SCD5 p.Ala241=
c.723C>T · rs75025667 · VCV2654844
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.826%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6.2 | GERP -3.8 |
| Overall | ||
| CADD | 3.518 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.826%
African / African-American · 620/75,038 alleles
Filtering AF
0.772%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.751%
Overall
0.0571%
921/1,614,206 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.826% | 121 |
| Admixed American | 0.142% | 706 |
| Middle Eastern | 0.066% | 1,516 |
| Remaining individualsnot grpmax-eligible | 0.0624% | 1,603 |
| European (non-Finnish) | 0.0145% | 6,901 |
| South Asian | 0.0022% | 45,541 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- SCD5
- Protein
- p.Ala241=
- Coding
- c.723C>T
- MANE Select
- NM_001037582
- dbSNP
- rs75025667
- Type
- single nucleotide variant
- Location
- chr4:82636670 (GRCh38)
- Gene constraint
- LOEUF 0.907 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.99
Similar variants
- SCD5 p.Arg186Gly Uncertain significance ★★ ⚠ same type
- SCD5 p.Ala16Ser Uncertain significance ★ ⚠ same type
- SCD5 p.Ala22Asp Uncertain significance ★ ⚠ same type
- SCD5 p.Ala78Val Uncertain significance ★ ⚠ same type
- SCD5 p.Arg103Trp Uncertain significance ★ ⚠ same type
- SCD5 p.Arg148His Uncertain significance ★ ⚠ same type
- SCD5 p.Arg162Cys Uncertain significance ★ ⚠ same type
- SCD5 p.Arg21Pro Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/scd5-p-ala241 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown