SCD5

stearoyl-CoA desaturase 5, the group of Fatty acid desaturases|MicroRNA protein coding host genes

Basic information

Region (hg38): 4:82629538-82798796

Previous symbols: [ "SCD4" ]

Links

ENSG00000145284 ∙ NCBI:79966 ∙ OMIM:608370 ∙ HGNC:21088 ∙ Uniprot:Q86SK9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hearing loss, autosomal dominant 79 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal dominant 79	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Audiologic/Otolaryngologic	31972369

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCD5 gene.

• Inborn genetic diseases (14 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCD5 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				3		3
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	3	0

Variants in SCD5

This is a list of pathogenic ClinVar variants found in the SCD5 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-82631385-C-T		not specified	Uncertain significance (Jul 20, 2021)
4-82636609-C-T		not specified	Uncertain significance (Jul 16, 2021)
4-82636662-A-G		not specified	Uncertain significance (Apr 21, 2022)
4-82636670-G-A			Likely benign (Feb 01, 2023)
4-82636705-T-C		not specified	Uncertain significance (Dec 12, 2023)
4-82636751-C-G		not specified	Uncertain significance (Feb 07, 2023)
4-82636767-C-G		Hearing loss, autosomal dominant 79	Pathogenic (Nov 08, 2023)
4-82636801-G-A		not specified	Uncertain significance (Feb 23, 2023)
4-82680720-G-C		not specified	Uncertain significance (Dec 06, 2022)
4-82680854-T-C			Uncertain significance (Sep 01, 2023)
4-82705332-T-C		not specified	Uncertain significance (Feb 17, 2023)
4-82705362-C-T		not specified	Uncertain significance (Sep 12, 2023)
4-82705363-G-A		not specified	Uncertain significance (Jun 01, 2023)
4-82705408-A-T		not specified	Uncertain significance (May 03, 2023)
4-82798394-C-T			Likely benign (Feb 01, 2023)
4-82798413-C-G		not specified	Uncertain significance (May 06, 2022)
4-82798420-C-G		not specified	Uncertain significance (Nov 10, 2022)
4-82798444-C-T		not specified	Uncertain significance (Nov 17, 2022)
4-82798459-A-G		not specified	Uncertain significance (Feb 27, 2023)
4-82798517-G-A			Likely benign (Jul 01, 2023)
4-82798521-G-C		not specified	Uncertain significance (Nov 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCD5	protein_coding	protein_coding	ENST00000319540	5	169319

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00104	0.954	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.917	172	209	0.822	0.0000124	2155
Missense in Polyphen		47	67.628	0.69498		750
Synonymous	-0.500	90	84.2	1.07	0.00000474	674
Loss of Function	1.77	7	14.2	0.494	7.56e-7	144

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000323	0.000323
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
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. 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:15610069). Gives rise to a mixture of 16:1 and 18:1 unsaturated fatty acids. {ECO:0000269|PubMed:15610069, ECO:0000269|PubMed:15907797}.
• Pathway: Biosynthesis of unsaturated fatty acids - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);Metabolism of lipids;Fatty acyl-CoA biosynthesis;Metabolism;Fatty acid metabolism;oleate biosynthesis (Consensus)

Recessive Scores

• pRec: 0.295

Intolerance Scores

• loftool: 0.225
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.61

Haploinsufficiency Scores

• pHI: 0.206
• hipred: N
• hipred_score: 0.321
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.955

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;fatty-acyl-CoA biosynthetic process;oxidation-reduction process;monounsaturated fatty acid biosynthetic process
• Cellular component: endoplasmic reticulum membrane;integral component of membrane
• Molecular function: stearoyl-CoA 9-desaturase activity;iron ion binding;oxidoreductase activity