SLC27A3
protein-codingsolute carrier family 27 member 3, the group of Solute carrier family 27|Acyl-CoA synthetase family
Gene summary
This gene belongs to a family of integral membrane proteins and encodes a protein that is involved in lipid metabolism. The increased expression of this gene in human neural stem cells derived from induced pluripotent stem cells suggests that it plays an important role in early brain development. Naturally occurring mutations in this gene are associated with autism spectrum disorders. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~5.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SLC27A3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024330.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | 4 | |||
| missense | 141 | 4 | 145 | |||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 149 | 6 | 0 | 155 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_077306.3 | 10 | MANE Select | |
| Ensembl | ENSP00000485061.2 | 10 | MANE Select | |
| RefSeq | NP_001304858.3 | 10 | Standard | |
| Ensembl | ENSP00000271857.2 | 10 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Insulin resistance - Homo sapiens (human)
- Metabolism of lipids
- Fatty acyl-CoA biosynthesis
- Metabolism
- Fatty acid metabolism
Biological Process
- long-chain fatty acid metabolic process
- long-chain fatty acid transport
Molecular Function
- nucleotide binding
- long-chain fatty acid-CoA ligase activity
- long-chain fatty acid transporter activity
- very long-chain fatty acid-CoA ligase activity
Cellular Component
- mitochondrion
- endoplasmic reticulum
- membrane
- integral component of membrane
- mitochondrial membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000368661
- Coding exons
- 10
- Length
- 5804
- Individuals with no LoFs
- 124968
- Homozygous LoFs
- 4
- Heterozygous LoFs
- 776
- Defined
- 125748
- p
- 0.00311
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.35 | 485 | 408 | 1.19 | 0.0000233 | 4544 |
| Missense (PolyPhen) | 205 | 165.82 | 1.2363 | 1813 | ||
| Synonymous | -2.19 | 214 | 177 | 1.21 | 0.00000999 | 1642 |
| Loss of Function | -0.476 | 31 | 28.3 | 1.10 | 0.00000139 | 308 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0026 | 0.0026 | notable |
| Latino/Admixed American | 0.0028 | 0.0028 | notable |
| Ashkenazi Jewish | 0.00060 | 0.00060 | rare |
| East Asian | 0.015 | 0.015 | notable |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.0018 | 0.0018 | notable |
| South Asian | 0.0044 | 0.0044 | notable |
| Other | 0.0047 | 0.0047 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Has acyl-CoA ligase activity for long-chain and very- long-chain fatty acids. Does not exhibit fatty acid transport activity (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- LoFtool
- 0.971
- RVIS EVS
- -0.82
- RVIS percentile EVS
- 12.01
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.161
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |