SCD5

Chr 4AD

stearoyl-CoA desaturase 5

Also known as: ACOD4, DFNA79, FADS4, HSCD5, SCD2, SCD4

NCBI Gene: 79966ENSG00000145284UniProt: Q86SK9

Stearoyl-CoA desaturase 5 catalyzes the insertion of double bonds into saturated fatty acids, converting them to monounsaturated fatty acids essential for cellular membrane composition and signaling. Mutations cause autosomal dominant deafness (DFNA79), though the gene shows low constraint to loss-of-function variation suggesting the association may require further validation. This gene is unique to primates and differs significantly from other stearoyl-CoA desaturase isoforms found in rodents.

Summary from RefSeq, OMIM, UniProt
Research Assistant →

Primary Disease Associations & Inheritance

?Deafness, autosomal dominant 79MIM #619086
AD
0
Active trials
17
Pubs (1 yr)
38
P/LP submissions
3%
P/LP missense
0.93
LOEUF
DN
Mechanism· predicted
Clinical Summary— SCD5
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
38 unique Pathogenic / Likely Pathogenic· 50 VUS of 97 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.93LOEUF
pLI 0.001
Z-score 1.77
OE 0.49 (0.28–0.93)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.92Z-score
OE missense 0.82 (0.72–0.93)
172 obs / 209.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.49 (0.28–0.93)
0≤0.351.4
Missense OE0.82 (0.72–0.93)
0≤0.61.4
Synonymous OE1.07
0≤1.21.6
LoF obs/exp: 7 / 14.2Missense obs/exp: 172 / 209.3Syn Z: -0.50
DN
0.6743th %ile
GOF
0.5170th %ile
LOF
0.3939th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

97 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic35
Likely Pathogenic3
VUS50
Likely Benign3
35
Pathogenic
3
Likely Pathogenic
50
VUS
3
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
1
34
0
35
Likely Pathogenic
0
0
3
0
3
VUS
0
44
6
0
50
Likely Benign
0
0
0
3
3
Benign
0
0
0
0
0
Total04543391

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

SCD5 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients