SC5D p.Phe58=
c.174C>T · rs200792246 · VCV731620
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.06%, amr)
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 1.5 | GERP -1.8, phastCons 0.97 |
| Overall | ||
| CADD | 12.83 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.06%
Admixed American · 36/59,964 alleles
Filtering AF
0.0445%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0392%
Overall
0.00713%
115/1,613,310 alleles · ultra-rare
exomes 80/1,461,446 · genomes 35/151,864 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.06% | 1,666 |
| South Asian | 0.0286% | 3,501 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,249 |
| African / African-American | 0.00801% | 12,482 |
| European (non-Finnish) | 0.00314% | 31,881 |
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.Phe58=
- Coding
- c.174C>T
- MANE Select
- NM_006918
- dbSNP
- rs200792246
- Type
- single nucleotide variant
- Location
- chr11:121303549 (GRCh38)
- Gene constraint
- LOEUF 1.303 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.05
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-phe58 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown