SCD
stearoyl-CoA desaturase, the group of Fatty acid desaturases
Basic information
Region (hg38): 10:100347232-100364826
Previous symbols: [ "SCDOS" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (4 variants)
- Inborn genetic diseases (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCD gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | ||||
| missense | 4 | 1 | 5 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 0 | |||||
| non coding | 1 | 1 | ||||
| Total | 0 | 0 | 4 | 0 | 4 |
Variants in SCD
This is a list of pathogenic ClinVar variants found in the SCD region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 10-100347540-C-T | Benign (Dec 31, 2019) | |||
| 10-100348146-C-G | Inborn genetic diseases | Uncertain significance (Aug 13, 2021) | ||
| 10-100348179-C-G | Benign (May 08, 2018) | |||
| 10-100348240-G-A | Benign (Jun 29, 2018) | |||
| 10-100348304-A-G | Inborn genetic diseases | Uncertain significance (Jan 10, 2023) | ||
| 10-100352368-G-A | Inborn genetic diseases | Uncertain significance (Jul 20, 2021) | ||
| 10-100356613-A-T | Inborn genetic diseases | Uncertain significance (Oct 26, 2022) | ||
| 10-100356761-G-A | Inborn genetic diseases | Uncertain significance (Oct 27, 2022) | ||
| 10-100360777-C-T | Benign (Dec 31, 2019) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SCD | protein_coding | protein_coding | ENST00000370355 | 6 | 17711 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.970 | 0.0303 | 125745 | 0 | 3 | 125748 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.04 | 130 | 214 | 0.608 | 0.0000126 | 2353 |
| Missense in Polyphen | 34 | 87.384 | 0.38909 | 964 | ||
| Synonymous | -0.600 | 87 | 80.2 | 1.09 | 0.00000441 | 705 |
| Loss of Function | 3.38 | 1 | 15.2 | 0.0657 | 7.34e-7 | 180 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000624 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000881 | 0.00000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Stearyl-CoA desaturase that utilizes O(2) and electrons from reduced cytochrome b5 to introduce the first double bond into saturated fatty acyl-CoA substrates (PubMed:15907797, PubMed:18765284). Catalyzes the insertion of a cis double bond at the delta-9 position into fatty acyl-CoA substrates including palmitoyl-CoA and stearoyl-CoA (PubMed:15907797, PubMed:18765284). Gives rise to a mixture of 16:1 and 18:1 unsaturated fatty acids (PubMed:15610069). Plays an important role in lipid biosynthesis. Plays an important role in regulating the expression of genes that are involved in lipogenesis and in regulating mitochondrial fatty acid oxidation (By similarity). Plays an important role in body energy homeostasis (By similarity). Contributes to the biosynthesis of membrane phospholipids, cholesterol esters and triglycerides (By similarity). {ECO:0000250|UniProtKB:P13516, ECO:0000269|PubMed:15610069, ECO:0000269|PubMed:15907797, ECO:0000269|PubMed:18765284}.;
- Pathway
- Biosynthesis of unsaturated fatty acids - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);Sterol Regulatory Element-Binding Proteins (SREBP) signalling;SREBF and miR33 in cholesterol and lipid homeostasis;Activation of gene expression by SREBF (SREBP);Adipogenesis;Liver X Receptor Pathway;Nuclear Receptors Meta-Pathway;Fatty Acid Biosynthesis;Angiopoietin Like Protein 8 Regulatory Pathway;PPAR signaling pathway;Liver steatosis AOP;Steatosis AOP;Metabolism of lipids;Fatty acyl-CoA biosynthesis;Regulation of cholesterol biosynthesis by SREBP (SREBF);Metabolism;Fatty acid metabolism;Metabolism of steroids;De novo fatty acid biosynthesis;Activation of gene expression by SREBF (SREBP);oleate biosynthesis
(Consensus)
Recessive Scores
- pRec
- 0.575
Intolerance Scores
- loftool
- 0.212
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.49
Haploinsufficiency Scores
- pHI
- 0.831
- hipred
- Y
- hipred_score
- 0.737
- ghis
- 0.443
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.934
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Scd4
- Phenotype
Gene ontology
- Biological process
- unsaturated fatty acid biosynthetic process;regulation of cholesterol biosynthetic process;fatty-acyl-CoA biosynthetic process;oxidation-reduction process;response to fatty acid;positive regulation of cold-induced thermogenesis;monounsaturated fatty acid biosynthetic process
- Cellular component
- nucleolus;endoplasmic reticulum;endoplasmic reticulum membrane;membrane;integral component of membrane;integral component of endoplasmic reticulum membrane
- Molecular function
- stearoyl-CoA 9-desaturase activity;iron ion binding;protein binding;oxidoreductase activity;palmitoyl-CoA 9-desaturase activity