SCD

stearoyl-CoA desaturase, the group of Fatty acid desaturases

Basic information

Region (hg38): 10:100347233-100364826

Previous symbols: [ "SCDOS" ]

Links

ENSG00000099194 ∙ NCBI:6319 ∙ OMIM:604031 ∙ HGNC:10571 ∙ Uniprot:O00767 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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	2
missense			11	1	1	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	11	1	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)
10-100348121-C-A		not specified	Uncertain significance (Oct 23, 2024)
10-100348146-C-G		not specified	Uncertain significance (Aug 13, 2021)
10-100348149-T-C		not specified	Likely benign (Oct 19, 2024)
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)
10-100352461-C-T		not specified	Uncertain significance (Nov 15, 2024)
10-100354514-T-C		not specified	Uncertain significance (Jul 31, 2024)
10-100354579-T-G		not specified	Uncertain significance (Jul 02, 2024)
10-100356542-C-T		not specified	Uncertain significance (Nov 14, 2024)
10-100356613-A-T		not specified	Uncertain significance (Oct 26, 2022)
10-100356626-G-A		not specified	Uncertain significance (Aug 06, 2024)
10-100356761-G-A		not specified	Uncertain significance (Oct 27, 2022)
10-100360777-C-T			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

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: 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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Scd4

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