ELOVL3
protein-codingELOVL fatty acid elongase 3
Gene summary
This gene encodes a protein that belongs to the GNS1/SUR4 family. Members of this family play a role in elongation of long chain fatty acids to provide precursors for synthesis of sphingolipids and ceramides. [provided by RefSeq, Jul 2013]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.3 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 ELOVL3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_152310.3. 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 | 0 | |||||
| missense | 40 | 3 | 43 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 41 | 3 | 0 | 44 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_689523.1 | 4 | MANE Select | |
| Ensembl | ENSP00000359022.3 | 4 | MANE Select | |
| Ensembl | ENSP00000809648.1 | 4 | Standard | |
| RefSeq | XP_011538547.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Fatty acid elongation - Homo sapiens (human)
- NR1D1 (REV-ERBA) represses gene expression
- Circadian Clock
- Metabolism of lipids
- Fatty acyl-CoA biosynthesis
Biological Process
- unsaturated fatty acid biosynthetic process
- fatty acid elongation, saturated fatty acid
- sphingolipid biosynthetic process
- fatty acid elongation, monounsaturated fatty acid
- fatty acid elongation, polyunsaturated fatty acid
Molecular Function
- protein binding
- fatty acid elongase activity
- 3-oxo-arachidoyl-CoA synthase activity
- 3-oxo-cerotoyl-CoA synthase activity
- 3-oxo-lignoceronyl-CoA synthase activity
Cellular Component
- endoplasmic reticulum
- endoplasmic reticulum membrane
- integral component of endoplasmic reticulum membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000370005
- Coding exons
- 4
- Length
- 3262
- Individuals with no LoFs
- 125741
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 125748
- p
- 0.0000278
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.746 | 129 | 155 | 0.831 | 0.00000807 | 1801 |
| Missense (PolyPhen) | 44 | 55.225 | 0.79673 | 689 | ||
| Synonymous | 0.331 | 57 | 60.3 | 0.946 | 0.00000335 | 508 |
| Loss of Function | 1.51 | 4 | 8.83 | 0.453 | 3.78e-7 | 93 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the first and rate-limiting reaction of the four that constitute the long-chain fatty acids elongation cycle. This endoplasmic reticulum-bound enzymatic process, allows the addition of 2 carbons to the chain of long- and very long-chain fatty acids/VLCFAs per cycle. Condensing enzyme with higher activity toward C18 acyl-CoAs, especially C18:0 acyl-CoAs. May participate in the production of saturated and monounsaturated VLCFAs of different chain lengths that are involved in multiple biological processes as precursors of membrane lipids and lipid mediators. {ECO:0000255|HAMAP-Rule:MF_03203, ECO:0000269|PubMed:20937905}.;
Recessive Scores
- pRec
- 0.0923
Intolerance Scores
- LoFtool
- 0.675
- RVIS EVS
- 0.17
- RVIS percentile EVS
- 65.56
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.000995
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |