CAPN5 p.Gly43=
c.129C>T · rs376307716 · VCV2994396
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00988%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.45 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.29 | gain · loss 0.08 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -3.7 | GERP -3.2 |
| Overall | ||
| CADD | 11.97 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00988%
South Asian · 9/91,084 alleles
Filtering AF
0.00514%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00375%
Overall
0.00161%
26/1,613,554 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00988% | 10,120 |
| African / African-American | 0.004% | 24,984 |
| East Asian | 0.00223% | 44,894 |
| European (non-Finnish) | 0.0011% | 90,773 |
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
- CAPN5
- Protein
- p.Gly43=
- Coding
- c.129C>T
- MANE Select
- NM_004055
- dbSNP
- rs376307716
- Type
- single nucleotide variant
- Location
- chr11:77085015 (GRCh38)
- Gene constraint
- LOEUF 0.928 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 91.71 · 1 PDB
- Residue 43
- the calpain catalytic domain
Similar variants
- CAPN5 p.Gly43Asp Uncertain significance ★ ⚠ same residue
- CAPN5 p.Gly43Ser Uncertain significance ★ ⚠ same residue
- CAPN5 p.Arg243Leu Pathogenic ★★ ⚠ same type
- CAPN5 p.Arg289Trp Pathogenic ★★ ⚠ same type
- CAPN5 p.Ala118Val Uncertain significance ★★ ⚠ same type
- CAPN5 p.Ala183Ser Uncertain significance ★★ ⚠ same type
- CAPN5 p.Ala185Val Uncertain significance ★★ ⚠ same type
- CAPN5 p.Ala237Val 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/capn5-p-gly43 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown