CDSN p.Phe202Ser
c.605T>C · rs707913 · VCV1231588
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 38%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.044 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 5.2 | phastCons 1 |
| Overall | ||
| CADD | 13.26 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
38%
African / African-American · 28,475/74,958 alleles
Filtering AF
37.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 37.5%
Overall
21.8%
351,147/1,613,866 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 38% | 3 |
| East Asian | 32.3% | 3 |
| Admixed American | 32% | 3 |
| Remaining individualsnot grpmax-eligible | 21.1% | 5 |
| Ashkenazi Jewishnot grpmax-eligible | 21.1% | 5 |
| European (non-Finnish) | 21% | 5 |
| Finnishnot grpmax-eligible | 20.6% | 5 |
| Middle Eastern | 16.8% | 6 |
| Amishnot grpmax-eligible | 10.5% | 10 |
| South Asian | 7.83% | 13 |
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.Phe202Ser
- Coding
- c.605T>C
- MANE Select
- NM_001264
- dbSNP
- rs707913
- Type
- single nucleotide variant
- Location
- chr6:31117010 (GRCh38)
- Gene constraint
- LOEUF 0.77 · pLI 0.08 (gnomAD)
- Structure
- AlphaFold pLDDT 38.13
- Residue 202
- a UniProt-annotated variant site (in allele 1.41, allele 1.42 and allele 1.43); the 'disordered' region
Similar variants
- CDSN p.Lys59Ter Pathogenic ★★ same type
- CDSN p.Cys423Ser Uncertain significance ★★ same type
- CDSN p.Gly335Ala Uncertain significance ★★ same type
- CDSN p.Pro226Ser Uncertain significance ★★ same type
- CDSN p.Pro282Thr Uncertain significance ★★ same type
- CDSN p.Pro447Leu Uncertain significance ★★ same type
- CDSN p.Pro471Leu Uncertain significance ★★ same type
- CDSN p.Ser159Gly 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/cdsn-p-phe202ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown