SCD

stearoyl-CoA desaturase, the group of Fatty acid desaturases

Basic information

Region (hg38): 10:100347232-100364826

Previous symbols: [ "SCDOS" ]

Links

ENSG00000099194NCBI:6319OMIM:604031HGNC:10571Uniprot:O00767AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCD gene.

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
clinvar
2
missense
5
clinvar
1
clinvar
6
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
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)781943
10-100348146-C-G not specified Uncertain significance (Aug 13, 2021)2244825
10-100348179-C-G Benign (May 08, 2018)731905
10-100348240-G-A Benign (Jun 29, 2018)787080
10-100348304-A-G not specified Uncertain significance (Jan 10, 2023)2462405
10-100352368-G-A not specified Uncertain significance (Jul 20, 2021)2238608
10-100356613-A-T not specified Uncertain significance (Oct 26, 2022)2320181
10-100356761-G-A not specified Uncertain significance (Oct 27, 2022)2226762
10-100360777-C-T Benign (Dec 31, 2019)773538

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SCDprotein_codingprotein_codingENST00000370355 617711
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9700.0303125745031257480.0000119
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.041302140.6080.00001262353
Missense in Polyphen3487.3840.38909964
Synonymous-0.6008780.21.090.00000441705
Loss of Function3.38115.20.06577.34e-7180

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006240.0000615
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.000008810.00000879
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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