CDSN p.Arg11His
c.32G>A · rs371334209 · VCV2057245
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.19%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.034 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.2 | |
| Overall | ||
| CADD | 18.33 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.19%
South Asian · 2,789/87,414 alleles
Filtering AF
3.09%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.05%
Overall
0.196%
3,131/1,593,800 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 3.19% | 31 |
| Remaining individualsnot grpmax-eligible | 0.376% | 266 |
| East Asian | 0.121% | 826 |
| Middle Eastern | 0.0693% | 1,442 |
| Admixed American | 0.0192% | 5,196 |
| African / African-American | 0.0161% | 6,221 |
| European (non-Finnish) | 0.00256% | 39,029 |
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.Arg11His
- Coding
- c.32G>A
- MANE Select
- NM_001264
- dbSNP
- rs371334209
- Type
- single nucleotide variant
- Location
- chr6:31120388 (GRCh38)
- Gene constraint
- LOEUF 0.77 · pLI 0.08 (gnomAD)
- Structure
- AlphaFold pLDDT 38.13
Similar variants
- CDSN p.Arg11fs Likely pathogenic ★ 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-arg11his (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown