Human Gene Module / Chromosome 10 / SLC35G1

SLC35G1solute carrier family 35 member G1

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
4 / 4
Rare Variants / Common Variants
5 / 0
Aliases
-
Associated Syndromes
-
Chromosome Band
10q23.33
Associated Disorders
-
Relevance to Autism

SLC35G1 was identified in an ASD candidate gene in Wang et al., 2023 based on reaching a false discovery rate (FDR) threshold of <0.1 following TADA analysis in both a discovery cohort of 1,141 Chinese ASD probands and a combined cohort consisting of the discovery cohort of Chinese ASD probands and 42,607 ASD probands originally published in Zhou et al., 2022. Wang et al., 2023 also demonstrated that mice harboring a heterozygous deletion of Slc35g1 exhibited defects in interactive social behaviors and increased marble-burying activity compared to wild-type mice. In total, four de novo coding variants in SLC35G1 (two loss-of-function variants and two missense variants) have been reported in ASD probands (Yuen et al., 2017; Zhou et al., 2022; Wang et al., 2023).

Molecular Function

This gene encodes a transmembrane protein which is a member of the drug/metabolite transporter protein superfamily. The encoded protein may play a role in the regulation of calcium levels inside the cell.

External Links
Gene CardOpen Targets PlatformgnomAD browserPubMed
Human
Entrez GeneOMIMUniProtHumanBaseVariCarta
Mouse
Entrez GeneMouse Genome InformaticsAllen Brain Atlas
SFARI Genomic Platforms
GPF browser SFARI genome browser
Reports related to SLC35G1 (4 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Support Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder C Yuen RK et al. (2017) Yes -
2 Support - Zhou X et al. (2022) Yes -
3 Primary - Wang J et al. (2023) Yes -
4 Support - Cirnigliaro M et al. (2023) Yes -
Rare Variants   (5)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.31G>C p.Glu11Gln missense_variant De novo - - 35982159 Zhou X et al. (2022)
c.360-1G>C - splice_site_variant De novo - Simplex 28263302 C Yuen RK et al. (2017)
c.931G>C p.Ala311Pro missense_variant De novo - Simplex 37393044 Wang J et al. (2023)
c.358_359del p.Lys120AsnfsTer38 frameshift_variant De novo - Simplex 37393044 Wang J et al. (2023)
c.71_83del p.Pro24LeufsTer71 frameshift_variant Familial Paternal Multiplex 37506195 Cirnigliaro M et al. (2023)
Common Variants  

No common variants reported.

SFARI Gene score
2

Strong Candidate

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.

7/1/2023
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2

Increased from to 2

Krishnan Probability Score

Score 0.44766339531143

Ranking 12083/25841 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 0.91713593802814

Ranking 3064/18225 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 0.88767177932945

Ranking 5343/18665 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 -0.42059781852575

Ranking 18561/20870 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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