FADS2
Basic information
Region (hg38): 11:61792980-61867354
Previous symbols: [ "LLCDL2" ]
Links
Transcripts
Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 19.
| Transcript ID | Protein ID | Coding exons | MANE Select | MANE Plus Clinical |
|---|---|---|---|---|
NM_004265.4 | NP_004256.1 | 12 | yes | - |
ENST00000278840.9 | ENSP00000278840.4 | 12 | yes | - |
NM_001281501.1 | NP_001268430.1 | 12 | - | - |
NM_001281502.1 | NP_001268431.1 | 12 | - | - |
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (19 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FADS2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_004265.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | 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 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FADS2 | protein_coding | protein_coding | ENST00000278840 | 12 | 74375 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 125744 | 0 | 3 | 125747 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.19 | 118 | 264 | 0.447 | 0.0000150 | 2974 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000901 | 0.00000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000375 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
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}.;
- Pathway
- 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;miR-targeted genes in muscle cell - TarBase;PPAR signaling pathway;Metabolism of lipids;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;γ-linolenate biosynthesis;Linoleate metabolism;Omega-6 fatty acid metabolism;icosapentaenoate biosynthesis II (metazoa);docosahexaenoate biosynthesis III (mammals)
(Consensus)
Recessive Scores
- pRec
- 0.278
Intolerance Scores
- loftool
- 0.277
- rvis_EVS
- -0.38
- rvis_percentile_EVS
- 27.42
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.992
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- unsaturated fatty acid biosynthetic process;alpha-linolenic acid metabolic process;linoleic acid metabolic process;oxidation-reduction process
- Cellular component
- endoplasmic reticulum membrane;integral component of plasma membrane;membrane
- Molecular function
- stearoyl-CoA 9-desaturase activity;linoleoyl-CoA desaturase activity