Human Gene Module / Chromosome X / FAM47A

FAM47Afamily with sequence similarity 47 member A

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
1 / 1
Rare Variants / Common Variants
4 / 0
EAGLE Score
0.45
Limited Learn More
Aliases
-
Associated Syndromes
-
Chromosome Band
Xp21.1
Associated Disorders
-
Genetic Category
Rare Single Gene Mutation
Relevance to Autism

Maternally-inherited loss-of-function variants in the FAM47A gene were identified in two male ASD probands by whole genome sequencing as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of multiple LoF variants and a probability of LoF intolerance rate (pLI) > 0.65, FAM47A was determined to be an ASD candidate gene in this report.

Molecular Function

This gene encodes a protein of unknown function.

External Links
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SFARI Genomic Platforms
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Reports related to FAM47A (1 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder C Yuen RK et al. (2017) Yes -
Rare Variants   (4)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.1590del p.Gly531ValfsTer50 frameshift_variant Familial Maternal Simplex 28263302 C Yuen RK et al. (2017)
c.1504_1540del p.Ser502ArgfsTer67 frameshift_variant Familial Maternal Simplex 28263302 C Yuen RK et al. (2017)
c.1542_1543del p.Ser515GlnfsTer82 frameshift_variant Familial Maternal Simplex 28263302 C Yuen RK et al. (2017)
c.1551_1588del p.Glu520GlyfsTer65 frameshift_variant Familial Maternal Simplex 28263302 C Yuen RK et al. (2017)
Common Variants  

No common variants reported.

SFARI Gene score
2

Strong Candidate

Maternally-inherited loss-of-function variants in the FAM47A gene were identified in two male ASD probands by whole genome sequencing as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of multiple LoF variants and a probability of LoF intolerance rate (pLI) > 0.65, FAM47A was determined to be an ASD candidate gene in this report.

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

Maternally-inherited loss-of-function variants in the FAM47A gene were identified in two male ASD probands by whole genome sequencing as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of multiple LoF variants and a probability of LoF intolerance rate (pLI) > 0.65, FAM47A was determined to be an ASD candidate gene in this report.

10/1/2019
4
icon
3

Decreased from 4 to 3

New Scoring Scheme
Description

Maternally-inherited loss-of-function variants in the FAM47A gene were identified in two male ASD probands by whole genome sequencing as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of multiple LoF variants and a probability of LoF intolerance rate (pLI) > 0.65, FAM47A was determined to be an ASD candidate gene in this report.

Reports Added
[New Scoring Scheme]
4/1/2017
icon
4

Increased from to 4

Description

Maternally-inherited loss-of-function variants in the FAM47A gene were identified in two male ASD probands by whole genome sequencing as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of multiple LoF variants and a probability of LoF intolerance rate (pLI) > 0.65, FAM47A was determined to be an ASD candidate gene in this report.

Krishnan Probability Score

Score 0.49127421854811

Ranking 5678/25841 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 0.74840041834631

Ranking 4218/18225 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 0.9410010765346

Ranking 14772/18665 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 0.099692664223492

Ranking 6144/20870 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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