Human Gene Module / Chromosome 9 / SLC27A4

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

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
2 / 3
Rare Variants / Common Variants
4 / 1
Aliases
SLC27A4, ACSVL4,  FATP4,  IPS
Associated Syndromes
-
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).

SFARI Genomic Platforms
Reports related to SLC27A4 (3 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 -
2 Support - Mir A et al. (2021) No -
3 Support - Zhou X et al. (2022) Yes -
Rare Variants   (4)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.778C>T p.His260Tyr missense_variant De novo - - 35982159 Zhou X et al. (2022)
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)
c.848A>G p.Tyr283Cys missense_variant Familial Both parents - 34797406 Mir A et al. (2021)
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
2

Strong Candidate

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: Score remained at 2

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

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).

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 0.0012218397150002

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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