CDSN p.Ser439=
c.1317C>A · rs3130982 · VCV1174929
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 8.32%, sas) — 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. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.2 | |
| Overall | ||
| CADD | 0.506 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.32%
South Asian · 7,576/91,072 alleles
Filtering AF
8.16%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.1%
Overall
0.635%
10,252/1,613,738 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 8.32% | 12 |
| Middle Eastern | 3.98% | 25 |
| Remaining individualsnot grpmax-eligible | 0.653% | 153 |
| African / African-American | 0.391% | 256 |
| East Asian | 0.241% | 415 |
| Ashkenazi Jewishnot grpmax-eligible | 0.22% | 456 |
| Admixed American | 0.198% | 504 |
| European (non-Finnish) | 0.122% | 823 |
| Finnishnot grpmax-eligible | 0.0125% | 7,997 |
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.Ser439=
- Coding
- c.1317C>A
- MANE Select
- NM_001264
- dbSNP
- rs3130982
- Type
- single nucleotide variant
- Location
- chr6:31116298 (GRCh38)
- Gene constraint
- LOEUF 0.77 · pLI 0.08 (gnomAD)
- Structure
- AlphaFold pLDDT 38.13
- Residue 439
- 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-ser439 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown