Human Gene Module / Chromosome 17 / SLC38A10

SLC38A10solute carrier family 38, member 10

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
3 / 3
Rare Variants / Common Variants
5 / 0
Aliases
SLC38A10, PP1744,  FLJ35718,  FLJ46399,  MGC15523
Associated Syndromes
-
Chromosome Band
17q25.3
Associated Disorders
-
Relevance to Autism

A rare deletion in the SLC38A10 gene has been identified with autism (Celestino-Soper et al., 2011).

Molecular Function

This protein is a putative sodium-dependent neutral amino acid transporter.

External Links
Gene CardOpen Targets PlatformgnomAD browserPubMed
Human
Entrez GeneUniProtHumanBaseVariCarta
SFARI Genomic Platforms
GPF browser SFARI genome browser
Reports related to SLC38A10 (3 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary Use of array CGH to detect exonic copy number variants throughout the genome in autism families detects a novel deletion in TMLHE Celestino-Soper PB , et al. (2011) Yes -
2 Support Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks Ruzzo EK , et al. (2019) Yes -
3 Support - Zhou X et al. (2022) Yes -
Rare Variants   (5)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.645C>T p.Tyr215%3D synonymous_variant De novo - - 35982159 Zhou X et al. (2022)
c.645C>T p.Tyr215%3D synonymous_variant De novo - Multiplex 35982159 Zhou X et al. (2022)
- - copy_number_loss Familial Both parents Simplex 21865298 Celestino-Soper PB , et al. (2011)
c.1585G>T p.Gly529Ter stop_gained Familial Paternal Multiplex 31398340 Ruzzo EK , et al. (2019)
c.3332_3335del p.Gln1111ArgfsTer14 frameshift_variant Familial Paternal Multiplex 31398340 Ruzzo EK , et al. (2019)
Common Variants  

No common variants reported.

SFARI Gene score
2

Strong Candidate

A rare deletion in the SLC38A10 gene has been identified with autism (PMID 21865298). In addition, multiple mutations and deletions were identified with autism above controls, as well as metabolic evidence of associated function (PMID ?? Celestino-Soper PB 2012)

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.

10/1/2019
3
icon
2

Decreased from 3 to 2

New Scoring Scheme
Description

A rare deletion in the SLC38A10 gene has been identified with autism (PMID 21865298). In addition, multiple mutations and deletions were identified with autism above controls, as well as metabolic evidence of associated function (PMID ?? Celestino-Soper PB 2012)

Reports Added
[New Scoring Scheme]
7/1/2019
3
icon
3

Decreased from 3 to 3

Description

A rare deletion in the SLC38A10 gene has been identified with autism (PMID 21865298). In addition, multiple mutations and deletions were identified with autism above controls, as well as metabolic evidence of associated function (PMID ?? Celestino-Soper PB 2012)

Reports Added
[Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks.2019]
7/1/2014
No data
icon
3

Increased from No data to 3

Description

A rare deletion in the SLC38A10 gene has been identified with autism (PMID 21865298). In addition, multiple mutations and deletions were identified with autism above controls, as well as metabolic evidence of associated function (PMID ?? Celestino-Soper PB 2012)

4/1/2014
No data
icon
3

Increased from No data to 3

Description

A rare deletion in the SLC38A10 gene has been identified with autism (PMID 21865298). In addition, multiple mutations and deletions were identified with autism above controls, as well as metabolic evidence of associated function (PMID ?? Celestino-Soper PB 2012)

Krishnan Probability Score

Score 0

Ranking 25808/25841 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 4.0924218098235E-8

Ranking 15896/18225 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 0.94828465916119

Ranking 17621/18665 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
Larsen Cumulative Evidence Score

Score 3

Ranking 359/461 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.
Original Source
Zhang D Score

Score -0.15304764587233

Ranking 14210/20870 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
Submit New Gene

Report an Error