Human Gene Module / Chromosome 2 / SH3RF3

SH3RF3SH3 domain containing ring finger 3

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
4 / 4
Rare Variants / Common Variants
4 / 0
Aliases
SH3RF3, POSH2,  SH3MD4
Associated Syndromes
-
Chromosome Band
2q13
Associated Disorders
-
Relevance to Autism

A de novo damaging missense variant in the SH3RF3 gene was identified in an ASD proband from the Simons Simplex Collection (Iossifov et al., 2014), while a de novo likely gene-disruptive variant in this gene was identified in an ASD proband from the SPARK cohort (Feliciano et al., 2019). A meta-analysis of de novo variants in 4773 published ASD trios and 465 SPARK trios using TADA identified SH3RF3 as a gene with a false discovery rate 0.2.

Molecular Function

The protein encoded by this gene has E3 ubiquitin-protein ligase activity.

External Links
Gene CardOpen Targets PlatformgnomAD browserPubMed
Human
Entrez GeneUniProtHumanBaseVariCarta
SFARI Genomic Platforms
GPF browser SFARI genome browser
Reports related to SH3RF3 (4 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary The contribution of de novo coding mutations to autism spectrum disorder Iossifov I et al. (2014) Yes -
2 Support Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes Feliciano P et al. (2019) Yes -
3 Support A recurrent PJA1 variant in trigonocephaly and neurodevelopmental disorders Suzuki T et al. (2020) Yes -
4 Support - Suhua Chang et al. () Yes -
Rare Variants   (4)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.2485C>T p.Arg829Cys missense_variant De novo - Simplex 32530565 Suzuki T et al. (2020)
c.2608C>T p.Arg870Cys missense_variant De novo - Simplex 25363768 Iossifov I et al. (2014)
c.1544del p.Phe515SerfsTer6 frameshift_variant De novo - - 31452935 Feliciano P et al. (2019)
c.114_131del p.Ala39_Glu44del inframe_deletion De novo - Simplex 39126614 Suhua Chang et al. ()
Common Variants  

No common variants reported.

SFARI Gene score
2

Strong Candidate

A de novo damaging missense variant in the SH3RF3 gene was identified in an ASD proband from the Simons Simplex Collection (Iossifov et al., 2014), while a de novo likely gene-disruptive variant in this gene was identified in an ASD proband from the SPARK cohort (Feliciano et al., 2019). A meta-analysis of de novo variants in 4773 published ASD trios and 465 SPARK trios using TADA identified SH3RF3 as a gene with a false discovery rate 0.2.

Score Delta: Score remained at 2

criteria met
See SFARI Gene'scoring criteria
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.

4/1/2022
3
icon
2

Decreased from 3 to 2

Description

A de novo damaging missense variant in the SH3RF3 gene was identified in an ASD proband from the Simons Simplex Collection (Iossifov et al., 2014), while a de novo likely gene-disruptive variant in this gene was identified in an ASD proband from the SPARK cohort (Feliciano et al., 2019). A meta-analysis of de novo variants in 4773 published ASD trios and 465 SPARK trios using TADA identified SH3RF3 as a gene with a false discovery rate 0.2.

7/1/2020
3
icon
3

Decreased from 3 to 3

Description

A de novo damaging missense variant in the SH3RF3 gene was identified in an ASD proband from the Simons Simplex Collection (Iossifov et al., 2014), while a de novo likely gene-disruptive variant in this gene was identified in an ASD proband from the SPARK cohort (Feliciano et al., 2019). A meta-analysis of de novo variants in 4773 published ASD trios and 465 SPARK trios using TADA identified SH3RF3 as a gene with a false discovery rate 0.2.

Reports Added
[A recurrent PJA1 variant in trigonocephaly and neurodevelopmental disorders2020]
10/1/2019
icon
3

Increased from to 3

New Scoring Scheme
Description

A de novo damaging missense variant in the SH3RF3 gene was identified in an ASD proband from the Simons Simplex Collection (Iossifov et al., 2014), while a de novo likely gene-disruptive variant in this gene was identified in an ASD proband from the SPARK cohort (Feliciano et al., 2019). A meta-analysis of de novo variants in 4773 published ASD trios and 465 SPARK trios using TADA identified SH3RF3 as a gene with a false discovery rate 0.2.

Reports Added
[New Scoring Scheme]
Krishnan Probability Score

Score 0.4629314149223

Ranking 9293/25841 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.
Original Source
ExAC Score

Score 0.98110087172834

Ranking 2100/18225 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
Original Source
Sanders TADA Score

Score 0.75340447353293

Ranking 1589/18665 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).
Original Source
Zhang D Score

Score 0.36463271021993

Ranking 1852/20870 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.
Original Source
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