FAR2
protein-codingfatty acyl-CoA reductase 2, the group of Short chain dehydrogenase/reductase superfamily
Gene summary
This gene belongs to the short chain dehydrogenase/reductase superfamily. It encodes a reductase enzyme involved in the first step of wax biosynthesis wherein fatty acids are converted to fatty alcohols. The encoded peroxisomal protein utilizes saturated fatty acids of 16 or 18 carbons as preferred substrates. Alternatively spliced transcript variants have been observed for this gene. Related pseudogenes have been identified on chromosomes 2, 14 and 22. [provided by RefSeq, Nov 2012]
- MLSTD1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~192.1 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 FAR2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001271783.2. 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 | 1 | 3 | |||
| missense | 61 | 1 | 62 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 65 | 1 | 1 | 67 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001258712.1 | 11 | MANE Select | |
| Ensembl | ENSP00000443291.2 | 11 | MANE Select | |
| RefSeq | NP_001258713.1 | 10 | Standard | |
| RefSeq | NP_060569.3 | 11 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Peroxisome - Homo sapiens (human)
- Metabolism of lipids
- Metabolism
- Wax biosynthesis
Biological Process
- lipid metabolic process
- wax biosynthetic process
- long-chain fatty-acyl-CoA metabolic process
- oxidation-reduction process
Molecular Function
- oxidoreductase activity
- fatty-acyl-CoA reductase (alcohol-forming) activity
- alcohol-forming fatty acyl-CoA reductase activity
Cellular Component
- peroxisome
- integral component of peroxisomal membrane
- peroxisomal matrix
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000536681
- Coding exons
- 11
- Length
- 191878
- Individuals with no LoFs
- 125737
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 11
- Defined
- 125748
- p
- 0.0000437
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.70 | 210 | 292 | 0.720 | 0.0000156 | 3417 |
| Missense (PolyPhen) | 75 | 115.84 | 0.64745 | 1408 | ||
| Synonymous | -0.407 | 108 | 103 | 1.05 | 0.00000569 | 956 |
| Loss of Function | 3.62 | 5 | 24.2 | 0.206 | 0.00000111 | 298 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000053 | 0.000053 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the reduction of saturated but not unsaturated C16 or C18 fatty acyl-CoA to fatty alcohols. A lower activity can be observed with shorter fatty acyl-CoA substrates (PubMed:15220348). It may play a role in the production of ether lipids/plasmalogens and wax monoesters which synthesis requires fatty alcohols as substrates (By similarity). {ECO:0000250|UniProtKB:Q8WVX9, ECO:0000269|PubMed:15220348}.;
Recessive Scores
- pRec
- 0.135
Intolerance Scores
- RVIS EVS
- -0.84
- RVIS percentile EVS
- 11.18
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- 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 |