FADS1
protein-codingfatty acid desaturase 1, the group of Fatty acid desaturases|MicroRNA protein coding host genes
Gene summary
The protein encoded by this gene is a member of the fatty acid desaturase (FADS) gene family. Desaturase enzymes regulate unsaturation of fatty acids through the introduction of double bonds between defined carbons of the fatty acyl chain. FADS family members are considered fusion products composed of an N-terminal cytochrome b5-like domain and a C-terminal multiple membrane-spanning desaturase portion, both of which are characterized by conserved histidine motifs. This gene is clustered with family members FADS1 and FADS2 at 11q12-q13.1; this cluster is thought to have arisen evolutionarily from gene duplication based on its similar exon/intron organization. [provided by RefSeq, Jul 2008]
- LLCDL1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~29.7 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 FADS1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_013402.7. 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 | ||||
| missense | 22 | 2 | 24 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 22 | 4 | 0 | 26 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_037534.5 | 12 | MANE Select | |
| Ensembl | ENSP00000322229.9 | 12 | MANE Select | |
| Ensembl | ENSP00000416043.1 | 4 | Standard | |
| Ensembl | ENSP00000407895.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Biosynthesis of unsaturated fatty acids - Homo sapiens (human)
- Alpha Linolenic Acid and Linoleic Acid Metabolism
- miR-targeted genes in adipocytes - TarBase
- miR-targeted genes in epithelium - TarBase
- miR-targeted genes in leukocytes - TarBase
Biological Process
- regulation of transcription, DNA-templated
- unsaturated fatty acid biosynthetic process
- cell-cell signaling
- phospholipid biosynthetic process
- cellular response to starvation
Molecular Function
- C-5 sterol desaturase activity
- oxidoreductase activity
- omega-6 fatty acid desaturase activity
- acyl-CoA delta5-desaturase activity
Cellular Component
- mitochondrion
- endoplasmic reticulum membrane
- membrane
- integral component of membrane
- intracellular membrane-bounded organelle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000350997
- Coding exons
- 12
- Length
- 29692
- Individuals with no LoFs
- 125667
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 11
- Defined
- 125678
- p
- 0.0000438
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.67 | 98 | 267 | 0.367 | 0.0000136 | 3288 |
| Missense (PolyPhen) | 26 | 94.661 | 0.27467 | 1176 | ||
| Synonymous | 1.56 | 88 | 109 | 0.810 | 0.00000564 | 976 |
| Loss of Function | 3.70 | 6 | 26.6 | 0.225 | 0.00000129 | 276 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00017 | 0.00016 | rare |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.000044 | 0.000044 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Isoform 2 does not exhibit any catalytic activity toward 20:3n-6, but it may enhance FADS2 activity (By similarity). Isoform 1 is a component of a lipid metabolic pathway that catalyzes biosynthesis of highly unsaturated fatty acids (HUFA) from precursor essential polyunsaturated fatty acids (PUFA) linoleic acid (LA) (18:2n-6) and alpha-linolenic acid (ALA) (18:3n-3). Catalyzes the desaturation of dihomo-gamma-linoleic acid (DHGLA) (20:3n-6) and eicosatetraenoic acid (20:4n-3) to generate arachidonic acid (AA) (20:4n-6) and eicosapentaenoic acid (EPA)(20:5n-3), respectively. {ECO:0000250, ECO:0000269|PubMed:10601301, ECO:0000269|PubMed:10769175}.;
Recessive Scores
- pRec
- 0.239
Intolerance Scores
- LoFtool
- 0.562
- RVIS EVS
- -0.12
- RVIS percentile EVS
- 44.54
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.931
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |