Human Gene Module / Chromosome 15 / GABRB3

GABRB3gamma-aminobutyric acid (GABA) A receptor, beta 3

Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
21 / 37
Rare Variants / Common Variants
47 / 30
Aliases
GABRB3, MGC9051
Associated Syndromes
-
Genetic Category
Rare Single Gene Mutation, Genetic Association
Chromosome Band
15q12
Associated Disorders
ADHD, ASD, DD/NDD, ID
Relevance to Autism

Rare variants in the GABRB3 gene have been identified with autism (e.g. Cook et al., 1998) and genetic association has been found between GABRB3 and childhood absence epilepsy (CAE) (Urak et al., 2006). As well, a number of studies have found genetic association between the GABRB3 gene and autism (including one that enriched for savant skills). Populations studied include Caucasian, African-American, Hispanic, as well as AGRE, SARC and CLSA cohorts. However, other studies found no genetic association between the GABRB3 gene and autism in IMGSAC and other cohorts.

Molecular Function

The encoded protein is a subunit of GABA-A receptor. Neurotransmission is predominantly mediated by a gated chloride channel activity intrinsic to the receptor.

Reports related to GABRB3 (37 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Negative Association Serotonin transporter (5-HTT) and gamma-aminobutyric acid receptor subunit beta3 (GABRB3) gene polymorphisms are not associated with autism in the ... Maestrini E , et al. (1999) Yes -
2 Negative Association Absence of linkage and linkage disequilibrium to chromosome 15q11-q13 markers in 139 multiplex families with autism. Salmon B , et al. (1999) Yes -
3 Positive Association Association between a GABRB3 polymorphism and autism. Buxbaum JD , et al. (2002) Yes -
4 Positive Association Association analysis of chromosome 15 gabaa receptor subunit genes in autistic disorder. Menold MM , et al. (2002) Yes -
5 Positive Association Exploratory subsetting of autism families based on savant skills improves evidence of genetic linkage to 15q11-q13. Nurmi EL , et al. (2003) Yes -
6 Positive Association A linkage disequilibrium map of the 1-Mb 15q12 GABA(A) receptor subunit cluster and association to autism. McCauley JL , et al. (2004) Yes -
7 Positive Association An association analysis of microsatellite markers across the Prader-Willi/Angelman critical region on chromosome 15 (q11-13) and autism spectrum di... Curran S , et al. (2005) Yes -
8 Positive Association An analysis paradigm for investigating multi-locus effects in complex disease: examination of three GABA receptor subunit genes on 15q11-q13 as ris... Ashley-Koch AE , et al. (2006) Yes -
9 Recent Recommendation A GABRB3 promoter haplotype associated with childhood absence epilepsy impairs transcriptional activity. Urak L , et al. (2006) No -
10 Recent Recommendation Gabrb3 gene deficient mice exhibit impaired social and exploratory behaviors, deficits in non-selective attention and hypoplasia of cerebellar verm... DeLorey TM , et al. (2007) No -
11 Positive Association Maternal transmission of a rare GABRB3 signal peptide variant is associated with autism. Delahanty RJ , et al. (2009) Yes -
12 Recent Recommendation Somatosensory and sensorimotor consequences associated with the heterozygous disruption of the autism candidate gene, Gabrb3. DeLorey TM , et al. (2010) No -
13 Recent Recommendation Altered ultrasonic vocalization and impaired learning and memory in Angelman syndrome mouse model with a large maternal deletion from Ube3a to Gabrb3. Jiang YH , et al. (2010) No -
14 Support De novo gene disruptions in children on the autistic spectrum. Iossifov I , et al. (2012) Yes -
15 Recent Recommendation Variation in the autism candidate gene GABRB3 modulates tactile sensitivity in typically developing children. Tavassoli T , et al. (2012) No -
16 Support Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder. Girirajan S , et al. (2013) Yes -
17 Positive Association De novo mutations in epileptic encephalopathies. Epi4K Consortium , et al. (2013) No IS, LGS, DD, ID, ASD, ADHD
18 Positive Association Genetic variation in GABRB3 is associated with Asperger syndrome and multiple endophenotypes relevant to autism. Warrier V , et al. (2013) Yes ALTs
19 Negative Association Genetic analysis of GABRB3 as a candidate gene of autism spectrum disorders. Chen CH , et al. (2014) Yes -
20 Support De novo mutations in moderate or severe intellectual disability. Hamdan FF , et al. (2014) No Autistic features
21 Recent Recommendation Synaptic, transcriptional and chromatin genes disrupted in autism. De Rubeis S , et al. (2014) Yes -
22 Support Large-scale discovery of novel genetic causes of developmental disorders. Deciphering Developmental Disorders Study (2014) No -
23 Support Excess of rare, inherited truncating mutations in autism. Krumm N , et al. (2015) Yes -
24 Recent Recommendation Incorporating Functional Information in Tests of Excess De Novo Mutational Load. Jiang Y , et al. (2015) No -
25 Recent Recommendation Low load for disruptive mutations in autism genes and their biased transmission. Iossifov I , et al. (2015) Yes -
26 Support Gene Mutation Analysis in 253 Chinese Children with Unexplained Epilepsy and Intellectual/Developmental Disabilities. Zhang Y , et al. (2015) No -
27 Recent Recommendation Compromising the phosphodependent regulation of the GABAAR 3 subunit reproduces the core phenotypes of autism spectrum disorders. Vien TN , et al. (2015) No -
28 Recent Recommendation Systems genetics identifies a convergent gene network for cognition and neurodevelopmental disease. Johnson MR , et al. (2015) No -
29 Support Comprehensive molecular testing in patients with high functioning autism spectrum disorder. Alvarez-Mora MI , et al. (2016) Yes -
30 Support De Novo Mutations in SLC1A2 and CACNA1A Are Important Causes of Epileptic Encephalopathies. Epi4K Consortium. Electronic address: epi4k@columbia.edu and Epi4K Consortium (2016) No -
31 Support Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability. Lelieveld SH , et al. (2016) No -
32 Support De novo genic mutations among a Chinese autism spectrum disorder cohort. Wang T , et al. (2016) Yes -
33 Support Diagnostic Targeted Resequencing in 349 Patients with Drug-Resistant Pediatric Epilepsies Identifies Causative Mutations in 30 Different Genes. Parrini E , et al. (2016) No Microcephaly
34 Positive Association GABAA receptor subunit gene polymorphisms predict symptom-based and developmental deficits in Chinese Han children and adolescents with autistic sp... Yang S , et al. (2017) Yes -
35 Negative Association Meta-analysis of GABRB3 Gene Polymorphisms and Susceptibility to Autism Spectrum Disorder. Noroozi R , et al. (2018) Yes -
36 Highly Cited GABAA-receptor heterogeneity in the adult rat brain: differential regional and cellular distribution of seven major subunits. Fritschy JM and Mohler H (1995) No -
37 Primary Linkage-disequilibrium mapping of autistic disorder, with 15q11-13 markers. Cook EH Jr , et al. (1998) Yes -
Rare Variants   (47)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.31C>T p.Pro11Ser missense_variant Familial - - 19935738 Delahanty RJ , et al. (2009)
c.489G>A p.Met163Ile missense_variant De novo - Simplex 22542183 Iossifov I , et al. (2012)
- - copy_number_gain De novo - Simplex 23375656 Girirajan S , et al. (2013)
c.328A>C p.Asn110His missense_variant De novo - - 23934111 Epi4K Consortium , et al. (2013)
c.905A>G p.Tyr302Cys missense_variant De novo - - 23934111 Epi4K Consortium , et al. (2013)
c.358G>A p.Asp120Asn missense_variant De novo - - 23934111 Epi4K Consortium , et al. (2013)
c.539A>G p.Glu180Gly missense_variant De novo - - 23934111 Epi4K Consortium , et al. (2013)
g.-1571T>C - 2KB_upstream_variant Unknown Not maternal Multiplex 24999380 Chen CH , et al. (2014)
g.-1528T>C - 2KB_upstream_variant Familial Maternal Simplex 24999380 Chen CH , et al. (2014)
c.-1533_-1526delCCTCATAinsTCCATTAGACAAAAGTCTG - indel, 2KB_upstream_variant Familial Paternal Simplex 24999380 Chen CH , et al. (2014)
c.-1442G>A - 2KB_upstream_variant Unknown Not maternal Multi-generational 24999380 Chen CH , et al. (2014)
c.-1437G>T - 2KB_upstream_variant Familial Paternal Simplex 24999380 Chen CH , et al. (2014)
c.-1090A>G - 2KB_upstream_variant Familial Paternal Simplex 24999380 Chen CH , et al. (2014)
c.-541T>C - 2KB_upstream_variant Familial Paternal Simplex 24999380 Chen CH , et al. (2014)
c.-534C>T - 2KB_upstream_variant Familial Paternal Simplex 24999380 Chen CH , et al. (2014)
c.-232G>T - 2KB_upstream_variant Familial Paternal Simplex 24999380 Chen CH , et al. (2014)
c.-169G>T - 2KB_upstream_variant Familial Paternal Simplex 24999380 Chen CH , et al. (2014)
c.-142G>T - 2KB_upstream_variant Familial Paternal Simplex 24999380 Chen CH , et al. (2014)
c.-142G>T - 2KB_upstream_variant Familial Maternal Simplex 24999380 Chen CH , et al. (2014)
c.-140A>T - 2KB_upstream_variant Familial Paternal Simplex 24999380 Chen CH , et al. (2014)
c.-53G>T - 2KB_upstream_variant Familial Paternal Simplex 24999380 Chen CH , et al. (2014)
c.557C>T p.Thr186Met missense_variant Familial Paternal Simplex 24999380 Chen CH , et al. (2014)
c.942C>T p.(=) synonymous_variant Familial Paternal Simplex 24999380 Chen CH , et al. (2014)
c.1006C>T p.Pro336Ser missense_variant Familial Maternal Simplex 24999380 Chen CH , et al. (2014)
c.413_415dupACC p.Asn138_Arg139insHis inframe_insertion De novo - Simplex 25356899 Hamdan FF , et al. (2014)
del(A) - frameshift_variant De novo - Simplex 25363760 De Rubeis S , et al. (2014)
c.70G>T p.Glu24Ter stop_gained Unknown - Unknown 25363760 De Rubeis S , et al. (2014)
ins(A) - frameshift_variant Unknown - Unknown 25363760 De Rubeis S , et al. (2014)
c.662T>C p.Ile221Thr missense_variant De novo - Simplex 25533962 Deciphering Developmental Disorders Study (2014)
c.232G>A p.Val78Ile missense_variant De novo - Simplex 25961944 Krumm N , et al. (2015)
c.914C>T p.Ala305Val missense_variant De novo - Simplex 26544041 Zhang Y , et al. (2015)
c.509T>G p.Leu170Arg missense_variant De novo - Simplex 26544041 Zhang Y , et al. (2015)
c.31C>T p.Pro11Ser missense_variant Familial Paternal Multi-generational 26845707 Alvarez-Mora MI , et al. (2016)
c.358G>A p.Asp120Asn missense_variant De novo - - 27476654 Epi4K Consortium. Electronic address: epi4k@columbia.edu and Epi4K Consortium (2016)
c.470C>T p.Thr157Met missense_variant Familial - - 27476654 Epi4K Consortium. Electronic address: epi4k@columbia.edu and Epi4K Consortium (2016)
c.545A>T p.Tyr182Phe missense_variant De novo - - 27476654 Epi4K Consortium. Electronic address: epi4k@columbia.edu and Epi4K Consortium (2016)
c.745C>A p.Gln249Lys missense_variant De novo - - 27476654 Epi4K Consortium. Electronic address: epi4k@columbia.edu and Epi4K Consortium (2016)
c.767T>A p.Leu256Gln missense_variant De novo - - 27476654 Epi4K Consortium. Electronic address: epi4k@columbia.edu and Epi4K Consortium (2016)
c.878T>A p.Leu293His missense_variant Unknown - - 27476654 Epi4K Consortium. Electronic address: epi4k@columbia.edu and Epi4K Consortium (2016)
c.913G>A p.Ala305Thr missense_variant De novo - - 27476654 Epi4K Consortium. Electronic address: epi4k@columbia.edu and Epi4K Consortium (2016)
c.1412A>G p.Tyr471Cys missense_variant De novo - - 27479843 Lelieveld SH , et al. (2016)
c.5G>A p.Trp2Ter stop_gained Familial Maternal - 27824329 Wang T , et al. (2016)
c.5G>A p.Trp2Ter stop_gained Familial Paternal - 27824329 Wang T , et al. (2016)
c.844C>T p.Arg282Cys missense_variant Familial - - 27824329 Wang T , et al. (2016)
c.761C>T p.Ser254Phe missense_variant De novo - - 27864847 Parrini E , et al. (2016)
c.372A>C p.Leu124Phe missense_variant De novo - - 27864847 Parrini E , et al. (2016)
- - copy_number_gain Familial Maternal - 9545402 Cook EH Jr , et al. (1998)
Common Variants   (30)
Status Allele Change Residue Change Variant Type Inheritance Pattern Paternal Transmission Family Type PubMed ID Author, Year
- - intron_variant - - - 11920158 Buxbaum JD , et al. (2002)
- - intron_variant - - - 11920158 Buxbaum JD , et al. (2002)
- - microsatellite, intron_variant - - - 12819446 Nurmi EL , et al. (2003)
- - intergenic_variant - - - 15389768 McCauley JL , et al. (2004)
c.835+2039T>C;c.580+2039T>C;c.622+2039T>C A/G intron_variant - - - 15389768 McCauley JL , et al. (2004)
c.241-728G>A - intron_variant - - - 15389768 McCauley JL , et al. (2004)
c.241-1250G>A;c.-15-1250G>A;c.28-1250G>A T/C intron_variant - - - 15389768 McCauley JL , et al. (2004)
c.241-62255G>A;c.-16+32825G>A;c.-111-41261G>A C/T intron_variant - - - 15389768 McCauley JL , et al. (2004)
- - microsatellite - - - 15952184 Curran S , et al. (2005)
c.241-55520T>G;c.-16+39560T>G;c.-111-34526T>G - intron_variant - - - 16674551 Ashley-Koch AE , et al. (2006)
c.-1437T>G T/G 2KB_upstream_variant - - - 16835263 Urak L , et al. (2006)
c.-1852G>A;c.-2203G>A;c.-1090G>A G/A 2KB_upstream_variant - - - 16835263 Urak L , et al. (2006)
c.-1659T>C;c.-2010T>C;c.-897T>C T/C 2KB_upstream_variant - - - 16835263 Urak L , et al. (2006)
c.-1493G>A;c.-1493G>C;c.-1493G>T;c.-1844G>A;c.-1844G>C;c.-1844G>T;c.-731G>A;c.-731G>C;c.-731G>T G/A 2KB_upstream_variant - - - 16835263 Urak L , et al. (2006)
c.-1303C>T;c.-1654C>T;c.-541C>T T/C 2KB_upstream_variant - - - 16835263 Urak L , et al. (2006)
- T/C 2KB_upstream_variant - - - 16835263 Urak L , et al. (2006)
c.-931G>T;c.-1282G>T;c.-169G>T T/G 2KB_upstream_variant - - - 16835263 Urak L , et al. (2006)
c.-828C>G;c.-1179C>G;c.-66C>G G/C 2KB_upstream_variant - - - 16835263 Urak L , et al. (2006)
c.-732C>T;c.-1083C>T;c.31C>T p.Pro11Ser missense_variant, 2_KB_upstream_variant - - - 16835263 Urak L , et al. (2006)
c.-688C>T;c.-1039C>T;c.75C>T p.(=) synonymous_variant, 2KB_upstream_variant - - - 16835263 Urak L , et al. (2006)
C473A - 2KB_upstream_variant - - - 16835263 Urak L , et al. (2006)
C662T - 2KB_upstream_variant - - - 16835263 Urak L , et al. (2006)
c.240+12C>T;c.-112+12C>T - intron_variant - - - 16835263 Urak L , et al. (2006)
c.240+39311C>T;c.-112+39311C>T A/G intron_variant - - - 24321478 Warrier V , et al. (2013)
c.240+23093A>G;c.-112+23093A>G C/T intron_variant - - - 24321478 Warrier V , et al. (2013)
c.240+29417T>G;c.-112+29417T>G C/A intron_variant - - - 24321478 Warrier V , et al. (2013)
c.241-26347G>A;c.-15-26347G>A;c.-111-5353G>A T/C intron_variant - - - 24321478 Warrier V , et al. (2013)
c.241-26705C>T;c.-15-26705C>T;c.-111-5711C>T A/G intron_variant - - - 24321478 Warrier V , et al. (2013)
c.1081-4918A>G;c.826-4918A>G;c.868-4918A>G;c.904-4918A>G - intron_variant - - - 28607477 Yang S , et al. (2017)
- - intron_variant - - - 9545402 Cook EH Jr , et al. (1998)
SFARI Gene score
2

Strong Candidate

2

Score Delta: Score remained at 2.1

2

Strong Candidate

See all Category 2 Genes

We considered a rigorous statistical comparison between cases and controls, yielding genome-wide statistical significance, with independent replication, to be the strongest possible evidence for a gene. These criteria were relaxed slightly for category 2.

7/1/2017
2
icon
2

Score remained at 2

Description

The gene lies within the 15q11-q13 duplication that, when maternally inherited, causes autism. There have been multiple gene-based association studies with mixed results; the gene has not been implicated in genome-wide association studies, nor have any of the gene-based associations been replicated. Knockout mice show social deficits and cerebellar vermis hypoplasia, and deficiency of MECP2 (a category S gene) causes decreased expression of GABRB3. A de novo LoF variant in the GABRB3 gene was identified in one ASD proband from 2,270 trios screened by the Autism Sequencing Consortium (PMID 25363760), while a de novo likely damaging missense variant in this gene has been observed in an ASD case from the Simons Simplex Collection (PMID 22542183). Analysis of rare coding variation in 3,871 ASD cases and 9,937 ancestry-matched or paternal controls from the Autism Sequencing Consortium (ASC) identified GABRB3 as a gene meeting high statistical significance with a 0.01 < FDR ? 0.05, meaning that this gene had a ? 95% chance of being a true autism gene (PMID 25363760).

4/1/2017
2
icon
2

Score remained at 2

Description

The gene lies within the 15q11-q13 duplication that, when maternally inherited, causes autism. There have been multiple gene-based association studies with mixed results; the gene has not been implicated in genome-wide association studies, nor have any of the gene-based associations been replicated. Knockout mice show social deficits and cerebellar vermis hypoplasia, and deficiency of MECP2 (a category S gene) causes decreased expression of GABRB3. A de novo LoF variant in the GABRB3 gene was identified in one ASD proband from 2,270 trios screened by the Autism Sequencing Consortium (PMID 25363760), while a de novo likely damaging missense variant in this gene has been observed in an ASD case from the Simons Simplex Collection (PMID 22542183). Analysis of rare coding variation in 3,871 ASD cases and 9,937 ancestry-matched or paternal controls from the Autism Sequencing Consortium (ASC) identified GABRB3 as a gene meeting high statistical significance with a 0.01< FDR ?0.05, meaning that this gene had a ?95% chance of being a true autism gene (PMID 25363760).

Reports Added
[Altered ultrasonic vocalization and impaired learning and memory in Angelman syndrome mouse model with a large maternal deletion from Ube3a to Gabrb3.2010] [An association analysis of microsatellite markers across the Prader-Willi/Angelman critical region on chromosome 15 (q11-13) and autism spectrum di...2005] [Comprehensive molecular testing in patients with high functioning autism spectrum disorder.2016] [Gabrb3 gene deficient mice exhibit impaired social and exploratory behaviors, deficits in non-selective attention and hypoplasia of cerebellar verm...2007] [An analysis paradigm for investigating multi-locus effects in complex disease: examination of three GABA receptor subunit genes on 15q11-q13 as ris...2006] [Genetic analysis of GABRB3 as a candidate gene of autism spectrum disorders.2014] [Incorporating Functional Information in Tests of Excess De Novo Mutational Load.2015] [De novo gene disruptions in children on the autistic spectrum.2012] [A GABRB3 promoter haplotype associated with childhood absence epilepsy impairs transcriptional activity.2006] [GABAA-receptor heterogeneity in the adult rat brain: differential regional and cellular distribution of seven major subunits.1995] [De novo mutations in moderate or severe intellectual disability.2014] [De novo mutations in epileptic encephalopathies.2013] [Linkage-disequilibrium mapping of autistic disorder, with 15q11-13 markers.1998] [Serotonin transporter (5-HTT) and gamma-aminobutyric acid receptor subunit beta3 (GABRB3) gene polymorphisms are not associated with autism in the ...1999] [Absence of linkage and linkage disequilibrium to chromosome 15q11-q13 markers in 139 multiplex families with autism.1999] [Compromising the phosphodependent regulation of the GABAAR 3 subunit reproduces the core phenotypes of autism spectrum disorders.2015] [Gene Mutation Analysis in 253 Chinese Children with Unexplained Epilepsy and Intellectual/Developmental Disabilities.2015] [Diagnostic Targeted Resequencing in 349 Patients with Drug-Resistant Pediatric Epilepsies Identifies Causative Mutations in 30 Different Genes.2016] [Systems genetics identifies a convergent gene network for cognition and neurodevelopmental disease.2015] [Excess of rare, inherited truncating mutations in autism.2015] [Genetic variation in GABRB3 is associated with Asperger syndrome and multiple endophenotypes relevant to autism.2013] [Association between a GABRB3 polymorphism and autism.2002] [De Novo Mutations in SLC1A2 and CACNA1A Are Important Causes of Epileptic Encephalopathies.2016] [Association analysis of chromosome 15 gabaa receptor subunit genes in autistic disorder.2002] [Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.2013] [Synaptic, transcriptional and chromatin genes disrupted in autism.2014] [A linkage disequilibrium map of the 1-Mb 15q12 GABA(A) receptor subunit cluster and association to autism.2004] [Exploratory subsetting of autism families based on savant skills improves evidence of genetic linkage to 15q11-q13.2003] [De novo genic mutations among a Chinese autism spectrum disorder cohort.2016] [Maternal transmission of a rare GABRB3 signal peptide variant is associated with autism.2009] [Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability.2016] [Somatosensory and sensorimotor consequences associated with the heterozygous disruption of the autism candidate gene, Gabrb3.2010] [Large-scale discovery of novel genetic causes of developmental disorders.2014] [Low load for disruptive mutations in autism genes and their biased transmission.2015] [Variation in the autism candidate gene GABRB3 modulates tactile sensitivity in typically developing children.2012]
1/1/2017
2
icon
2

Score remained at 2

Description

The gene lies within the 15q11-q13 duplication that, when maternally inherited, causes autism. There have been multiple gene-based association studies with mixed results; the gene has not been implicated in genome-wide association studies, nor have any of the gene-based associations been replicated. Knockout mice show social deficits and cerebellar vermis hypoplasia, and deficiency of MECP2 (a category S gene) causes decreased expression of GABRB3. A de novo LoF variant in the GABRB3 gene was identified in one ASD proband from 2,270 trios screened by the Autism Sequencing Consortium (PMID 25363760), while a de novo likely damaging missense variant in this gene has been observed in an ASD case from the Simons Simplex Collection (PMID 22542183). Analysis of rare coding variation in 3,871 ASD cases and 9,937 ancestry-matched or paternal controls from the Autism Sequencing Consortium (ASC) identified GABRB3 as a gene meeting high statistical significance with a 0.01 < FDR ?0.05, meaning that this gene had a ?95% chance of being a true autism gene (PMID 25363760).

10/1/2016
2
icon
2

Score remained at 2

Description

The gene lies within the 15q11-q13 duplication that, when maternally inherited, causes autism. There have been multiple gene-based association studies with mixed results; the gene has not been implicated in genome-wide association studies, nor have any of the gene-based associations been replicated. Knockout mice show social deficits and cerebellar vermis hypoplasia, and deficiency of MECP2 (a category S gene) causes decreased expression of GABRB3. A de novo LoF variant in the GABRB3 gene was identified in one ASD proband from 2,270 trios screened by the Autism Sequencing Consortium (PMID 25363760), while a de novo likely damaging missense variant in this gene has been observed in an ASD case from the Simons Simplex Collection (PMID 22542183). Analysis of rare coding variation in 3,871 ASD cases and 9,937 ancestry-matched or paternal controls from the Autism Sequencing Consortium (ASC) identified GABRB3 as a gene meeting high statistical significance with a 0.01

7/1/2016
2
icon
2

Score remained at 2

Description

The gene lies within the 15q11-q13 duplication that, when maternally inherited, causes autism. There have been multiple gene-based association studies with mixed results; the gene has not been implicated in genome-wide association studies, nor have any of the gene-based associations been replicated. Knockout mice show social deficits and cerebellar vermis hypoplasia, and deficiency of MECP2 (a category S gene) causes decreased expression of GABRB3. A de novo LoF variant in the GABRB3 gene was identified in one ASD proband from 2,270 trios screened by the Autism Sequencing Consortium (PMID 25363760), while a de novo likely damaging missense variant in this gene has been observed in an ASD case from the Simons Simplex Collection (PMID 22542183). Analysis of rare coding variation in 3,871 ASD cases and 9,937 ancestry-matched or paternal controls from the Autism Sequencing Consortium (ASC) identified GABRB3 as a gene meeting high statistical significance with a 0.01

1/1/2016
2
icon
2

Score remained at 2

Description

The gene lies within the 15q11-q13 duplication that, when maternally inherited, causes autism. There have been multiple gene-based association studies with mixed results; the gene has not been implicated in genome-wide association studies, nor have any of the gene-based associations been replicated. Knockout mice show social deficits and cerebellar vermis hypoplasia, and deficiency of MECP2 (a category S gene) causes decreased expression of GABRB3. A de novo LoF variant in the GABRB3 gene was identified in one ASD proband from 2,270 trios screened by the Autism Sequencing Consortium (PMID 25363760), while a de novo likely damaging missense variant in this gene has been observed in an ASD case from the Simons Simplex Collection (PMID 22542183). Analysis of rare coding variation in 3,871 ASD cases and 9,937 ancestry-matched or paternal controls from the Autism Sequencing Consortium (ASC) identified GABRB3 as a gene meeting high statistical significance with a 0.01

Reports Added
[An association analysis of microsatellite markers across the Prader-Willi/Angelman critical region on chromosome 15 (q11-13) and autism spectrum di...2005] [GABAA-receptor heterogeneity in the adult rat brain: differential regional and cellular distribution of seven major subunits.1995] [Comprehensive molecular testing in patients with high functioning autism spectrum disorder.2016] [Compromising the phosphodependent regulation of the GABAAR 3 subunit reproduces the core phenotypes of autism spectrum disorders.2015] [Gabrb3 gene deficient mice exhibit impaired social and exploratory behaviors, deficits in non-selective attention and hypoplasia of cerebellar verm...2007] [An analysis paradigm for investigating multi-locus effects in complex disease: examination of three GABA receptor subunit genes on 15q11-q13 as ris...2006] [De novo gene disruptions in children on the autistic spectrum.2012] [De novo mutations in epileptic encephalopathies.2013] [A GABRB3 promoter haplotype associated with childhood absence epilepsy impairs transcriptional activity.2006] [Genetic analysis of GABRB3 as a candidate gene of autism spectrum disorders.2014] [Linkage-disequilibrium mapping of autistic disorder, with 15q11-13 markers.1998] [Serotonin transporter (5-HTT) and gamma-aminobutyric acid receptor subunit beta3 (GABRB3) gene polymorphisms are not associated with autism in the ...1999] [Absence of linkage and linkage disequilibrium to chromosome 15q11-q13 markers in 139 multiplex families with autism.1999] [Gene Mutation Analysis in 253 Chinese Children with Unexplained Epilepsy and Intellectual/Developmental Disabilities.2015] [Systems genetics identifies a convergent gene network for cognition and neurodevelopmental disease.2015] [Excess of rare, inherited truncating mutations in autism.2015] [Association between a GABRB3 polymorphism and autism.2002] [Association analysis of chromosome 15 gabaa receptor subunit genes in autistic disorder.2002] [Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.2013] [Synaptic, transcriptional and chromatin genes disrupted in autism.2014] [Exploratory subsetting of autism families based on savant skills improves evidence of genetic linkage to 15q11-q13.2003] [Genetic variation in GABRB3 is associated with Asperger syndrome and multiple endophenotypes relevant to autism.2013] [Low load for disruptive mutations in autism genes and their biased transmission.2015] [Incorporating Functional Information in Tests of Excess De Novo Mutational Load.2015] [Maternal transmission of a rare GABRB3 signal peptide variant is associated with autism.2009] [Somatosensory and sensorimotor consequences associated with the heterozygous disruption of the autism candidate gene, Gabrb3.2010] [A linkage disequilibrium map of the 1-Mb 15q12 GABA(A) receptor subunit cluster and association to autism.2004] [Large-scale discovery of novel genetic causes of developmental disorders.2014] [Variation in the autism candidate gene GABRB3 modulates tactile sensitivity in typically developing children.2012] [Altered ultrasonic vocalization and impaired learning and memory in Angelman syndrome mouse model with a large maternal deletion from Ube3a to Gabrb3.2010]
7/1/2015
2
icon
2

Score remained at 2

Description

The gene lies within the 15q11-q13 duplication that, when maternally inherited, causes autism. There have been multiple gene-based association studies with mixed results; the gene has not been implicated in genome-wide association studies, nor have any of the gene-based associations been replicated. Knockout mice show social deficits and cerebellar vermis hypoplasia, and deficiency of MECP2 (a category S gene) causes decreased expression of GABRB3. A de novo LoF variant in the GABRB3 gene was identified in one ASD proband from 2,270 trios screened by the Autism Sequencing Consortium (PMID 25363760), while a de novo likely damaging missense variant in this gene has been observed in an ASD case from the Simons Simplex Collection (PMID 22542183). Analysis of rare coding variation in 3,871 ASD cases and 9,937 ancestry-matched or paternal controls from the Autism Sequencing Consortium (ASC) identified GABRB3 as a gene meeting high statistical significance with a 0.01

Reports Added
[Altered ultrasonic vocalization and impaired learning and memory in Angelman syndrome mouse model with a large maternal deletion from Ube3a to Gabrb3.2010] [An association analysis of microsatellite markers across the Prader-Willi/Angelman critical region on chromosome 15 (q11-13) and autism spectrum di...2005] [Incorporating Functional Information in Tests of Excess De Novo Mutational Load.2015] [GABAA-receptor heterogeneity in the adult rat brain: differential regional and cellular distribution of seven major subunits.1995] [Gabrb3 gene deficient mice exhibit impaired social and exploratory behaviors, deficits in non-selective attention and hypoplasia of cerebellar verm...2007] [An analysis paradigm for investigating multi-locus effects in complex disease: examination of three GABA receptor subunit genes on 15q11-q13 as ris...2006] [De novo gene disruptions in children on the autistic spectrum.2012] [Genetic analysis of GABRB3 as a candidate gene of autism spectrum disorders.2014] [De novo mutations in epileptic encephalopathies.2013] [Serotonin transporter (5-HTT) and gamma-aminobutyric acid receptor subunit beta3 (GABRB3) gene polymorphisms are not associated with autism in the ...1999] [Absence of linkage and linkage disequilibrium to chromosome 15q11-q13 markers in 139 multiplex families with autism.1999] [Excess of rare, inherited truncating mutations in autism.2015] [Linkage-disequilibrium mapping of autistic disorder, with 15q11-13 markers.1998] [Association between a GABRB3 polymorphism and autism.2002] [Association analysis of chromosome 15 gabaa receptor subunit genes in autistic disorder.2002] [Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.2013] [Synaptic, transcriptional and chromatin genes disrupted in autism.2014] [Exploratory subsetting of autism families based on savant skills improves evidence of genetic linkage to 15q11-q13.2003] [Genetic variation in GABRB3 is associated with Asperger syndrome and multiple endophenotypes relevant to autism.2013] [A GABRB3 promoter haplotype associated with childhood absence epilepsy impairs transcriptional activity.2006] [Maternal transmission of a rare GABRB3 signal peptide variant is associated with autism.2009] [Somatosensory and sensorimotor consequences associated with the heterozygous disruption of the autism candidate gene, Gabrb3.2010] [A linkage disequilibrium map of the 1-Mb 15q12 GABA(A) receptor subunit cluster and association to autism.2004] [Large-scale discovery of novel genetic causes of developmental disorders.2014] [Variation in the autism candidate gene GABRB3 modulates tactile sensitivity in typically developing children.2012]
4/1/2015
2
icon
2

Score remained at 2

Description

The gene lies within the 15q11-q13 duplication that, when maternally inherited, causes autism. There have been multiple gene-based association studies with mixed results; the gene has not been implicated in genome-wide association studies, nor have any of the gene-based associations been replicated. Knockout mice show social deficits and cerebellar vermis hypoplasia, and deficiency of MECP2 (a category S gene) causes decreased expression of GABRB3. A de novo LoF variant in the GABRB3 gene was identified in one ASD proband from 2,270 trios screened by the Autism Sequencing Consortium (PMID 25363760), while a de novo likely damaging missense variant in this gene has been observed in an ASD case from the Simons Simplex Collection (PMID 22542183). Analysis of rare coding variation in 3,871 ASD cases and 9,937 ancestry-matched or paternal controls from the Autism Sequencing Consortium (ASC) identified GABRB3 as a gene meeting high statistical significance with a 0.01

1/1/2015
2
icon
2

Score remained at 2

Description

The gene lies within the 15q11-q13 duplication that, when maternally inherited, causes autism. There have been multiple gene-based association studies with mixed results; the gene has not been implicated in genome-wide association studies, nor have any of the gene-based associations been replicated. Knockout mice show social deficits and cerebellar vermis hypoplasia, and deficiency of MECP2 (a category S gene) causes decreased expression of GABRB3. A de novo LoF variant in the GABRB3 gene was identified in one ASD proband from 2,270 trios screened by the Autism Sequencing Consortium (PMID 25363760), while a de novo likely damaging missense variant in this gene has been observed in an ASD case from the Simons Simplex Collection (PMID 22542183). Analysis of rare coding variation in 3,871 ASD cases and 9,937 ancestry-matched or paternal controls from the Autism Sequencing Consortium (ASC) identified GABRB3 as a gene meeting high statistical significance with a 0.01

10/1/2014
4
icon
2

Decreased from 4 to 2

Description

The gene lies within the 15q11-q13 duplication that, when maternally inherited, causes autism. There have been multiple gene-based association studies with mixed results; the gene has not been implicated in genome-wide association studies, nor have any of the gene-based associations been replicated. Knockout mice show social deficits and cerebellar vermis hypoplasia, and deficiency of MECP2 (a category S gene) causes decreased expression of GABRB3. A de novo LoF variant in the GABRB3 gene was identified in one ASD proband from 2,270 trios screened by the Autism Sequencing Consortium (PMID 25363760), while a de novo likely damaging missense variant in this gene has been observed in an ASD case from the Simons Simplex Collection (PMID 22542183). Analysis of rare coding variation in 3,871 ASD cases and 9,937 ancestry-matched or paternal controls from the Autism Sequencing Consortium (ASC) identified GABRB3 as a gene meeting high statistical significance with a 0.01

7/1/2014
No data
icon
4

Increased from No data to 4

Description

There is minimal evidence for the role of GABRB3 in autism. The gene lies within the 15q11q13 duplication that, when maternally inherited, causes autism. There have been multiple gene-based association studies with mixed results; the gene has not been implicated in genome-wide association studies, nor have any of the gene-based associations been replicated. Knockout mice show social deficits and cerebellar vermis hypoplasia, and deficiency of MECP2 (a category X gene), causes decreased expression of GABRB3.

Reports Added
[Exploratory subsetting of autism families based on savant skills improves evidence of genetic linkage to 15q11-q13.2003] [A linkage disequilibrium map of the 1-Mb 15q12 GABA(A) receptor subunit cluster and association to autism.2004] [An association analysis of microsatellite markers across the Prader-Willi/Angelman critical region on chromosome 15 (q11-13) and autism spectrum di...2005] [An analysis paradigm for investigating multi-locus effects in complex disease: examination of three GABA receptor subunit genes on 15q11-q13 as ris...2006] [A GABRB3 promoter haplotype associated with childhood absence epilepsy impairs transcriptional activity.2006] [Gabrb3 gene deficient mice exhibit impaired social and exploratory behaviors, deficits in non-selective attention and hypoplasia of cerebellar verm...2007] [Maternal transmission of a rare GABRB3 signal peptide variant is associated with autism.2009] [Somatosensory and sensorimotor consequences associated with the heterozygous disruption of the autism candidate gene, Gabrb3.2010] [Altered ultrasonic vocalization and impaired learning and memory in Angelman syndrome mouse model with a large maternal deletion from Ube3a to Gabrb3.2010] [De novo gene disruptions in children on the autistic spectrum.2012] [Variation in the autism candidate gene GABRB3 modulates tactile sensitivity in typically developing children.2012] [Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.2013] [De novo mutations in epileptic encephalopathies.2013] [Genetic variation in GABRB3 is associated with Asperger syndrome and multiple endophenotypes relevant to autism.2013] [Genetic analysis of GABRB3 as a candidate gene of autism spectrum disorders.2014] [GABAA-receptor heterogeneity in the adult rat brain: differential regional and cellular distribution of seven major subunits.1995] [Linkage-disequilibrium mapping of autistic disorder, with 15q11-13 markers.1998] [Serotonin transporter (5-HTT) and gamma-aminobutyric acid receptor subunit beta3 (GABRB3) gene polymorphisms are not associated with autism in the ...1999] [Absence of linkage and linkage disequilibrium to chromosome 15q11-q13 markers in 139 multiplex families with autism.1999] [Association between a GABRB3 polymorphism and autism.2002] [Association analysis of chromosome 15 gabaa receptor subunit genes in autistic disorder.2002]
4/1/2014
No data
icon
4

Increased from No data to 4

Description

There is minimal evidence for the role of GABRB3 in autism. The gene lies within the 15q11q13 duplication that, when maternally inherited, causes autism. There have been multiple gene-based association studies with mixed results; the gene has not been implicated in genome-wide association studies, nor have any of the gene-based associations been replicated. Knockout mice show social deficits and cerebellar vermis hypoplasia, and deficiency of MECP2 (a category X gene), causes decreased expression of GABRB3.

Krishnan Probability Score

Score 0.76491725651352

Ranking 27/25841 scored genes


[Show Scoring Methodology]
Krishnan and colleagues generated probability scores genome-wide by using a machine learning approach on a human brain-specific gene network. The method was first presented in Nat Neurosci 19, 1454-1462 (2016), and scores for more than 25,000 RefSeq genes can be accessed in column G of supplementary table 3 (see: http://www.nature.com/neuro/journal/v19/n11/extref/nn.4353-S5.xlsx). A searchable browser, with the ability to view networks of associated ASD risk genes, can be found at asd.princeton.edu.
ExAC Score

Score 0.99707396027166

Ranking 1358/18225 scored genes


[Show Scoring Methodology]
The Exome Aggregation Consortium (ExAC) is a summary database of 60,706 exomes that has been widely used to estimate 'constraint' on mutation for individual genes. It was introduced by Lek et al. Nature 536, 285-291 (2016), and the ExAC browser can be found at exac.broadinstitute.org. The pLI score was developed as measure of intolerance to loss-of- function mutation. A pLI > 0.9 is generally viewed as highly constrained, and thus any loss-of- function mutations in autism in such a gene would be more likely to confer risk. For a full list of pLI scores see: ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/functional_gene_constraint/fordist_cle aned_exac_nonTCGA_z_pli_rec_null_data.txt
Iossifov Probability Score

Score 0.812

Ranking 223/239 scored genes


[Show Scoring Methodology]
Supplementary dataset S2 in the paper by Iossifov et al. (PNAS 112, E5600-E5607 (2015)) lists 239 genes with a probability of at least 0.8 of being associated with autism risk (column I). This probability metric combines the evidence from de novo likely-gene- disrupting and missense mutations and assesses it against the background mutation rate in unaffected individuals from the University of Washington’s Exome Variant Sequence database (evs.gs.washington.edu/EVS/). The list of probability scores can be found here: www.pnas.org/lookup/suppl/doi:10.1073/pnas.1516376112/- /DCSupplemental/pnas.1516376112.sd02.xlsx
Sanders TADA Score

Score 0.04494292732921

Ranking 44/18665 scored genes


[Show Scoring Methodology]
The TADA score ('Transmission and De novo Association') was introduced by He et al. PLoS Genet 9(8):e1003671 (2013), and is a statistic that integrates evidence from both de novo and transmitted mutations. It forms the basis for the claim of 65 individual genes being strongly associated with autism risk at a false discovery rate of 0.1 (Sanders et al. Neuron 87, 1215-1233 (2015)). The calculated TADA score for 18,665 RefSeq genes can be found in column P of Supplementary Table 6 in the Sanders et al. paper (the column headed 'tadaFdrAscSscExomeSscAgpSmallDel'), which represents a combined analysis of exome data and small de novo deletions (see www.cell.com/cms/attachment/2038545319/2052606711/mmc7.xlsx).
Larsen Cumulative Evidence Score

Score 85.5

Ranking 11/461 scored genes


[Show Scoring Methodology]
Larsen and colleagues generated gene scores based on the sum of evidence for all available ASD-associated variants in a gene, with assessments based on mode of inheritance, effect size, and variant frequency in the general population. The approach was first presented in Mol Autism 7:44 (2016), and scores for 461 genes can be found in column I in supplementary table 4 from that paper.
Zhang D Score

Score 0.25275803209956

Ranking 3442/20870 scored genes


[Show Scoring Methodology]
The DAMAGES score (disease-associated mutation analysis using gene expression signatures), or D score, was developed to combine evidence from de novo loss-of- function mutation with evidence from cell-type- specific gene expression in the mouse brain (specifically translational profiles of 24 specific mouse CNS cell types isolated from 6 different brain regions). Genes with positive D scores are more likely to be associated with autism risk, with higher-confidence genes having higher D scores. This statistic was first presented by Zhang & Shen (Hum Mutat 38, 204- 215 (2017), and D scores for more than 20,000 RefSeq genes can be found in column M in supplementary table 2 from that paper.
CNVs associated with GABRB3(1 CNVs)
15q12 9 Deletion-Duplication 16  /  18
Interaction Table
Interactor Symbol Interactor Name Interactor Organism Interactor Type Entrez ID Uniprot ID
ACCN4 Acid-sensing ion channel 4 Human Protein Binding 55515 Q96FT7-4
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