CAPN6 p.Thr472=
c.1416C>T · rs17879776 · VCV777822
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.38%, afr)
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 2.2 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 9.077 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.38%
African / African-American · 1,358/57,134 alleles
Filtering AF
2.27%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.23%
Overall
0.129%
1,562/1,207,994 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.38% | 42 |
| Remaining individualsnot grpmax-eligible | 0.168% | 594 |
| Admixed American | 0.14% | 715 |
| Middle Eastern | 0.121% | 825 |
| European (non-Finnish) | 0.00604% | 16,565 |
| South Asian | 0.00353% | 28,343 |
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.Thr472=
- Coding
- c.1416C>T
- MANE Select
- NM_014289
- dbSNP
- rs17879776
- Type
- single nucleotide variant
- Location
- chrX:111248637 (GRCh38)
- Structure
- AlphaFold pLDDT 91.57
- Residue 472
- the 'domain iii' region
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-thr472 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown