Human Gene Module / Chromosome 5 / NR2F1

NR2F1nuclear receptor subfamily 2 group F member 1

SFARI Gene Score
3S
Suggestive Evidence, Syndromic Criteria 3.1, Syndromic
Autism Reports / Total Reports
8 / 19
Rare Variants / Common Variants
53 / 0
Aliases
NR2F1, BBOAS,  BBSOAS,  COUP-TFI,  EAR-3,  EAR3,  ERBAL3,  NR2F2,  SVP44,  TCFCOUP1,  TFCOUP1
Associated Syndromes
Bosch-Boonstra-Schaaf optic atrophy syndrome
Genetic Category
Rare Single Gene Mutation, Syndromic, Functional
Chromosome Band
5q15
Associated Disorders
DD/NDD, ADHD, EPS, ASD, ID
Relevance to Autism

One of the six patients with Bosch-Boonstra-Schaaf optic atrophy syndrome described in Bosch et al., 2014 presented with autism spectrum disorder with marked obsessive-compulsive behaviors. Evaluation of the clinical features of 20 individuals with novel pathogenic NR2F1 variants demonstrated that, in addition to visual and cognitive deficits, individuals with BBSOAS manifested hypotonia (75%), seizures (40%), repetitive behavior (40%), autism spectrum disorder (35%), oromotor dysfunction (60%), thinning of the corpus callosum (53%), and hearing defects (20%) (Chen et al., 2016). De novo probably damaging missense variants in NR2F1 have also been observed in two ASD probands: one from the Simons Simplex Collection (Sanders et al., 2012), the other from the Autism Sequencing Consortium (De Rubeis et al., 2014).

Molecular Function

The protein encoded by this gene is a nuclear hormone receptor and transcriptional regulator that binds to 5'-AGGTCA-3' repeats. Heterozygous mutations in this gene are a cause of Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS; OMIM 615722), an autosomal dominant disorder characterized by delayed development, moderate intellectual disability, and optic atrophy (Bosch et al., 2014).

Reports related to NR2F1 (19 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Support De novo mutations revealed by whole-exome sequencing are strongly associated with autism Sanders SJ , et al. (2012) Yes -
2 Primary NR2F1 mutations cause optic atrophy with intellectual disability Bosch DG , et al. (2014) No ID, ASD
3 Support Synaptic, transcriptional and chromatin genes disrupted in autism De Rubeis S , et al. (2014) Yes -
4 Recent Recommendation The expanding clinical phenotype of Bosch-Boonstra-Schaaf optic atrophy syndrome: 20 new cases and possible genotype-phenotype correlations Chen CA , et al. (2016) No ID, ASD, epilepsy/seizures, ADHD
5 Support Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability Lelieveld SH et al. (2016) No -
6 Support The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies Redin C , et al. (2016) No Multiple congenital anomalies
7 Support Lessons learned from additional research analyses of unsolved clinical exome cases Eldomery MK , et al. (2017) Yes -
8 Support A clinical utility study of exome sequencing versus conventional genetic testing in pediatric neurology Vissers LE , et al. (2017) No -
9 Support Leveraging blood serotonin as an endophenotype to identify de novo and rare variants involved in autism Chen R , et al. (2017) Yes -
10 Support Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder Lim ET , et al. (2017) Yes -
11 Support The combination of whole-exome sequencing and copy number variation sequencing enables the diagnosis of rare neurological disorders Jiao Q , et al. (2019) No DD, ID
12 Support Increased diagnostic and new genes identification outcome using research reanalysis of singleton exome sequencing Bruel AL , et al. (2019) No -
13 Support Autism risk in offspring can be assessed through quantification of male sperm mosaicism Breuss MW , et al. (2019) Yes -
14 Support Rare genetic susceptibility variants assessment in autism spectrum disorder: detection rate and practical use Husson T , et al. (2020) Yes -
15 Recent Recommendation Phenotypic expansion of Bosch-Boonstra-Schaaf optic atrophy syndrome and further evidence for genotype-phenotype correlations Rech ME et al. (2020) No ASD or autistic features, ADHD
16 Recent Recommendation Imbalance of Excitatory/Inhibitory Neuron Differentiation in Neurodevelopmental Disorders with an NR2F1 Point Mutation Zhang K et al. (2020) Yes -
17 Support Missense NR2F1 variant in monozygotic twins affected with the Bosch-Boonstra-Schaaf optic atrophy syndrome Mio C et al. (2020) No -
18 Support NR2F1 regulates regional progenitor dynamics in the mouse neocortex and cortical gyrification in BBSOAS patients Bertacchi M et al. (2020) No -
19 Support Novel dominant-negative NR2F1 frameshift mutation and a phenotypic expansion of the Bosch-Boonstra-Schaaf optic atrophy syndrome Walsh S et al. (2020) No ASD, DD, epilepsy/seizures
Rare Variants   (53)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
- - copy_number_loss Unknown - - 32275123 Rech ME et al. (2020)
- - copy_number_loss Unknown - - 26986877 Chen CA , et al. (2016)
- - copy_number_loss Unknown - - 24462372 Bosch DG , et al. (2014)
- - copy_number_loss De novo NA - 26986877 Chen CA , et al. (2016)
- - copy_number_loss De novo NA - 24462372 Bosch DG , et al. (2014)
- - copy_number_loss Familial Maternal - 32275123 Rech ME et al. (2020)
- - complex_structural_alteration De novo NA - 27841880 Redin C , et al. (2016)
c.1117C>T p.Arg373Ter stop_gained De novo NA - 32275123 Rech ME et al. (2020)
- - copy_number_loss Familial Paternal Simplex 26986877 Chen CA , et al. (2016)
c.284G>T p.Gly95Val missense_variant Unknown - - 32275123 Rech ME et al. (2020)
c.290A>C p.His97Pro missense_variant Unknown - - 32275123 Rech ME et al. (2020)
c.323G>T p.Ser108Ile missense_variant Unknown - - 32275123 Rech ME et al. (2020)
c.365G>C p.Cys122Ser missense_variant Unknown - - 32275123 Rech ME et al. (2020)
c.931G>C p.Ala311Pro missense_variant Unknown - - 32275123 Rech ME et al. (2020)
c.256T>C p.Cys86Arg missense_variant De novo NA - 32275123 Rech ME et al. (2020)
c.262G>A p.Val88Met missense_variant De novo NA - 32275123 Rech ME et al. (2020)
c.293A>G p.Tyr98Cys missense_variant De novo NA - 32275123 Rech ME et al. (2020)
c.311A>G p.Glu104Gly missense_variant De novo NA - 32275123 Rech ME et al. (2020)
c.417A>T p.Gln139His missense_variant De novo NA - 32275123 Rech ME et al. (2020)
c.954G>C p.Glu318Asp missense_variant De novo NA - 32275123 Rech ME et al. (2020)
c.82C>T p.Gln28Ter stop_gained De novo NA Simplex 28344757 Chen R , et al. (2017)
c.1217T>C p.Met406Thr missense_variant De novo NA - 32275123 Rech ME et al. (2020)
c.2T>C p.Met1? initiator_codon_variant De novo NA - 30945278 Jiao Q , et al. (2019)
c.1A>G p.Met1? initiator_codon_variant De novo NA - 32275123 Rech ME et al. (2020)
c.2T>C p.Met1? initiator_codon_variant De novo NA - 32275123 Rech ME et al. (2020)
c.382T>C p.Cys128Arg missense_variant De novo NA - 26986877 Chen CA , et al. (2016)
c.403C>A p.Arg135Ser missense_variant De novo NA - 26986877 Chen CA , et al. (2016)
c.413G>A p.Cys138Tyr missense_variant De novo NA - 26986877 Chen CA , et al. (2016)
c.425G>T p.Arg142Leu missense_variant De novo NA - 26986877 Chen CA , et al. (2016)
c.436T>C p.Cys146Arg missense_variant De novo NA - 26986877 Chen CA , et al. (2016)
c.463G>A p.Ala155Thr missense_variant De novo NA - 26986877 Chen CA , et al. (2016)
c.289C>T p.His97Tyr missense_variant De novo NA - 31231135 Bruel AL , et al. (2019)
c.1103G>A p.Gly368Asp missense_variant De novo NA - 26986877 Chen CA , et al. (2016)
c.2T>G p.Met1? initiator_codon_variant De novo NA - 26986877 Chen CA , et al. (2016)
c.339C>A p.Ser113Arg missense_variant De novo NA - 24462372 Bosch DG , et al. (2014)
c.344G>C p.Arg115Pro missense_variant De novo NA - 24462372 Bosch DG , et al. (2014)
c.755T>C p.Leu252Pro missense_variant De novo NA - 24462372 Bosch DG , et al. (2014)
c.403C>T p.Arg135Cys missense_variant De novo NA - 31873310 Breuss MW , et al. (2019)
c.314G>A p.Gly105Asp missense_variant De novo NA - 28333917 Vissers LE , et al. (2017)
c.328_330del p.Phe110del inframe_deletion De novo NA - 26986877 Chen CA , et al. (2016)
c.305C>T p.Thr102Ile missense_variant De novo NA - 25363760 De Rubeis S , et al. (2014)
c.314G>A p.Gly105Asp missense_variant De novo NA - 27479843 Lelieveld SH et al. (2016)
c.531C>G p.Asp177Glu missense_variant De novo NA Simplex 28714951 Lim ET , et al. (2017)
c.380dup p.Asn127LysfsTer270 frameshift_variant Unknown - - 32275123 Rech ME et al. (2020)
c.291del p.Tyr98ThrfsTer21 frameshift_variant De novo NA - 26986877 Chen CA , et al. (2016)
c.335G>A p.Arg112Lys missense_variant De novo NA Simplex 24462372 Bosch DG , et al. (2014)
c.1184G>C p.Gly395Ala missense_variant De novo NA Simplex 32094338 Husson T , et al. (2020)
c.1211G>A p.Arg404His missense_variant De novo NA Simplex 22495306 Sanders SJ , et al. (2012)
c.413G>A p.Cys138Tyr missense_variant De novo NA Simplex 28327206 Eldomery MK , et al. (2017)
c.2_4delinsGGA p.MetAla1_?2 initiator_codon_variant De novo NA - 26986877 Chen CA , et al. (2016)
c.1083del p.Asn362ThrfsTer33 frameshift_variant De novo NA Simplex 32712214 Walsh S et al. (2020)
c.103_113delinsCGCCGCCGC p.Gly35ArgfsTer361 frameshift_variant De novo NA - 26986877 Chen CA , et al. (2016)
c.313G>A p.Gly105Ser missense_variant De novo NA Multiplex (monozygotic twins) 32412696 Mio C et al. (2020)
Common Variants  

No common variants reported.

SFARI Gene score
3S

Suggestive Evidence, Syndromic

Heterozygous mutations in this gene are a cause of Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS; OMIM 615722), an autosomal dominant disorder characterized by delayed development, moderate intellectual disability, and optic atrophy (Bosch et al., 2014). One of the six patients with Bosch-Boonstra-Schaaf optic atrophy syndrome described in Bosch et al., 2014 presented with autism spectrum disorder with marked obsessive-compulsive behaviors. Evaluation of the clinical features of 20 individuals with novel pathogenic NR2F1 variants demonstrated that, in addition to visual and cognitive deficits, individuals with BBSOAS manifested hypotonia (75%), seizures (40%), repetitive behavior (40%), autism spectrum disorder (35%), oromotor dysfunction (60%), thinning of the corpus callosum (53%), and hearing defects (20%) (Chen et al., 2016). De novo probably damaging missense variants in NR2F1 have also been observed in two ASD probands: one from the Simons Simplex Collection (Sanders et al., 2012), the other from the Autism Sequencing Consortium (De Rubeis et al., 2014).

Score Delta: Score remained at 4S

3

Suggestive Evidence

See all Category 3 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.

The syndromic category includes mutations that are associated with a substantial degree of increased risk and consistently linked to additional characteristics not required for an ASD diagnosis. If there is independent evidence implicating a gene in idiopathic ASD, it will be listed as "#S" (e.g., 2S, 3S, etc.). If there is no such independent evidence, the gene will be listed simply as "S."

7/1/2020
4S
icon
4S

Score remained at 4S

Description

Heterozygous mutations in this gene are a cause of Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS; OMIM 615722), an autosomal dominant disorder characterized by delayed development, moderate intellectual disability, and optic atrophy (Bosch et al., 2014). One of the six patients with Bosch-Boonstra-Schaaf optic atrophy syndrome described in Bosch et al., 2014 presented with autism spectrum disorder with marked obsessive-compulsive behaviors. Evaluation of the clinical features of 20 individuals with novel pathogenic NR2F1 variants demonstrated that, in addition to visual and cognitive deficits, individuals with BBSOAS manifested hypotonia (75%), seizures (40%), repetitive behavior (40%), autism spectrum disorder (35%), oromotor dysfunction (60%), thinning of the corpus callosum (53%), and hearing defects (20%) (Chen et al., 2016). De novo probably damaging missense variants in NR2F1 have also been observed in two ASD probands: one from the Simons Simplex Collection (Sanders et al., 2012), the other from the Autism Sequencing Consortium (De Rubeis et al., 2014).

4/1/2020
4S
icon
4S

Score remained at 4S

Description

Heterozygous mutations in this gene are a cause of Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS; OMIM 615722), an autosomal dominant disorder characterized by delayed development, moderate intellectual disability, and optic atrophy (Bosch et al., 2014). One of the six patients with Bosch-Boonstra-Schaaf optic atrophy syndrome described in Bosch et al., 2014 presented with autism spectrum disorder with marked obsessive-compulsive behaviors. Evaluation of the clinical features of 20 individuals with novel pathogenic NR2F1 variants demonstrated that, in addition to visual and cognitive deficits, individuals with BBSOAS manifested hypotonia (75%), seizures (40%), repetitive behavior (40%), autism spectrum disorder (35%), oromotor dysfunction (60%), thinning of the corpus callosum (53%), and hearing defects (20%) (Chen et al., 2016). De novo probably damaging missense variants in NR2F1 have also been observed in two ASD probands: one from the Simons Simplex Collection (Sanders et al., 2012), the other from the Autism Sequencing Consortium (De Rubeis et al., 2014).

1/1/2020
4S
icon
4S

Score remained at 4S

Description

Heterozygous mutations in this gene are a cause of Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS; OMIM 615722), an autosomal dominant disorder characterized by delayed development, moderate intellectual disability, and optic atrophy (Bosch et al., 2014). One of the six patients with Bosch-Boonstra-Schaaf optic atrophy syndrome described in Bosch et al., 2014 presented with autism spectrum disorder with marked obsessive-compulsive behaviors. Evaluation of the clinical features of 20 individuals with novel pathogenic NR2F1 variants demonstrated that, in addition to visual and cognitive deficits, individuals with BBSOAS manifested hypotonia (75%), seizures (40%), repetitive behavior (40%), autism spectrum disorder (35%), oromotor dysfunction (60%), thinning of the corpus callosum (53%), and hearing defects (20%) (Chen et al., 2016). De novo probably damaging missense variants in NR2F1 have also been observed in two ASD probands: one from the Simons Simplex Collection (Sanders et al., 2012), the other from the Autism Sequencing Consortium (De Rubeis et al., 2014).

10/1/2019
4S
icon
3S

Decreased from 4S to 3S

New Scoring Scheme
Description

Heterozygous mutations in this gene are a cause of Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS; OMIM 615722), an autosomal dominant disorder characterized by delayed development, moderate intellectual disability, and optic atrophy (Bosch et al., 2014). One of the six patients with Bosch-Boonstra-Schaaf optic atrophy syndrome described in Bosch et al., 2014 presented with autism spectrum disorder with marked obsessive-compulsive behaviors. Evaluation of the clinical features of 20 individuals with novel pathogenic NR2F1 variants demonstrated that, in addition to visual and cognitive deficits, individuals with BBSOAS manifested hypotonia (75%), seizures (40%), repetitive behavior (40%), autism spectrum disorder (35%), oromotor dysfunction (60%), thinning of the corpus callosum (53%), and hearing defects (20%) (Chen et al., 2016). De novo probably damaging missense variants in NR2F1 have also been observed in two ASD probands: one from the Simons Simplex Collection (Sanders et al., 2012), the other from the Autism Sequencing Consortium (De Rubeis et al., 2014).

Reports Added
[New Scoring Scheme]
7/1/2019
4S
icon
4S

Decreased from 4S to 4S

Description

Heterozygous mutations in this gene are a cause of Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS; OMIM 615722), an autosomal dominant disorder characterized by delayed development, moderate intellectual disability, and optic atrophy (Bosch et al., 2014). One of the six patients with Bosch-Boonstra-Schaaf optic atrophy syndrome described in Bosch et al., 2014 presented with autism spectrum disorder with marked obsessive-compulsive behaviors. Evaluation of the clinical features of 20 individuals with novel pathogenic NR2F1 variants demonstrated that, in addition to visual and cognitive deficits, individuals with BBSOAS manifested hypotonia (75%), seizures (40%), repetitive behavior (40%), autism spectrum disorder (35%), oromotor dysfunction (60%), thinning of the corpus callosum (53%), and hearing defects (20%) (Chen et al., 2016). De novo probably damaging missense variants in NR2F1 have also been observed in two ASD probands: one from the Simons Simplex Collection (Sanders et al., 2012), the other from the Autism Sequencing Consortium (De Rubeis et al., 2014).

4/1/2019
4S
icon
4S

Decreased from 4S to 4S

Description

Heterozygous mutations in this gene are a cause of Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS; OMIM 615722), an autosomal dominant disorder characterized by delayed development, moderate intellectual disability, and optic atrophy (Bosch et al., 2014). One of the six patients with Bosch-Boonstra-Schaaf optic atrophy syndrome described in Bosch et al., 2014 presented with autism spectrum disorder with marked obsessive-compulsive behaviors. Evaluation of the clinical features of 20 individuals with novel pathogenic NR2F1 variants demonstrated that, in addition to visual and cognitive deficits, individuals with BBSOAS manifested hypotonia (75%), seizures (40%), repetitive behavior (40%), autism spectrum disorder (35%), oromotor dysfunction (60%), thinning of the corpus callosum (53%), and hearing defects (20%) (Chen et al., 2016). De novo probably damaging missense variants in NR2F1 have also been observed in two ASD probands: one from the Simons Simplex Collection (Sanders et al., 2012), the other from the Autism Sequencing Consortium (De Rubeis et al., 2014).

7/1/2017
4S
icon
4S

Decreased from 4S to 4S

Description

Heterozygous mutations in this gene are a cause of Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS; OMIM 615722), an autosomal dominant disorder characterized by delayed development, moderate intellectual disability, and optic atrophy (Bosch et al., 2014). One of the six patients with Bosch-Boonstra-Schaaf optic atrophy syndrome described in Bosch et al., 2014 presented with autism spectrum disorder with marked obsessive-compulsive behaviors. Evaluation of the clinical features of 20 individuals with novel pathogenic NR2F1 variants demonstrated that, in addition to visual and cognitive deficits, individuals with BBSOAS manifested hypotonia (75%), seizures (40%), repetitive behavior (40%), autism spectrum disorder (35%), oromotor dysfunction (60%), thinning of the corpus callosum (53%), and hearing defects (20%) (Chen et al., 2016). De novo probably damaging missense variants in NR2F1 have also been observed in two ASD probands: one from the Simons Simplex Collection (Sanders et al., 2012), the other from the Autism Sequencing Consortium (De Rubeis et al., 2014).

4/1/2017
4S
icon
4S

Decreased from 4S to 4S

Description

Heterozygous mutations in this gene are a cause of Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS; OMIM 615722), an autosomal dominant disorder characterized by delayed development, moderate intellectual disability, and optic atrophy (Bosch et al., 2014). One of the six patients with Bosch-Boonstra-Schaaf optic atrophy syndrome described in Bosch et al., 2014 presented with autism spectrum disorder with marked obsessive-compulsive behaviors. Evaluation of the clinical features of 20 individuals with novel pathogenic NR2F1 variants demonstrated that, in addition to visual and cognitive deficits, individuals with BBSOAS manifested hypotonia (75%), seizures (40%), repetitive behavior (40%), autism spectrum disorder (35%), oromotor dysfunction (60%), thinning of the corpus callosum (53%), and hearing defects (20%) (Chen et al., 2016). De novo probably damaging missense variants in NR2F1 have also been observed in two ASD probands: one from the Simons Simplex Collection (Sanders et al., 2012), the other from the Autism Sequencing Consortium (De Rubeis et al., 2014).

10/1/2016
4S
icon
4S

Decreased from 4S to 4S

Description

Heterozygous mutations in this gene are a cause of Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS; OMIM 615722), an autosomal dominant disorder characterized by delayed development, moderate intellectual disability, and optic atrophy (Bosch et al., 2014). One of the six patients with Bosch-Boonstra-Schaaf optic atrophy syndrome described in Bosch et al., 2014 presented with autism spectrum disorder with marked obsessive-compulsive behaviors. Evaluation of the clinical features of 20 individuals with novel pathogenic NR2F1 variants demonstrated that, in addition to visual and cognitive deficits, individuals with BBSOAS manifested hypotonia (75%), seizures (40%), repetitive behavior (40%), autism spectrum disorder (35%), oromotor dysfunction (60%), thinning of the corpus callosum (53%), and hearing defects (20%) (Chen et al., 2016). De novo probably damaging missense variants in NR2F1 have also been observed in two ASD probands: one from the Simons Simplex Collection (Sanders et al., 2012), the other from the Autism Sequencing Consortium (De Rubeis et al., 2014).

7/1/2016
4S
icon
4S

Decreased from 4S to 4S

Description

Heterozygous mutations in this gene are a cause of Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS; OMIM 615722), an autosomal dominant disorder characterized by delayed development, moderate intellectual disability, and optic atrophy (Bosch et al., 2014). One of the six patients with Bosch-Boonstra-Schaaf optic atrophy syndrome described in Bosch et al., 2014 presented with autism spectrum disorder with marked obsessive-compulsive behaviors. Evaluation of the clinical features of 20 individuals with novel pathogenic NR2F1 variants demonstrated that, in addition to visual and cognitive deficits, individuals with BBSOAS manifested hypotonia (75%), seizures (40%), repetitive behavior (40%), autism spectrum disorder (35%), oromotor dysfunction (60%), thinning of the corpus callosum (53%), and hearing defects (20%) (Chen et al., 2016). De novo probably damaging missense variants in NR2F1 have also been observed in two ASD probands: one from the Simons Simplex Collection (Sanders et al., 2012), the other from the Autism Sequencing Consortium (De Rubeis et al., 2014).

4/1/2016
icon
4S

Increased from to 4S

Description

Heterozygous mutations in this gene are a cause of Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS; OMIM 615722), an autosomal dominant disorder characterized by delayed development, moderate intellectual disability, and optic atrophy (Bosch et al., 2014). One of the six patients with Bosch-Boonstra-Schaaf optic atrophy syndrome described in Bosch et al., 2014 presented with autism spectrum disorder with marked obsessive-compulsive behaviors. Evaluation of the clinical features of 20 individuals with novel pathogenic NR2F1 variants demonstrated that, in addition to visual and cognitive deficits, individuals with BBSOAS manifested hypotonia (75%), seizures (40%), repetitive behavior (40%), autism spectrum disorder (35%), oromotor dysfunction (60%), thinning of the corpus callosum (53%), and hearing defects (20%) (Chen et al., 2016). De novo probably damaging missense variants in NR2F1 have also been observed in two ASD probands: one from the Simons Simplex Collection (Sanders et al., 2012), the other from the Autism Sequencing Consortium (De Rubeis et al., 2014).

Krishnan Probability Score

Score 0.56619311657082

Ranking 1220/25841 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.
Sanders TADA Score

Score 0.40393677506562

Ranking 284/18665 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).
Zhang D Score

Score 0.2346314388017

Ranking 3695/20870 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.
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