SCD
Basic information
Region (hg38): 10:100347232-100364826
Previous symbols: [ "SCDOS" ]
Links
Phenotypes
GenCC
Source:
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 SCD 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 | 1 | |||||
Total | 0 | 0 | 5 | 0 | 4 |
Variants in SCD
This is a list of pathogenic ClinVar variants found in the SCD region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
10-100347540-C-T | Benign (Dec 31, 2019) | |||
10-100348146-C-G | not specified | 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 | not specified | Uncertain significance (Jan 10, 2023) | ||
10-100352368-G-A | not specified | Uncertain significance (Jul 20, 2021) | ||
10-100356613-A-T | not specified | Uncertain significance (Oct 26, 2022) | ||
10-100356761-G-A | not specified | 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