Is CAPN10 p.Cys218Arg (c.652T>C) pathogenic?

CAPN10 p.Cys218Arg (c.652T>C) is classified Uncertain significance in CAPN10 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-16). AlphaMissense: likely pathogenic (0.6547); Ultra-rare (popmax 0.023%, nfe); Associated with Inborn genetic diseases.

What condition is associated with CAPN10 p.Cys218Arg (c.652T>C)?

CAPN10 p.Cys218Arg (c.652T>C) is associated with Inborn genetic diseases (ClinVar).

How common is CAPN10 p.Cys218Arg (c.652T>C) in the general population?

CAPN10 p.Cys218Arg (c.652T>C) is ultra-rare (popmax 0.023%, nfe) (gnomAD).

What do computational predictors say about CAPN10 p.Cys218Arg (c.652T>C)?

AlphaMissense predicts likely pathogenic (score 0.6547) — an in-silico prediction, not a clinical call.

CAPN10 p.Cys218Arg

c.652T>C · rs369247221 · VCV2391122

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6547 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.023%, nfe)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.6547	likely pathogenic
REVEL	0.569	indeterminate
SaProt	LLR -1.28	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.1	GERP 0.16, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 12 kb · p 0.013 · regional, not allelic
Overall
CADD	22.1	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.023% European (non-Finnish) · 268/1,166,650 alleles

Filtering AF 0.0207% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0198%

Overall 0.0176% 279/1,584,218 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.023%	4,353
Remaining individualsnot grpmax-eligible	0.013%	7,695
Admixed American	0.00375%	26,687
African / African-American	0.00134%	74,714

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: CAPN10
Protein: p.Cys218Arg
Coding: c.652T>C
MANE Select: NM_023083
dbSNP: rs369247221
Type: single nucleotide variant
Location: chr2:240592114 (GRCh38)
Gene constraint: LOEUF 1.121 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.91
Residue 218: the calpain catalytic domain

Full CAPN10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CAPN10 p.Arg127Cys Uncertain significance ★★ ⚠ same condition
CAPN10 p.Gly526Ser Uncertain significance ★★ ⚠ same condition
CAPN10 p.Pro46Ser Uncertain significance ★★ ⚠ same condition
CAPN10 p.Thr339Met Uncertain significance ★★ ⚠ same condition
CAPN10 p.Ala156Thr Uncertain significance ★ ⚠ same condition
CAPN10 p.Ala252Val Uncertain significance ★ ⚠ same condition
CAPN10 p.Ala341Thr Uncertain significance ★ ⚠ same condition
CAPN10 p.Ala389Val Uncertain significance ★ ⚠ same condition

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/capn10-p-cys218arg (accessed [today's date]).

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