Is CAPN5 p.Arg62= (c.186C>T) pathogenic?

CAPN5 p.Arg62= (c.186C>T) is classified Likely benign in CAPN5 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-04). Very rare (popmax 0.00134%, afr).

How common is CAPN5 p.Arg62= (c.186C>T) in the general population?

CAPN5 p.Arg62= (c.186C>T) is very rare (popmax 0.00134%, afr) (gnomAD).

CAPN5 p.Arg62=

c.186C>T · rs1950178158 · VCV2014168

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00134%, 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 0.11	GERP -1.8, phastCons 0.35
Overall
CADD	9.327	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00134% African / African-American · 1/74,858 alleles

Overall 6.23e-05% 1/1,605,174 alleles · very rare exomes 0/1,452,916 · genomes 1/152,258 · joint denominator

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.Arg62=
Coding: c.186C>T
MANE Select: NM_004055
dbSNP: rs1950178158
Type: single nucleotide variant
Location: chr11:77093702 (GRCh38)
Gene constraint: LOEUF 0.928 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 91.71 · 1 PDB
Residue 62: the calpain catalytic domain

Full CAPN5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CAPN5 p.Arg62His Uncertain significance ★★ ⚠ same residue
OMP p.Arg62Trp Uncertain significance ★ ⚠ same residue
CAPN5 p.Arg62fs 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

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-arg62 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown