SC5D p.Phe291=
c.873C>T · rs779699551 · VCV745582
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00119%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.2 | GERP 0.99, phastCons 0.89 |
| Overall | ||
| CADD | 11.28 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00119%
European (non-Finnish) · 14/1,176,846 alleles
Filtering AF
0.00069%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00054%
Overall
0.000872%
14/1,605,314 alleles · very rare
exomes 13/1,453,286 · genomes 1/152,028 · joint denominator
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
- SC5D
- Protein
- p.Phe291=
- Coding
- c.873C>T
- MANE Select
- NM_006918
- dbSNP
- rs779699551
- Type
- single nucleotide variant
- Location
- chr11:121307485 (GRCh38)
- Gene constraint
- LOEUF 1.303 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.05
- Residue 291
- the 'disordered' region
Similar variants
- SC5D p.Arg277Cys Uncertain significance ★★ ⚠ same type
- SC5D p.Asn292Ser Uncertain significance ★★ ⚠ same type
- SC5D p.Asp59Asn Uncertain significance ★★ ⚠ same type
- SC5D p.Lys148Glu Uncertain significance ★★ ⚠ same type
- SC5D p.Met234Val Uncertain significance ★★ ⚠ same type
- SC5D p.Tyr55Cys Uncertain significance ★★ ⚠ same type
- SC5D p.Val57Leu Uncertain significance ★★ ⚠ same type
- SC5D c.210+19T>A Benign/Likely benign ★★ 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/sc5d-p-phe291 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown