Human Gene Module / Chromosome 16 / GRIN2A

GRIN2Aglutamate receptor, ionotropic, N-methyl D-aspartate 2A

Score
4
Minimal Evidence Criteria 4.1
Autism Reports / Total Reports
6 / 34
Rare Variants / Common Variants
86 / 5
Aliases
GRIN2A, NR2A,  NMDAR2A
Associated Syndromes
-
Genetic Category
Rare Single Gene Mutation, Syndromic, Genetic Association
Chromosome Band
16p13.2
Associated Disorders
ASD, DD/NDD, EPS, ADHD, ID, EP
Relevance to Autism

Genetic association has been found between the GRIN2A gene and autism in an IMGSAC cohort (Barnby et al., 2005).

Molecular Function

The encoded protein is a subunit of N-methyl-D-aspartate (NMDA) selective glutamate receptors.

Reports related to GRIN2A (34 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary Candidate-gene screening and association analysis at the autism-susceptibility locus on chromosome 16p: evidence of association at GRIN2A and ABAT. Barnby G , et al. (2005) Yes -
2 Recent Recommendation Integrative properties of radial oblique dendrites in hippocampal CA1 pyramidal neurons. Losonczy A and Magee JC (2006) No -
3 Recent Recommendation Cholesterol-enriched diet affects spatial learning and synaptic function in hippocampal synapses. Dufour F , et al. (2006) No -
4 Recent Recommendation Zinc modulates bidirectional hippocampal plasticity by effects on NMDA receptors. Izumi Y , et al. (2006) No -
5 Recent Recommendation NMDA receptor function: subunit composition versus spatial distribution. Khr G (2006) No -
6 Support Mutations in GRIN2A and GRIN2B encoding regulatory subunits of NMDA receptors cause variable neurodevelopmental phenotypes. Endele S , et al. (2010) No ID
7 Support Exome sequencing of ion channel genes reveals complex profiles confounding personal risk assessment in epilepsy. Klassen T , et al. (2011) No -
8 Support Epileptic encephalopathies of the Landau-Kleffner and continuous spike and waves during slow-wave sleep types: genomic dissection makes the link wi... Lesca G , et al. (2012) No ADHD
9 Support Rare mutations in N-methyl-D-aspartate glutamate receptors in autism spectrum disorders and schizophrenia. Tarabeux J , et al. (2011) Yes -
10 Support Diagnostic exome sequencing in persons with severe intellectual disability. de Ligt J , et al. (2012) No Epilepsy, ASD
11 Support Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder. Girirajan S , et al. (2013) Yes -
12 Positive association Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis. Cross-Disorder Group of the Psychiatric Genomics Consortium (2013) Yes -
13 Recent Recommendation GRIN2A mutations cause epilepsy-aphasia spectrum disorders. Carvill GL , et al. (2013) No -
14 Recent Recommendation Mutations in GRIN2A cause idiopathic focal epilepsy with rolandic spikes. Lemke JR , et al. (2013) No DD, ID
15 Recent Recommendation GRIN2A mutations in acquired epileptic aphasia and related childhood focal epilepsies and encephalopathies with speech and language dysfunction. Lesca G , et al. (2013) No -
16 Support Gene Mutation Analysis in 253 Chinese Children with Unexplained Epilepsy and Intellectual/Developmental Disabilities. Zhang Y , et al. (2015) No -
17 Support Targeted DNA Sequencing from Autism Spectrum Disorder Brains Implicates Multiple Genetic Mechanisms. D'Gama AM , et al. (2015) Yes -
18 Recent recommendation Systems genetics identifies a convergent gene network for cognition and neurodevelopmental disease. Johnson MR , et al. (2015) No -
19 Support Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability. Lelieveld SH , et al. (2016) No -
20 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 ASD (1 case), epilepsy/seizures (1 case)
21 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 -
22 Support Epilepsy in patients with GRIN2A alterations: Genetics, neurodevelopment, epileptic phenotype and response to anticonvulsive drugs. von Stlpnagel C , et al. (2017) No DD, ID
23 Support A de novo loss-of-function GRIN2A mutation associated with childhood focal epilepsy and acquired epileptic aphasia. Gao K , et al. (2017) No -
24 Recent recommendation Epilepsy-associated GRIN2A mutations reduce NMDA receptor trafficking and agonist potency - molecular profiling and functional rescue. Addis L , et al. (2017) No -
25 Support A clinical utility study of exome sequencing versus conventional genetic testing in pediatric neurology. Vissers LE , et al. (2017) No -
26 Support Next-generation DNA sequencing identifies novel gene variants and pathways involved in specific language impairment. Chen XS , et al. (2017) No -
27 Support Functional assessment of the NMDA receptor variant GluN2A R586K. Marwick KFM , et al. (2017) No -
28 Support Genomic diagnosis for children with intellectual disability and/or developmental delay. Bowling KM , et al. (2017) No -
29 Support Functional Properties of Human NMDA Receptors Associated with Epilepsy-Related Mutations of GluN2A Subunit. Sibarov DA , et al. (2017) No -
30 Support Improved diagnostic yield compared with targeted gene sequencing panels suggests a role for whole-genome sequencing as a first-tier genetic test. Lionel AC , et al. (2017) No -
31 Highly Cited Endothelium-derived relaxing factor release on activation of NMDA receptors suggests role as intercellular messenger in the brain. Garthwaite J , et al. (1988) No -
32 Support Effect of Angiotensin-Converting Enzyme Inhibitor/Calcium Antagonist Combination Therapy on Renal Function in Hypertensive Patients With Chronic Ki... Okuda T , et al. (2018) Yes -
33 Positive association Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection. Pardias AF , et al. (2018) No -
34 Highly Cited Developmental and regional expression in the rat brain and functional properties of four NMDA receptors. Monyer H , et al. (1994) No -
Rare Variants   (86)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
- - translocation Familial Maternal & paternal Multi-generational 20890276 Endele S , et al. (2010)
c.652C>T p.Gln218Ter stop_gained Familial Maternal Multi-generational 20890276 Endele S , et al. (2010)
c.1845C>A p.Asn615Lys missense_variant De novo - - 20890276 Endele S , et al. (2010)
c.1757G>A p.Arg586Lys missense_variant Familial Maternal - 20890276 Endele S , et al. (2010)
c.3190A>G p.Thr1064Ala missense_variant - - - 20890276 Endele S , et al. (2010)
c.3228C>G p.Asn1076Lys missense_variant Unknown - - 20890276 Endele S , et al. (2010)
C>T p.(=) synonymous_variant Unknown - Unknown 21703448 Klassen T , et al. (2011)
G>T p.(=) synonymous_variant Unknown - Unknown 21703448 Klassen T , et al. (2011)
c.2332G>C p.Ala778Pro missense_variant Unknown - Unknown 21703448 Klassen T , et al. (2011)
C>T p.Met788Ile missense_variant Unknown - Unknown 21703448 Klassen T , et al. (2011)
c.2855A>G p.Lys952Arg missense_variant Unknown - Unknown 21703448 Klassen T , et al. (2011)
- - copy_number_loss De novo - Unknown 22738016 Lesca G , et al. (2012)
c.2902G>A p.Ala968Thr missense_variant De novo - Simplex 22833210 Tarabeux J , et al. (2011)
c.3669C>T p.(=) synonymous_variant De novo - Simplex 22833210 Tarabeux J , et al. (2011)
c.428C>T p.Thr143Ile missense_variant - - - 22833210 Tarabeux J , et al. (2011)
c.2765C>T p.Ala922Val missense_variant - - - 22833210 Tarabeux J , et al. (2011)
c.1945C>G p.Leu649Val missense_variant De novo - - 23033978 de Ligt J , et al. (2012)
c.1655C>G p.Pro552Arg missense_variant De novo - - 23033978 de Ligt J , et al. (2012)
- - copy_number_gain Familial Maternal Multiplex 23375656 Girirajan S , et al. (2013)
c.1007 + 1G>A p.Phe139IlefsTer15 splice_site_variant Familial Family A: maternal and paternal; family C: paternal Multi-generational 23933818 Carvill GL , et al. (2013)
c.2T>C p.Met1Thr initiator_codon_variant Familial Paternal Multi-generational 23933818 Carvill GL , et al. (2013)
c.1592C>T p.Thr531Met missense_variant Familial Maternal Multiplex 23933818 Carvill GL , et al. (2013)
c.728C>T p.Ala243Val missense_variant Unknown - Unknown 23933819 Lemke JR , et al. (2013)
c.2041C>T p.Arg681Ter stop_gained Familial Maternal Multi-generational 23933819 Lemke JR , et al. (2013)
c.1007 + 1G>A - splice_site_variant Unknown (n=2), Familial (n=2) Maternal (n=2) Unknown (n=1), multiplex (n=3) 23933819 Lemke JR , et al. (2013)
c.1108C>T p.Arg370Trp missense_variant Unknown - Unknown 23933819 Lemke JR , et al. (2013)
c.2140G>A p.Glu714Lys missense_variant Unknown - Unknown 23933819 Lemke JR , et al. (2013)
c.2927A>G p.Asn976Ser missense_variant Unknown (both cases) - Unknown (both cases) 23933819 Lemke JR , et al. (2013)
c.594G>A p.Trp198Ter stop_gained Unknown - Unknown 23933819 Lemke JR , et al. (2013)
c.1001T>A p.Leu334Ter stop_gained Familial Paternal Multi-generational 23933819 Lemke JR , et al. (2013)
c.2334_2338delCTTGC p.Leu779SerfsTer5 frameshift_variant Familial Paternal Simplex 23933819 Lemke JR , et al. (2013)
c.2829C>G p.Tyr943Ter stop_gained Familial Paternal Multi-generational 23933819 Lemke JR , et al. (2013)
c.2007 + 1G>A - splice_site_variant Familial Paternal Multi-generational 23933819 Lemke JR , et al. (2013)
c.236C>G p.Pro79Arg missense_variant Familial Maternal Multi-generational 23933819 Lemke JR , et al. (2013)
c.547T>A p.Phe183Ile missense_variant Familial Paternal Simplex 23933819 Lemke JR , et al. (2013)
c.692G>A p.Cys231Tyr missense_variant Familial Maternal Multiplex 23933819 Lemke JR , et al. (2013)
c.869C>T p.Ala290Val missense_variant Unknown - Unknown 23933819 Lemke JR , et al. (2013)
c.1306T>C p.Cys436Arg missense_variant De novo - Multiplex 23933819 Lemke JR , et al. (2013)
c.2095C>T p.Pro699Ser missense_variant De novo - Simplex 23933819 Lemke JR , et al. (2013)
c.2113A>G p.Met705Val missense_variant Familial Maternal Multiplex 23933819 Lemke JR , et al. (2013)
c.2179G>A p.Ala727Thr missense_variant Unknown - Unknown 23933819 Lemke JR , et al. (2013)
c.2200G>C p.Val734Leu missense_variant Familial Paternal Multiplex 23933819 Lemke JR , et al. (2013)
c.2314A>G p.Lys772Glu missense_variant Unknown - Unknown 23933819 Lemke JR , et al. (2013)
c.2441T>C p.Ile814Thr missense_variant Familial Paternal Simplex 23933819 Lemke JR , et al. (2013)
c.2710A>T p.Ile904Phe missense_variant Familial Paternal Multi-generational 23933819 Lemke JR , et al. (2013)
c.90delTins(T)2 p.Pro31SerfsTer107 frameshift_variant Familial Maternal Multi-generational 23933819 Lemke JR , et al. (2013)
c.1585delG p.Val529TrpfsTer22 frameshift_variant Familial Maternal Multi-generational 23933819 Lemke JR , et al. (2013)
c.1637_1639delCTT p.Ser547del inframe_deletion Unknown Not maternal Multiplex 23933819 Lemke JR , et al. (2013)
- - copy_number_loss Unknown - Unknown 23933819 Lemke JR , et al. (2013)
- - copy_number_loss Unknown - Unknown 23933819 Lemke JR , et al. (2013)
- - copy_number_loss Unknown - Unknown 23933819 Lemke JR , et al. (2013)
- - copy_number_gain Unknown - Unknown 23933819 Lemke JR , et al. (2013)
c.1123-2A>G p.Val375fs splice_site_variant Familial Maternal Multi-generational 23933820 Lesca G , et al. (2013)
- - copy_number_loss Familial Maternal Multiplex 23933820 Lesca G , et al. (2013)
- Phe670fs copy_number_loss Familial Maternal Multi-generational 23933820 Lesca G , et al. (2013)
c.4161C>A p.Tyr1387Ter stop_gained Familial Maternal Multi-generational 23933820 Lesca G , et al. (2013)
c.1510C>T p.Arg504Trp missense_variant Familial Maternal Multiplex 23933820 Lesca G , et al. (2013)
c.1447G>A p.Gly483Arg missense_variant Familial Maternal Multiplex 23933820 Lesca G , et al. (2013)
c.1553G>A p.Arg518His missense_variant Familial Paternal Multi-generational 23933820 Lesca G , et al. (2013)
c.2191G>A p.Asp731Asn missense_variant Familial Maternal Multi-generational 23933820 Lesca G , et al. (2013)
c.3751G>A p.Asp1251Asn missense_variant Familial Paternal - 23933820 Lesca G , et al. (2013)
c.2146G>A p.Ala716Thr missense_variant Familial Maternal Multi-generational 23933820 Lesca G , et al. (2013)
c.2797G>A p.Asp933Asn missense_variant Familial Paternal Simplex 23933820 Lesca G , et al. (2013)
c.551T>G p.Ile184Ser missense_variant Familial Maternal Simplex 23933820 Lesca G , et al. (2013)
c.2081T>C p.Ile694Thr missense_variant De novo - Simplex 23933820 Lesca G , et al. (2013)
c.1954T>G p.Phe652Val missense_variant De novo - Simplex 23933820 Lesca G , et al. (2013)
c.1642G>A p.Ala548Thr missense_variant De novo - Simplex 23933820 Lesca G , et al. (2013)
c.2007G>T p.Lys669Asn missense_variant Unknown - Simplex 23933820 Lesca G , et al. (2013)
c.883G>A p.Gly295Ser missense_variant Unknown Not maternal Simplex 23933820 Lesca G , et al. (2013)
c.3827C>G p.Ala1276Gly missense_variant Unknown - Unknown 23933820 Lesca G , et al. (2013)
c.2191G>A p.Asp731Asn missense_variant De novo - Simplex 26544041 Zhang Y , et al. (2015)
c.2650G>A p.Asp884Asn missense_variant Unknown - Unknown 26637798 D'Gama AM , et al. (2015)
c.2450T>C p.Met817Thr missense_variant De novo - - 27479843 Lelieveld SH , et al. (2016)
c.2054T>C p.Val685Gly missense_variant Unknown - - 27839871 Swanger SA , et al. (2016)
c.1586delT p.Phe528GlyfsTer22 frameshift_variant Unknown - Multi-generational 28109652 von Stlpnagel C , et al. (2017)
c.1818G>A p.Trp606Ter stop_gained Unknown - - 28109652 von Stlpnagel C , et al. (2017)
c.2407G>T p.Glu803Ter stop_gained De novo - - 28109652 von Stlpnagel C , et al. (2017)
c.2007+1G>A p.? splice_site_variant Familial Paternal - 28109652 von Stlpnagel C , et al. (2017)
- - copy_number_gain Unknown - - 28109652 von Stlpnagel C , et al. (2017)
c.1841A>G p.Asn614Ser missense_variant De novo - - 28109652 von Stlpnagel C , et al. (2017)
c.1936A>G p.Thr646Ala missense_variant De novo - - 28109652 von Stlpnagel C , et al. (2017)
c.2191G>A p.Asp731Asn missense_variant De novo - Simplex 28182669 Gao K , et al. (2017)
c.2450T>C p.Met817Thr missense_variant De novo - - 28333917 Vissers LE , et al. (2017)
c.2063G>C p.Gly688Ala missense_variant De novo - Possible multi-generational 28440294 Chen XS , et al. (2017)
c.4375A>G p.Ser1459Gly missense_variant De novo - - 28554332 Bowling KM , et al. (2017)
c.2050A>G p.Thr684Ala missense_variant De novo - - 28771251 Lionel AC , et al. (2017)
Common Variants   (5)
Status Allele Change Residue Change Variant Type Inheritance Pattern Paternal Transmission Family Type PubMed ID Author, Year
c.1576T>C p.(=) synonymous_variant - - - 15830322 Barnby G , et al. (2005)
c.2316-35G>C - intron_variant - - - 15830322 Barnby G , et al. (2005)
c.*1212C>T;c.*1418C>T - 3_prime_UTR_variant - - - 15830322 Barnby G , et al. (2005)
c.2168+4735G>T;c.2324+4735G>T;c.1697+4735G>T A/C intron_variant - - - 23453885 Cross-Disorder Group of the Psychiatric Genomics Consortium (2013)
c.2169-7736A>G;c.2325-7736A>G;c.1698-7736A>G - intron_variant - - - 29483656 Pardias AF , et al. (2018)
SFARI Gene score
4

Minimal Evidence

There is association and linkage evidence for the GRIN2A gene. For example, genetic association has been found between the GRIN2A gene and autism in an IMGSAC cohort (Barnby et al., 2005).

Score Delta: Score remained at 4

4

Minimal Evidence

See all Category 4 Genes

The literature is replete with relatively small studies of candidate genes, using either common or rare variant approaches, which do not reach the criteria set out for categories 1 and 2. Genes that had two such lines of supporting evidence were placed in category 3, and those with one line of evidence were placed in category 4. Some additional lines of "accessory evidence" (indicated as 'acc" in the score cards) could also boost a gene from category 4 to 3.

1/1/2018
4
icon
4

Score remained at 4

Description

There is association and linkage evidence for the GRIN2A gene. For example, genetic association has been found between the GRIN2A gene and autism in an IMGSAC cohort (Barnby et al., 2005).

7/1/2017
4
icon
4

Score remained at 4

Description

There is association and linkage evidence for the GRIN2A gene. For example, genetic association has been found between the GRIN2A gene and autism in an IMGSAC cohort (Barnby et al., 2005).

4/1/2017
4
icon
4

Score remained at 4

Description

There is association and linkage evidence for the GRIN2A gene. For example, genetic association has been found between the GRIN2A gene and autism in an IMGSAC cohort (Barnby et al., 2005).

Reports Added
[Epileptic encephalopathies of the Landau-Kleffner and continuous spike and waves during slow-wave sleep types: genomic dissection makes the link wi...2012] [Epilepsy in patients with GRIN2A alterations: Genetics, neurodevelopment, epileptic phenotype and response to anticonvulsive drugs.2017] [A de novo loss-of-function GRIN2A mutation associated with childhood focal epilepsy and acquired epileptic aphasia.2017] [A clinical utility study of exome sequencing versus conventional genetic testing in pediatric neurology.2017] [Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis.2013] [Diagnostic exome sequencing in persons with severe intellectual disability.2012] [Cholesterol-enriched diet affects spatial learning and synaptic function in hippocampal synapses.2006] [Zinc modulates bidirectional hippocampal plasticity by effects on NMDA receptors.2006] [GRIN2A mutations cause epilepsy-aphasia spectrum disorders.2013] [Mutations in GRIN2A cause idiopathic focal epilepsy with rolandic spikes.2013] [GRIN2A mutations in acquired epileptic aphasia and related childhood focal epilepsies and encephalopathies with speech and language dysfunction.2013] [Mechanistic Insight into NMDA Receptor Dysregulation by Rare Variants in the GluN2A and GluN2B Agonist Binding Domains.2016] [NMDA receptor function: subunit composition versus spatial distribution.2006] [Rare mutations in N-methyl-D-aspartate glutamate receptors in autism spectrum disorders and schizophrenia.2011] [Gene Mutation Analysis in 253 Chinese Children with Unexplained Epilepsy and Intellectual/Developmental Disabilities.2015] [Targeted DNA Sequencing from Autism Spectrum Disorder Brains Implicates Multiple Genetic Mechanisms.2015] [Systems genetics identifies a convergent gene network for cognition and neurodevelopmental disease.2015] [Functional assessment of the NMDA receptor variant GluN2A R586K.2017] [Endothelium-derived relaxing factor release on activation of NMDA receptors suggests role as intercellular messenger in the brain.1988] [Next-generation DNA sequencing identifies novel gene variants and pathways involved in specific language impairment.2017] [Mutations in GRIN2A and GRIN2B encoding regulatory subunits of NMDA receptors cause variable neurodevelopmental phenotypes.2010] [Epilepsy-associated GRIN2A mutations reduce NMDA receptor trafficking and agonist potency - molecular profiling and functional rescue.2017] [Developmental and regional expression in the rat brain and functional properties of four NMDA receptors.1994] [Exome sequencing of ion channel genes reveals complex profiles confounding personal risk assessment in epilepsy.2011] [Molecular Mechanism of Disease-Associated Mutations in the Pre-M1 Helix of NMDA Receptors and Potential Rescue Pharmacology.2017] [Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability.2016] [Genomic diagnosis for children with intellectual disability and/or developmental delay.2017] [Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.2013] [Candidate-gene screening and association analysis at the autism-susceptibility locus on chromosome 16p: evidence of association at GRIN2A and ABAT.2005] [Integrative properties of radial oblique dendrites in hippocampal CA1 pyramidal neurons.2006]
10/1/2016
4
icon
4

Score remained at 4

Description

There is association and linkage evidence for the GRIN2A gene. For example, genetic association has been found between the GRIN2A gene and autism in an IMGSAC cohort (Barnby et al., 2005).

7/1/2016
4
icon
4

Score remained at 4

Description

There is association and linkage evidence for the GRIN2A gene. For example, genetic association has been found between the GRIN2A gene and autism in an IMGSAC cohort (Barnby et al., 2005).

1/1/2016
4
icon
4

Score remained at 4

Description

There is association and linkage evidence for the GRIN2A gene. For example, genetic association has been found between the GRIN2A gene and autism in an IMGSAC cohort (Barnby et al., 2005).

Reports Added
[Developmental and regional expression in the rat brain and functional properties of four NMDA receptors.1994] [Cholesterol-enriched diet affects spatial learning and synaptic function in hippocampal synapses.2006] [Endothelium-derived relaxing factor release on activation of NMDA receptors suggests role as intercellular messenger in the brain.1988] [Epileptic encephalopathies of the Landau-Kleffner and continuous spike and waves during slow-wave sleep types: genomic dissection makes the link wi...2012] [NMDA receptor function: subunit composition versus spatial distribution.2006] [Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis.2013] [Mutations in GRIN2A cause idiopathic focal epilepsy with rolandic spikes.2013] [GRIN2A mutations in acquired epileptic aphasia and related childhood focal epilepsies and encephalopathies with speech and language dysfunction.2013] [Exome sequencing of ion channel genes reveals complex profiles confounding personal risk assessment in epilepsy.2011] [Diagnostic exome sequencing in persons with severe intellectual disability.2012] [Candidate-gene screening and association analysis at the autism-susceptibility locus on chromosome 16p: evidence of association at GRIN2A and ABAT.2005] [Zinc modulates bidirectional hippocampal plasticity by effects on NMDA receptors.2006] [GRIN2A mutations cause epilepsy-aphasia spectrum disorders.2013] [Mutations in GRIN2A and GRIN2B encoding regulatory subunits of NMDA receptors cause variable neurodevelopmental phenotypes.2010] [Rare mutations in N-methyl-D-aspartate glutamate receptors in autism spectrum disorders and schizophrenia.2011] [Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.2013] [Targeted DNA Sequencing from Autism Spectrum Disorder Brains Implicates Multiple Genetic Mechanisms.2015] [Integrative properties of radial oblique dendrites in hippocampal CA1 pyramidal neurons.2006] [Systems genetics identifies a convergent gene network for cognition and neurodevelopmental disease.2015] [Gene Mutation Analysis in 253 Chinese Children with Unexplained Epilepsy and Intellectual/Developmental Disabilities.2015]
7/1/2014
No data
icon
4

Increased from No data to 4

Description

There is association and linkage evidence for the GRIN2A gene. For example, genetic association has been found between the GRIN2A gene and autism in an IMGSAC cohort (Barnby et al., 2005).

4/1/2014
No data
icon
4

Increased from No data to 4

Description

There is association and linkage evidence for the GRIN2A gene. For example, genetic association has been found between the GRIN2A gene and autism in an IMGSAC cohort (Barnby et al., 2005).

Krishnan Probability Score

Score 0.63703855943237

Ranking 56/25841 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 0.99804480805101

Ranking 1249/18225 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
Sanders TADA Score

Score 0.94842664598765

Ranking 17679/18665 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 9

Ranking 197/461 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 -0.085195646077055

Ranking 11774/20870 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 GRIN2A(1 CNVs)
16p13.2 33 Deletion-Duplication 50  /  215
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