Is CAPN10 p.Pro574Ala (c.1720C>G) pathogenic?

CAPN10 p.Pro574Ala (c.1720C>G) is classified Uncertain significance in CAPN10 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-31). AlphaMissense: likely benign (0.1106); Very rare (popmax 0.0022%, nfe); Associated with diabetes mellitus, noninsulin-dependent, 1.

What condition is associated with CAPN10 p.Pro574Ala (c.1720C>G)?

CAPN10 p.Pro574Ala (c.1720C>G) is associated with diabetes mellitus, noninsulin-dependent, 1 (ClinVar).

How common is CAPN10 p.Pro574Ala (c.1720C>G) in the general population?

CAPN10 p.Pro574Ala (c.1720C>G) is very rare (popmax 0.0022%, nfe) (gnomAD).

What do computational predictors say about CAPN10 p.Pro574Ala (c.1720C>G)?

AlphaMissense predicts likely benign (score 0.1106) — an in-silico prediction, not a clinical call.

CAPN10 p.Pro574Ala

c.1720C>G · rs1175724176 · VCV1704371

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1106 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0022%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

diabetes mellitus, noninsulin-dependent, 1

Computational evidence

Protein change
AlphaMissense	0.1106	likely benign
REVEL	0.38	indeterminate
SaProt	LLR -3.90	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.3	GERP 0.23, phastCons 0.75
Regional constraint	o/e 0.92	unconstrained · MANE · 12 kb · p 0.013 · regional, not allelic
Overall
CADD	13.19	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0022% European (non-Finnish) · 26/1,180,038 alleles

Filtering AF 0.00153% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0013%

Overall 0.00167% 27/1,613,432 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0022%	45,386
Remaining individualsnot grpmax-eligible	0.0016%	62,482

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.Pro574Ala
Coding: c.1720C>G
MANE Select: NM_023083
dbSNP: rs1175724176
Type: single nucleotide variant
Location: chr2:240596919 (GRCh38)
Gene constraint: LOEUF 1.121 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.91
Residue 574: the 'domain iii 2' region

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

Disease context

diabetes mellitus, noninsulin-dependent, 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CAPN10 p.Trp302Ter Likely pathogenic ★ same condition
CAPN10 p.Arg127Cys Uncertain significance ★★ ⚠ same type
CAPN10 p.Gly526Ser Uncertain significance ★★ ⚠ same type
CAPN10 p.Pro46Ser Uncertain significance ★★ ⚠ same type
CAPN10 p.Thr339Met Uncertain significance ★★ ⚠ same type
CAPN10 p.Ala477= Benign ★★ same type
CAPN10 p.Ala477Thr Benign ★★ same type
CAPN10 p.Arg555Cys Likely benign ★★ 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/capn10-p-pro574ala (accessed [today's date]).

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