CDSN p.Ser152Arg
c.456C>G · rs144038841 · VCV732112
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.67%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.018 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.27 | |
| Overall | ||
| CADD | 14.46 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.67%
East Asian · 1,194/44,742 alleles
Filtering AF
2.54%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.49%
Overall
0.0967%
1,554/1,606,338 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 2.67% | 37 |
| Admixed American | 0.206% | 485 |
| Finnishnot grpmax-eligible | 0.138% | 725 |
| Remaining individualsnot grpmax-eligible | 0.0545% | 1,835 |
| South Asian | 0.0342% | 2,926 |
| Middle Eastern | 0.033% | 3,029 |
| African / African-American | 0.0247% | 4,052 |
| European (non-Finnish) | 0.00544% | 18,370 |
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.Ser152Arg
- Coding
- c.456C>G
- MANE Select
- NM_001264
- dbSNP
- rs144038841
- Type
- single nucleotide variant
- Location
- chr6:31117159 (GRCh38)
- Gene constraint
- LOEUF 0.77 · pLI 0.08 (gnomAD)
- Structure
- AlphaFold pLDDT 38.13
- Residue 152
- the 'disordered' region
Similar variants
- CDSN p.Ser152Gly Conflicting classifications of pathogenicity ★ same residue
- 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
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-ser152arg (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown