Human Gene Module / Chromosome 12 / GRIN2B

GRIN2Bglutamate receptor, inotropic, N-methyl D-apartate 2B

Score
1
High Confidence Criteria 1.1
Autism Reports / Total Reports
16 / 34
Rare Variants / Common Variants
63 / 32
Aliases
GRIN2B, NMDAR2B,  NR2B,  hNR3
Associated Syndromes
-
Genetic Category
Rare Single Gene Mutation, Syndromic, Genetic Association
Chromosome Band
12p13.1
Associated Disorders
ASD, DD/NDD, EPS, ADHD, ID, EP
Relevance to Autism

Several studies have identified rare mutations in the GRIN2B gene in individuals with autism. For example, O'Roak et al. (2011) found a single individual with a 3' splice mutation of GRIN2B, Myers et al. (2011) found an excess of rare non-synonymous mutations in GRIN2B in both autism and schizophrenia and Talkowski et al. (2012) found two CNVs involving GRIN2B in ASD patients. As well, Yoo et al. (2012) showed association of GRIN2B markers in a Korean cohort of 151 families. Studies have also found genetic association of the GRIN2B gene with obsessive-compulsive disorder (Arnold et al., 2004) as well as with schizophrenia (Ohtsuki et al., 2001).

Molecular Function

NMDA receptor subtype of glutamate-gated ion channels with high calcium permeability and voltage-dependent sensitivity to magnesium.

Reports related to GRIN2B (34 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Highly Cited Mutation analysis of the NMDAR2B (GRIN2B) gene in schizophrenia. Ohtsuki T , et al. (2001) No -
2 Highly Cited Association of a glutamate (NMDA) subunit receptor gene (GRIN2B) with obsessive-compulsive disorder: a preliminary study. Arnold PD , et al. (2004) No -
3 Recent recommendation Direct measure of the de novo mutation rate in autism and schizophrenia cohorts. Awadalla P , et al. (2010) No -
4 Support Mutations in GRIN2A and GRIN2B encoding regulatory subunits of NMDA receptors cause variable neurodevelopmental phenotypes. Endele S , et al. (2010) No -
5 Recent Recommendation Strain dependent effects of prenatal stress on gene expression in the rat hippocampus. Neeley EW , et al. (2011) No -
6 Recent Recommendation A population genetic approach to mapping neurological disorder genes using deep resequencing. Myers RA , et al. (2011) Yes -
7 Primary Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. O'Roak BJ , et al. (2011) Yes -
8 Support Exome sequencing of ion channel genes reveals complex profiles confounding personal risk assessment in epilepsy. Klassen T , et al. (2011) No -
9 Positive Association Family based association of GRIN2A and GRIN2B with Korean autism spectrum disorders. Yoo HJ , et al. (2012) Yes -
10 Support Sequencing chromosomal abnormalities reveals neurodevelopmental loci that confer risk across diagnostic boundaries. Talkowski ME , et al. (2012) Yes -
11 Support Rare mutations in N-methyl-D-aspartate glutamate receptors in autism spectrum disorders and schizophrenia. Tarabeux J , et al. (2011) Yes -
12 Support Diagnostic exome sequencing in persons with severe intellectual disability. de Ligt J , et al. (2012) No Epilepsy, ASD
13 Support Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. O'Roak BJ , et al. (2012) Yes -
14 Recent Recommendation Behavioral phenotype in five individuals with de novo mutations within the GRIN2B gene. Freunscht I , et al. (2013) No -
15 Support Interstitial 12p13.1 deletion involving GRIN2B in three patients with intellectual disability. Dimassi S , et al. (2013) No ASD, Epilepsy
16 Positive association De novo mutations in epileptic encephalopathies. Epi4K Consortium , et al. (2013) No IS, LGS, DD, ID, ASD, ADHD
17 Support Excess of rare novel loss-of-function variants in synaptic genes in schizophrenia and autism spectrum disorders. Kenny EM , et al. (2013) Yes -
18 Support GRIN2B mutations in West syndrome and intellectual disability with focal epilepsy. Lemke JR , et al. (2013) No West syndrome
19 Recent recommendation Neuronal excitation upregulates Tbr1, a high-confidence risk gene of autism, mediating Grin2b expression in the adult brain. Chuang HC , et al. (2014) No -
20 Positive association A candidate gene association study further corroborates involvement of contactin genes in autism. Poot M (2014) Yes -
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 Positive association Association of genetic variants of GRIN2B with autism. Pan Y , et al. (2015) Yes -
24 Recent recommendation Low load for disruptive mutations in autism genes and their biased transmission. Iossifov I , et al. (2015) Yes -
25 Support Gene Mutation Analysis in 253 Chinese Children with Unexplained Epilepsy and Intellectual/Developmental Disabilities. Zhang Y , et al. (2015) No -
26 Support Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability. Lelieveld SH , et al. (2016) No -
27 Support Mutation screening of GRIN2B in schizophrenia and autism spectrum disorder in a Japanese population. Takasaki Y , et al. (2016) Yes -
28 Support De novo genic mutations among a Chinese autism spectrum disorder cohort. Wang T , et al. (2016) Yes -
29 Recent recommendation Mechanistic Insight into NMDA Receptor Dysregulation by Rare Variants in the GluN2A and GluN2B Agonist Binding Domains. Swanger SA , et al. (2016) No -
30 Support The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies. Redin C , et al. (2016) Yes -
31 Support Clinical exome sequencing: results from 2819 samples reflecting 1000 families. Trujillano D , et al. (2016) No ASD (1 case)
32 Support Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights t... Nilsson D , et al. (2016) Yes -
33 Support Molecular Mechanism of Disease-Associated Mutations in the Pre-M1 Helix of NMDA Receptors and Potential Rescue Pharmacology. Ogden KK , et al. (2017) No -
34 Support Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases. Stessman HA , et al. (2017) Yes -
Rare Variants   (63)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
T>G p.Leu825Val missense_variant De novo - - 20797689 Awadalla P , et al. (2010)
- - translocation De novo - - 20890276 Endele S , et al. (2010)
- - translocation De novo - - 20890276 Endele S , et al. (2010)
c.411 + 1G>A - splice_site_variant De novo - - 20890276 Endele S , et al. (2010)
c.2044C>T p.Arg682Cys missense_variant De novo - - 20890276 Endele S , et al. (2010)
c.2360 - 2A>G - splice_site_variant De novo - - 20890276 Endele S , et al. (2010)
c.803_804delCA p.Thr268SerfsTer15 frameshift_variant De novo - - 20890276 Endele S , et al. (2010)
c.2172-2A>G, c.-43-2A>G - splice_site_variant De novo - Simplex 21572417 O'Roak BJ , et al. (2011)
c.834C>A p.(=) synonymous_variant Unknown - Unknown 21703448 Klassen T , et al. (2011)
c.1440G>A p.(=) synonymous_variant Unknown - Unknown 21703448 Klassen T , et al. (2011)
c.4107C>T p.(=) synonymous_variant Unknown - Unknown 21703448 Klassen T , et al. (2011)
c.731C>T p.Ala244Val missense_variant Unknown - Unknown 21703448 Klassen T , et al. (2011)
- - inversion De novo - - 22521361 Talkowski ME , et al. (2012)
c.2473T>G p.Leu825Val missense_variant De novo - Simplex 22833210 Tarabeux J , et al. (2011)
c.3076G>A p.Gly1026Ser missense_variant - - - 22833210 Tarabeux J , et al. (2011)
c.4244C>T p.Ser1415Leu missense_variant - - - 22833210 Tarabeux J , et al. (2011)
c.1658C>T p.Pro553Leu missense_variant De novo - - 23033978 de Ligt J , et al. (2012)
c.1677G>A p.Trp559Ter stop_gained De novo - Simplex 23160955 O'Roak BJ , et al. (2012)
c.1367G>A p.Cys456Tyr missense_variant De novo - Simplex 23160955 O'Roak BJ , et al. (2012)
c.99_100insC p.Ser34GlnfsTer25 frameshift_variant De novo - Simplex 23160955 O'Roak BJ , et al. (2012)
c.1906G>C p.Ala636Pro missense_variant De novo - - 23718928 Freunscht I , et al. (2013)
- - copy_number_loss De novo - - 23918416 Dimassi S , et al. (2013)
- - copy_number_loss De novo - - 23918416 Dimassi S , et al. (2013)
- - copy_number_loss De novo - - 23918416 Dimassi S , et al. (2013)
c.1382G>T p.Cys461Phe missense_variant De novo - - 23934111 Epi4K Consortium , et al. (2013)
c.2131C>T p.Gln711Ter stop_gained De novo - - 24126926 Kenny EM , et al. (2013)
c.1853T>G p.Val618Gly missense_variant De novo - - 24272827 Lemke JR , et al. (2013)
c.1844A>T p.Asn615Ile missense_variant De novo - - 24272827 Lemke JR , et al. (2013)
c.1619G>A p.Arg540His missense_variant De novo - - 24272827 Lemke JR , et al. (2013)
c.2011-5_2011-4delTC p.Phe671_Gln672del splice_site_variant Familial Paternal - 24272827 Lemke JR , et al. (2013)
del(TGAT) - frameshift_variant Unknown - Unknown 25363760 De Rubeis S , et al. (2014)
del(A) - frameshift_variant Unknown - Unknown 25363760 De Rubeis S , et al. (2014)
c.1555C>T p.Arg519Ter stop_gained Unknown - Unknown 25363760 De Rubeis S , et al. (2014)
c.2087G>A p.Arg696His missense_variant Unknown - Unknown 25363760 De Rubeis S , et al. (2014)
c.1619G>A p.Arg540His missense_variant Unknown - Unknown 25363760 De Rubeis S , et al. (2014)
c.3242G>A p.Arg1081His missense_variant Unknown - Unknown 25363760 De Rubeis S , et al. (2014)
c.2459G>C p.Gly820Ala missense_variant De novo - Simplex 25533962 Deciphering Developmental Disorders Study (2014)
c.2793C>T p.(=) synonymous_variant Unknown - Simplex 25656819 Pan Y , et al. (2015)
c.2877C>T p.(=) synonymous_variant Unknown - Simplex 25656819 Pan Y , et al. (2015)
c.3429A>G p.(=) synonymous_variant Unknown - Simplex 25656819 Pan Y , et al. (2015)
c.3564C>G p.(=) synonymous_variant Unknown - Simplex 25656819 Pan Y , et al. (2015)
c.3683C>T p.Thr1228Met missense_variant Unknown - Simplex 25656819 Pan Y , et al. (2015)
c.4015A>G p.Met1339Val missense_variant Familial Paternal Simplex 25656819 Pan Y , et al. (2015)
c.3818C>A p.Thr1273Lys missense_variant Familial Paternal Simplex 25656819 Pan Y , et al. (2015)
c.1985A>C p.Gln662Pro missense_variant De novo - Simplex 26544041 Zhang Y , et al. (2015)
c.1672G>A p.Val558Ile missense_variant De novo - - 27479843 Lelieveld SH , et al. (2016)
c.1570G>A p.Asp524Asn missense_variant De novo - - 27479843 Lelieveld SH , et al. (2016)
c.52G>A p.Val18Ile missense_variant Unknown - - 27616045 Takasaki Y , et al. (2016)
c.1768G>A p.Ala590Thr missense_variant Unknown - - 27616045 Takasaki Y , et al. (2016)
c.3118G>A p.Gly1040Ser missense_variant Unknown - - 27616045 Takasaki Y , et al. (2016)
c.3296G>A p.Arg1099His missense_variant Unknown - - 27616045 Takasaki Y , et al. (2016)
c.3875A>G p.Lys1292Arg missense_variant Unknown - - 27616045 Takasaki Y , et al. (2016)
c.1555C>T p.Arg519Ter stop_gained De novo - - 27824329 Wang T , et al. (2016)
c.2087G>A p.Arg696His missense_variant De novo - Possible multi-generational 27839871 Swanger SA , et al. (2016)
c.1306T>C p.Cys436Arg missense_variant De novo - - 27839871 Swanger SA , et al. (2016)
- - inversion De novo - - 27841880 Redin C , et al. (2016)
c.737C>A p.Ser246Ter stop_gained De novo - Simplex 27848944 Trujillano D , et al. (2016)
c.2252T>C p.Ile751Thr missense_variant De novo - - 27848944 Trujillano D , et al. (2016)
- - translocation De novo - - 27862604 Nilsson D , et al. (2016)
c.1460G>C p.Gly487Ala missense_variant De novo - - 28191889 Stessman HA , et al. (2017)
c.2384_2391del p.Leu795HisfsTer7 frameshift_variant De novo - - 28191889 Stessman HA , et al. (2017)
c.92_99delGCCCCCCCinsGCCCCCCCC p.Ser34GlnfsTer25 frameshift_variant De novo - - 28191889 Stessman HA , et al. (2017)
c.1376G>A p.Gly459Glu missense_variant De novo - - 28191889 Stessman HA , et al. (2017)
Common Variants   (32)
Status Allele Change Residue Change Variant Type Inheritance Pattern Paternal Transmission Family Type PubMed ID Author, Year
c.15G>T p.(=) synonymous_variant - - - 11317224 Ohtsuki T , et al. (2001)
c.366C>G p.(=) synonymous_variant - - - 11317224 Ohtsuki T , et al. (2001)
c.1665C>T p.(=) synonymous_variant - - - 11317224 Ohtsuki T , et al. (2001)
c.2664C>T p.(=) synonymous_variant - - - 11317224 Ohtsuki T , et al. (2001)
c.4197T>C p.(=) synonymous_variant - - - 11317224 Ohtsuki T , et al. (2001)
C4615T - 3_prime_UTR_variant - - - 11317224 Ohtsuki T , et al. (2001)
A5806A/C - 3_prime_UTR_variant - - - 11317224 Ohtsuki T , et al. (2001)
5988T/C - 3_prime_UTR_variant - - - 11317224 Ohtsuki T , et al. (2001)
T5072G N/A 3_prime_UTR_variant - - - 15083261 Arnold PD , et al. (2004)
T5988C N/A 3_prime_UTR_variant - - - 15083261 Arnold PD , et al. (2004)
c.-19+54228G>A A/G intron_variant - - - 25337070 Poot M (2014)
- G/A downstream_gene_variant - - - 25656819 Pan Y , et al. (2015)
c.2011-14090A>G;c.-43-16037A>G A/G intron_variant - - - 25656819 Pan Y , et al. (2015)
c.2011-17252A>C;c.-43-19199A>C - intron_variant - - - 25656819 Pan Y , et al. (2015)
c.2010+16493A>G;c.-44+16493A>G A/G intron_variant - - - 25656819 Pan Y , et al. (2015)
c.2010+10285C>A;c.-44+10285C>A A/C intron_variant - - - 25656819 Pan Y , et al. (2015)
c.2010+8705T>C;c.-44+8705T>C A/G intron_variant - - - 25656819 Pan Y , et al. (2015)
c.1125+15349G>A A/G intron_variant - - - 25656819 Pan Y , et al. (2015)
c.1125+8652A>G A/G intron_variant - - - 25656819 Pan Y , et al. (2015)
c.1125+6440G>A A/G intron_variant - - - 25656819 Pan Y , et al. (2015)
c.1125+3263A>G A/G intron_variant - - - 25656819 Pan Y , et al. (2015)
c.1125+2272T>C - intron_variant - - - 25656819 Pan Y , et al. (2015)
c.1011-13916G>A A/G intron_variant - - - 25656819 Pan Y , et al. (2015)
c.1010+23237C>T G/A intron_variant - - - 25656819 Pan Y , et al. (2015)
c.1010+9696T>C A/G intron_variant - - - 25656819 Pan Y , et al. (2015)
c.412-44918A>C C/A intron_variant - - - 25656819 Pan Y , et al. (2015)
c.412-46045T>C G/A intron_variant - - - 25656819 Pan Y , et al. (2015)
c.411+37406T>G C/A intron_variant - - - 25656819 Pan Y , et al. (2015)
c.411+18164C>A A/C intron_variant - - - 25656819 Pan Y , et al. (2015)
c.411+8818T>C G/A intron_variant - - - 25656819 Pan Y , et al. (2015)
c.4197T>C;c.1983T>C p.(=) synonymous_variant - - - 25656819 Pan Y , et al. (2015)
c.1806C>T;c.-248C>T p.(=) synonymous_variant - - - 25656819 Pan Y , et al. (2015)
SFARI Gene score
1

High Confidence

Studies have identified rare mutations in the GRIN2B gene with autism. In particular, O'Roak et al. (2011) found a single individual with a 3' splice mutation of GRIN2B, Myers et al. (2011) found an excess of rare non-synonymous mutations in GRIN2B in both autism and schizophrenia. As well, Yoo et al. (2012) showed association of GRIN2B markers in a Korean cohort of 151 families. Studies have also found genetic association of the GRIN2B gene with obsessive-compulsive disorder (Arnold et al., 2004) as well as with schizophrenia (Ohtsuki et al., 2001). PMID 22495309 and 23160955 reported 3 de novo LoF in GRIN2B. 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 GRIN2B as a gene meeting high statistical significance with a FDR ?0.01, meaning that this gene had a ?99% chance of being a true autism gene (PMID 25363760). This gene was identified in Iossifov et al. 2015 as a strong candidate to be an ASD risk gene based on a combination of de novo mutational evidence and the absence or very low frequency of mutations in controls (PMID 26401017).

1

High Confidence

See all Category 1 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.

01-01-2017
1

Initial score established: 1

Description

Studies have identified rare mutations in the GRIN2B gene with autism. In particular, O'Roak et al. (2011) found a single individual with a 3' splice mutation of GRIN2B, Myers et al. (2011) found an excess of rare non-synonymous mutations in GRIN2B in both autism and schizophrenia. As well, Yoo et al. (2012) showed association of GRIN2B markers in a Korean cohort of 151 families. Studies have also found genetic association of the GRIN2B gene with obsessive-compulsive disorder (Arnold et al., 2004) as well as with schizophrenia (Ohtsuki et al., 2001). PMID 22495309 and 23160955 reported 3 de novo LoF in GRIN2B. 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 GRIN2B as a gene meeting high statistical significance with a FDR ?0.01, meaning that this gene had a ?99% chance of being a true autism gene (PMID 25363760). This gene was identified in Iossifov et al. 2015 as a strong candidate to be an ASD risk gene based on a combination of de novo mutational evidence and the absence or very low frequency of mutations in controls (PMID 26401017).

CNVs associated with GRIN2B(1 CNVs)
12p13.1 9 Deletion 14  /  16
Animal Models associated with GRIN2B(10 Models)
Grin2B_10_TG_HT_Grin2A Genetic
Grin2b_1_CN_KO_HM Genetic
Grin2b_2_CN_KO_HM Genetic
Grin2b_3_WT_ANT Induced
Grin2B_4_TG Genetic
Grin2B_5_cKO_HM Genetic
Grin2B_6_cKO_HM Genetic
Grin2B_7_TG_HM_Grin2A Genetic
Grin2B_8_KO_HM Genetic
Grin2B_9_CKO_HM Genetic
Interaction Table
Interactor Symbol Interactor Name Interactor Organism Interactor Type Entrez ID Uniprot ID
GRIN3A glutamate receptor, ionotropic, N-methyl-D-aspartate 3A Human Protein Binding 116443 Q8TCU5
Il16 interleukin 16 Mouse Protein Binding 16170 O54824
Il1r1 interleukin 1 receptor, type I Rat Protein Binding 25663 Q05KR1
MIR223 microRNA 223 Human RNA Binding 407008 N/A
PLAT plasminogen activator, tissue Human Protein Modification 5327 P00750
Trpv1 transient receptor potential cation channel, subfamily V, member 1 Rat Protein Binding 83810 O35433
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