Is CAPN10 p.Ala511= (c.1533G>A) pathogenic?

CAPN10 p.Ala511= (c.1533G>A) is classified Likely benign in CAPN10 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-07-10). Rare (popmax 0.101%, mid); Associated with CAPN10-related disorder.

What condition is associated with CAPN10 p.Ala511= (c.1533G>A)?

CAPN10 p.Ala511= (c.1533G>A) is associated with CAPN10-related disorder (ClinVar).

How common is CAPN10 p.Ala511= (c.1533G>A) in the general population?

CAPN10 p.Ala511= (c.1533G>A) is rare (popmax 0.101%, mid) (gnomAD).

CAPN10 p.Ala511=

c.1533G>A · rs370128354 · VCV3050082

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.101%, mid)

Conditions

CAPN10-related disorder

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 -7.1	GERP -2.6
Overall
CADD	0.147	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.101% Middle Eastern · 6/5,944 alleles

Filtering AF 0.0439% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.03%

Overall 0.00899% 143/1,591,456 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.101%	991
European (non-Finnish)	0.0105%	9,569
Admixed American	0.0103%	9,756
Remaining individualsnot grpmax-eligible	0.00651%	15,365
Finnishnot grpmax-eligible	0.00645%	15,497
African / African-American	0.00134%	74,688

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.Ala511=
Coding: c.1533G>A
MANE Select: NM_023083
dbSNP: rs370128354
Type: single nucleotide variant
Location: chr2:240596732 (GRCh38)
Gene constraint: LOEUF 1.121 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.91

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

Disease context

CAPN10-related disorder

Similar variants

CAPN10 p.Ala511Thr Likely benign ★ same residue
CAPN10 c.1989+1G>A Pathogenic ★ same condition
CAPN10 p.Ala380= Uncertain significance ★ same condition
CAPN10 p.Arg395Gln Uncertain significance ★ ⚠ same condition
CAPN10 p.Lys366Thr Uncertain significance ⚠ same condition
CAPN10 c.1990-7T>C Benign same condition
CAPN10 p.Ala390= Likely benign same condition
CAPN10 p.Ala447= Likely benign 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-ala511 (accessed [today's date]).

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