CAPN6 p.Pro514=
c.1542G>A · rs746917930 · VCV2661203
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.157%, sas)
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 -7.4 | GERP -4.1 |
| Overall | ||
| CADD | 0.634 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.157%
South Asian · 89/56,770 alleles
Filtering AF
0.13%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.121%
Overall
0.00985%
119/1,208,118 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.157% | 638 |
| Remaining individualsnot grpmax-eligible | 0.0147% | 6,791 |
| Admixed American | 0.00656% | 15,255 |
| European (non-Finnish) | 0.00213% | 47,018 |
| African / African-American | 0.00175% | 57,215 |
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
- CAPN6
- Protein
- p.Pro514=
- Coding
- c.1542G>A
- MANE Select
- NM_014289
- dbSNP
- rs746917930
- Type
- single nucleotide variant
- Location
- chrX:111247935 (GRCh38)
- Structure
- AlphaFold pLDDT 91.57
- Residue 514
- the c2 domain
Similar variants
- CAPN6 c.1158+128A>T Benign ★★ same type
- CAPN6 c.1743+105G>A Benign ★★ same type
- CAPN6 c.297+86C>T Benign ★★ same type
- CAPN6 c.699+25C>T Benign ★★ same type
- CAPN6 c.700-159T>C Benign ★★ same type
- CAPN6 p.Tyr117= Benign ★★ same type
- CAPN6 p.Val277Leu Benign ★★ same type
- CAPN6 p.Arg260Cys 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/capn6-p-pro514 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown