Human Gene Module / Chromosome 9 / SLC27A4

SLC27A4Solute carrier family 27 (fatty acid transporter), member 4

Score
3
Suggestive Evidence Criteria 3.1
Autism Reports / Total Reports
1 / 1
Rare Variants / Common Variants
2 / 1
Aliases
SLC27A4, ACSVL4,  FATP4,  IPS
Associated Syndromes
-
Genetic Category
Rare Single Gene Mutation
Chromosome Band
9q34.11
Associated Disorders
-
Relevance to Autism

A functional polymorphism statistically enriched in Japanese ASD cases compared to ethnically-matched controls, as well as two novel case-specific missense variants in Japanese male ASD probands, were identified in the SLC27A4 gene (Maekawa et al., 2015).

Molecular Function

This gene encodes a member of a family of fatty acid transport proteins, which are involved in translocation of long-chain fatty acids cross the plasma membrane. Clinical studies suggest this gene as a candidate gene for the insulin resistance syndrome, and mutations in this gene have been associated with ichthyosis prematurity syndrome (OMIM 608649).

Reports related to SLC27A4 (1 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary Investigation of the fatty acid transporter-encoding genes SLC27A3 and SLC27A4 in autism. Maekawa M , et al. (2015) Yes -
Rare Variants   (2)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.250G>A p.Val84Ile missense_variant Unknown - Unknown 26548558 Maekawa M , et al. (2015)
c.272C>T p.Thr91Met missense_variant Unknown - Unknown 26548558 Maekawa M , et al. (2015)
Common Variants   (1)
Status Allele Change Residue Change Variant Type Inheritance Pattern Paternal Transmission Family Type PubMed ID Author, Year
c.625G>A p.Gly209Ser missense_variant - - - 26548558 Maekawa M , et al. (2015)
SFARI Gene score
3

Suggestive Evidence

A functional polymorphism statistically enriched in Japanese ASD cases compared to ethnically-matched controls, as well as two novel case-specific missense variants in Japanese male ASD probands, were identified in the SLC27A4 gene (Maekawa et al., 2015).

Score Delta: Decreased from 4 to 3

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 functional polymorphism statistically enriched in Japanese ASD cases compared to ethnically-matched controls, as well as two novel case-specific missense variants in Japanese male ASD probands, were identified in the SLC27A4 gene (Maekawa et al., 2015).

Reports Added
[New Scoring Scheme]
10/1/2015
icon
4

Increased from to 4

Description

A functional polymorphism statistically enriched in Japanese ASD cases compared to ethnically-matched controls, as well as two novel case-specific missense variants in Japanese male ASD probands, were identified in the SLC27A4 gene (Maekawa et al., 2015).

Krishnan Probability Score

Score 0.44722285501752

Ranking 13705/25841 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 0.0012218397150003

Ranking 11642/18225 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 0.94765496531366

Ranking 17364/18665 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 -0.10056300134017

Ranking 12373/20870 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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