CDSN p.Ser92Phe
c.275C>T · rs761952633 · VCV1049998
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0171%, nfe)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.193 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.1 | phastCons 0.062 |
| Overall | ||
| CADD | 19.36 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0171%
European (non-Finnish) · 199/1,161,926 alleles
Filtering AF
0.0152%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0144%
Overall
0.0127%
201/1,578,342 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0171% | 5,839 |
| Remaining individualsnot grpmax-eligible | 0.00328% | 30,526 |
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
- CDSN
- Protein
- p.Ser92Phe
- Coding
- c.275C>T
- MANE Select
- NM_001264
- dbSNP
- rs761952633
- Type
- single nucleotide variant
- Location
- chr6:31117340 (GRCh38)
- Gene constraint
- LOEUF 0.77 · pLI 0.08 (gnomAD)
- Structure
- AlphaFold pLDDT 38.13
- Residue 92
- the 'disordered' region
Similar variants
- CDSN p.Cys423Ser Uncertain significance ★★ same condition
- CDSN p.Gly335Ala Uncertain significance ★★ same condition
- CDSN p.Pro226Ser Uncertain significance ★★ same condition
- CDSN p.Pro471Leu Uncertain significance ★★ same condition
- CDSN p.Ser159Gly Uncertain significance ★★ same condition
- CDSN p.Ser274Asn Uncertain significance ★★ same condition
- CDSN p.Val506Met Uncertain significance ★★ same condition
- CDSN p.Pro192Leu Likely benign ★★ same condition
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/cdsn-p-ser92phe (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown