Human Gene Module / Chromosome 17 / SLC25A39

SLC25A39solute carrier family 25 member 39

Score
3
Suggestive Evidence Criteria 3.1
Autism Reports / Total Reports
3 / 3
Rare Variants / Common Variants
11 / 0
Aliases
SLC25A39, CGI-69,  CGI69
Associated Syndromes
-
Genetic Category
Rare Single Gene Mutation
Chromosome Band
17q21.31
Associated Disorders
-
Relevance to Autism

A de novo frameshift variant in the SLC25A39 gene was identified in an ASD proband from the Simons Simplex Collection in Iossifov et al., 2012. Rare inherited loss-of-function and damaging missense variants in this gene were observed in ASD probands from the Simons Simplex Collection (Krumm et al., 2015) and in a cohort of Chinese ASD probands (Guo et al., 2017). Transmission and De Novo Association (TADA) analysis of a combined cohort consisting of 536 Chinese ASD probands and 1457 Chinese controls, as well as ASD probands and controls from the Simons Simplex Collection and the Autism Sequencing Consortium, in Guo et al., 2017 identified SLC25A39 as an ASD candidate gene with a PTADA of 0.002017.

Molecular Function

his gene encodes a member of the SLC25 transporter or mitochondrial carrier family of proteins. Members of this family are encoded by the nuclear genome while their protein products are usually embedded in the inner mitochondrial membrane and exhibit wide-ranging substrate specificity. Although the encoded protein is currently considered an orphan transporter, this protein is related to other carriers known to transport amino acids. This protein may play a role in iron homeostasis and be required for normal heme biosynthesis.

Reports related to SLC25A39 (3 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary De novo gene disruptions in children on the autistic spectrum. Iossifov I , et al. (2012) Yes -
2 Support Excess of rare, inherited truncating mutations in autism. Krumm N , et al. (2015) Yes -
3 Recent Recommendation Targeted sequencing and functional analysis reveal brain-size-related genes and their networks in autism spectrum disorders. Li J , et al. (2017) Yes -
Rare Variants   (11)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.673C>T p.Arg225Ter stop_gained Familial - - 28831199 Li J , et al. (2017)
ACCT>CCCG p.? splice_site_variant Familial Maternal Simplex 25961944 Krumm N , et al. (2015)
c.100G>C p.Val34Leu missense_variant Familial Maternal Simplex 25961944 Krumm N , et al. (2015)
c.389C>T p.Thr130Ile missense_variant Familial Maternal Simplex 25961944 Krumm N , et al. (2015)
c.442C>A p.Leu148Met missense_variant Familial Paternal Simplex 25961944 Krumm N , et al. (2015)
c.991G>C p.Ala331Pro missense_variant Familial Paternal Simplex 25961944 Krumm N , et al. (2015)
c.998C>T p.Ser333Phe missense_variant Familial Maternal Simplex 25961944 Krumm N , et al. (2015)
c.1063C>T p.Arg355Trp missense_variant Familial Paternal Simplex 25961944 Krumm N , et al. (2015)
c.336del p.Lys113ArgfsTer3 frameshift_variant De novo NA Simplex 22542183 Iossifov I , et al. (2012)
c.798dup p.Thr267AspfsTer11 frameshift_variant Familial Maternal Simplex 25961944 Krumm N , et al. (2015)
c.799_800insG p.Thr267SerfsTer11 frameshift_variant Familial Maternal Simplex 25961944 Krumm N , et al. (2015)
Common Variants  

No common variants reported.

SFARI Gene score
3

Suggestive Evidence

A de novo frameshift variant in the SLC25A39 gene was identified in an ASD proband from the Simons Simplex Collection in Iossifov et al., 2012. Rare inherited loss-of-function and damaging missense variants in this gene were observed in ASD probands from the Simons Simplex Collection (Krumm et al., 2015) and in a cohort of Chinese ASD probands (Guo et al., 2017). Transmission and De Novo Association (TADA) analysis of a combined cohort consisting of 536 Chinese ASD probands and 1457 Chinese controls, as well as ASD probands and controls from the Simons Simplex Collection and the Autism Sequencing Consortium, in Guo et al., 2017 identified SLC25A39 as an ASD candidate gene with a PTADA of 0.002017.

Score Delta: Score remained at 4

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.

10/1/2019
4
icon
3

Decreased from 4 to 3

New Scoring Scheme
Description

A de novo frameshift variant in the SLC25A39 gene was identified in an ASD proband from the Simons Simplex Collection in Iossifov et al., 2012. Rare inherited loss-of-function and damaging missense variants in this gene were observed in ASD probands from the Simons Simplex Collection (Krumm et al., 2015) and in a cohort of Chinese ASD probands (Guo et al., 2017). Transmission and De Novo Association (TADA) analysis of a combined cohort consisting of 536 Chinese ASD probands and 1457 Chinese controls, as well as ASD probands and controls from the Simons Simplex Collection and the Autism Sequencing Consortium, in Guo et al., 2017 identified SLC25A39 as an ASD candidate gene with a PTADA of 0.002017.

Reports Added
[New Scoring Scheme]
7/1/2017
icon
4

Increased from to 4

Description

A de novo frameshift variant in the SLC25A39 gene was identified in an ASD proband from the Simons Simplex Collection in Iossifov et al., 2012. Rare inherited loss-of-function and damaging missense variants in this gene were observed in ASD probands from the Simons Simplex Collection (Krumm et al., 2015) and in a cohort of Chinese ASD probands (Guo et al., 2017). Transmission and De Novo Association (TADA) analysis of a combined cohort consisting of 536 Chinese ASD probands and 1457 Chinese controls, as well as ASD probands and controls from the Simons Simplex Collection and the Autism Sequencing Consortium, in Guo et al., 2017 identified SLC25A39 as an ASD candidate gene with a PTADA of 0.002017.

Krishnan Probability Score

Score 0.40710789131989

Ranking 23062/25841 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.
ExAC Score

Score 0.00010238545322193

Ranking 13073/18225 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
Sanders TADA Score

Score 0.40315981931577

Ranking 283/18665 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 -0.79569452072612

Ranking 20640/20870 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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SFARI Gene Update

We are pleased to announce some changes to the ongoing curation of the data in SFARI Gene. In the context of a continued effort to develop the human gene module and its manually curated list of autism risk genes, we are modifying other aspects of the site to focus on the information that is of greatest interest to the research community. The version of SFARI Gene that has been developed until now will be frozen and will remain available as “SFARI Gene Archive”. Please see the announcement for more details.
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