FADS1
fatty acid desaturase 1, the group of Fatty acid desaturases|MicroRNA protein coding host genes
Basic information
Region (hg38): 11:61799627-61829318
Previous symbols: [ "LLCDL1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FADS1 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 3 | 0 |
Variants in FADS1
This is a list of pathogenic ClinVar variants found in the FADS1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 11-61802839-C-A | not specified | Uncertain significance (Sep 06, 2022) | ||
| 11-61803420-C-A | not specified | Uncertain significance (Mar 19, 2024) | ||
| 11-61812491-C-A | not specified | Uncertain significance (Aug 02, 2021) | ||
| 11-61812622-C-T | not specified | Likely benign (Jan 31, 2022) | ||
| 11-61812623-G-A | not specified | Uncertain significance (Aug 15, 2023) | ||
| 11-61816744-C-A | Likely benign (Jul 26, 2018) | |||
| 11-61816789-A-C | Likely benign (Jun 01, 2020) | |||
| 11-61816814-G-C | not specified | Uncertain significance (May 11, 2022) | ||
| 11-61816847-C-T | not specified | Uncertain significance (Jan 03, 2024) | ||
| 11-61828430-C-T | not specified | Uncertain significance (Jan 24, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FADS1 | protein_coding | protein_coding | ENST00000350997 | 12 | 29692 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.374 | 0.626 | 125667 | 0 | 11 | 125678 | 0.0000438 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.67 | 98 | 267 | 0.367 | 0.0000136 | 3288 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000909 | 0.0000908 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000169 | 0.000163 |
| Finnish | 0.0000473 | 0.0000462 |
| European (Non-Finnish) | 0.0000442 | 0.0000440 |
| Middle Eastern | 0.000169 | 0.000163 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
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}.;
- Pathway
- 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;miR-targeted genes in lymphocytes - TarBase;Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);Metabolism of lipids;arachidonate biosynthesis III (metazoa);alpha-linolenic acid (ALA) metabolism;Linoleic acid (LA) metabolism;alpha-linolenic (omega3) and linoleic (omega6) acid metabolism;Omega-3 fatty acid metabolism;Metabolism;Fatty acid metabolism;Linoleate metabolism;Omega-6 fatty acid metabolism;icosapentaenoate biosynthesis II (metazoa)
(Consensus)
Recessive Scores
- pRec
- 0.239
Intolerance Scores
- loftool
- 0.562
- rvis_EVS
- -0.12
- rvis_percentile_EVS
- 44.54
Haploinsufficiency Scores
- pHI
- 0.106
- hipred
- Y
- hipred_score
- 0.693
- ghis
- 0.596
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.931
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fads1
- Phenotype
- immune system phenotype; digestive/alimentary phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- regulation of transcription, DNA-templated;unsaturated fatty acid biosynthetic process;cell-cell signaling;phospholipid biosynthetic process;cellular response to starvation;regulation of lipid metabolic process;alpha-linolenic acid metabolic process;linoleic acid metabolic process;regulation of cell differentiation;icosanoid biosynthetic process;oxidation-reduction process
- Cellular component
- mitochondrion;endoplasmic reticulum membrane;membrane;integral component of membrane;intracellular membrane-bounded organelle
- Molecular function
- C-5 sterol desaturase activity;oxidoreductase activity;omega-6 fatty acid desaturase activity;acyl-CoA delta5-desaturase activity