Is CAPN5 p.Arg499Cys (c.1495C>T) pathogenic?

CAPN5 p.Arg499Cys (c.1495C>T) is classified Conflicting classifications of pathogenicity in CAPN5 (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2026-01-13). AlphaMissense: likely benign (0.0715); Rare (popmax 0.18%, nfe); Associated with Inborn genetic diseases.

What condition is associated with CAPN5 p.Arg499Cys (c.1495C>T)?

CAPN5 p.Arg499Cys (c.1495C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CAPN5 p.Arg499Cys (c.1495C>T) in the general population?

CAPN5 p.Arg499Cys (c.1495C>T) is rare (popmax 0.18%, nfe) (gnomAD).

What do computational predictors say about CAPN5 p.Arg499Cys (c.1495C>T)?

AlphaMissense predicts likely benign (score 0.0715) — an in-silico prediction, not a clinical call.

CAPN5 p.Arg499Cys

c.1495C>T · rs151286594 · VCV789210

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.0715 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.18%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0715	likely benign
REVEL	0.156	moderately benign-leaning
SaProt	LLR -5.26	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -3.1	GERP -3.7
Regional constraint	o/e 0.89	unconstrained · MANE · 39 kb · p 0.00098 · regional, not allelic
Overall
CADD	16.88	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 0.18% European (non-Finnish) · 2,061/1,143,470 alleles

Filtering AF 0.174% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.171%

Overall 0.151% 2,335/1,544,826 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.18%	555
Finnishnot grpmax-eligible	0.17%	588
Remaining individualsnot grpmax-eligible	0.132%	758
South Asian	0.0759%	1,317
African / African-American	0.026%	3,840
Admixed American	0.0198%	5,047
Middle Eastern	0.0168%	5,956
East Asian	0.00245%	40,736

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.Arg499Cys
Coding: c.1495C>T
MANE Select: NM_004055
dbSNP: rs151286594
Type: single nucleotide variant
Location: chr11:77121941 (GRCh38)
Gene constraint: LOEUF 0.928 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 91.71 · 1 PDB
Residue 499: the c2 domain

Full CAPN5 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

CAPN5 p.Arg499His Conflicting classifications of pathogenicity ★ ⚠ same residue
CAPN5 p.Ala183Ser Uncertain significance ★★ ⚠ same condition
CAPN5 p.Ala237Val Uncertain significance ★★ ⚠ same condition
CAPN5 p.Ala253Thr Uncertain significance ★★ ⚠ same condition
CAPN5 p.Ala34Val Uncertain significance ★★ ⚠ same condition
CAPN5 p.Ala357Val Uncertain significance ★★ ⚠ same condition
CAPN5 p.Ala362Gly Uncertain significance ★★ ⚠ same condition
CAPN5 p.Ala447Thr 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/capn5-p-arg499cys (accessed [today's date]).

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