FADS2
protein-codingfatty acid desaturase 2, the group of Fatty acid desaturases
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 at 11q12-q13.1; this cluster is thought to have arisen evolutionarily from gene duplication based on its similar exon/intron organization. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]
- LLCDL2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~74.4 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 FADS2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004265.4. 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 | 1 | 3 | |||
| missense | 19 | 1 | 20 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 23 | 1 | 1 | 25 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004256.1 | 12 | MANE Select | |
| Ensembl | ENSP00000278840.4 | 12 | MANE Select | |
| RefSeq | NP_001268430.1 | 12 | Standard | |
| RefSeq | NP_001268431.1 | 12 | 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 metabolism - Homo sapiens (human)
- PPAR signaling pathway - Homo sapiens (human)
- Alpha Linolenic Acid and Linoleic Acid Metabolism
- miR-targeted genes in lymphocytes - TarBase
Biological Process
- unsaturated fatty acid biosynthetic process
- alpha-linolenic acid metabolic process
- linoleic acid metabolic process
- oxidation-reduction process
Molecular Function
- stearoyl-CoA 9-desaturase activity
- linoleoyl-CoA desaturase activity
Cellular Component
- endoplasmic reticulum membrane
- integral component of plasma membrane
- membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000278840
- Coding exons
- 12
- Length
- 74375
- Individuals with no LoFs
- 125744
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 3
- Defined
- 125747
- p
- 0.0000119
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.19 | 118 | 264 | 0.447 | 0.0000150 | 2974 |
| Missense (PolyPhen) | 9 | 57.676 | 0.15604 | 705 | ||
| Synonymous | 0.641 | 103 | 112 | 0.923 | 0.00000727 | 804 |
| Loss of Function | 4.48 | 2 | 27.2 | 0.0735 | 0.00000127 | 280 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0000090 | 0.0000088 | rare |
| South Asian | 0.000037 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: 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 first and rate limiting step in this pathway which is the desaturation of LA (18:2n-6) and ALA (18:3n-3) into gamma- linoleic acid (GLA) (18:3n-6) and stearidonic acid (18:4n-3) respectively and other desaturation steps. Highly unsaturated fatty acids (HUFA) play pivotal roles in many biological functions. It catalizes as well the introduction of a cis double bond in palmitate to produce the mono-unsaturated fatty acid sapienate, the most abundant fatty acid in sebum. {ECO:0000269|PubMed:12713571, ECO:0000269|PubMed:9867867}.;
Recessive Scores
- pRec
- 0.278
Intolerance Scores
- LoFtool
- 0.277
- RVIS EVS
- -0.38
- RVIS percentile EVS
- 27.42
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.992
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |