Is CAPN15 p.Val195= (c.585C>T) pathogenic?

CAPN15 p.Val195= (c.585C>T) is classified Likely benign in CAPN15 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-08-21). Rare (popmax 0.563%, eas); Associated with CAPN15-related disorder.

What condition is associated with CAPN15 p.Val195= (c.585C>T)?

CAPN15 p.Val195= (c.585C>T) is associated with CAPN15-related disorder (ClinVar).

How common is CAPN15 p.Val195= (c.585C>T) in the general population?

CAPN15 p.Val195= (c.585C>T) is rare (popmax 0.563%, eas) (gnomAD).

CAPN15 p.Val195=

c.585C>T · rs369551311 · VCV3052432

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.563%, eas)

Conditions

CAPN15-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 -6.4	GERP -2.8
Overall
CADD	0.069	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.563% East Asian · 243/43,198 alleles

Filtering AF 0.505% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.482%

Overall 0.0244% 384/1,576,482 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.563%	178
Remaining individualsnot grpmax-eligible	0.0652%	1,534
South Asian	0.0577%	1,732
African / African-American	0.00807%	12,386
European (non-Finnish)	0.00368%	27,181
Admixed American	0.00174%	57,350

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: CAPN15
Protein: p.Val195=
Coding: c.585C>T
MANE Select: NM_005632
dbSNP: rs369551311
Type: single nucleotide variant
Location: chr16:547423 (GRCh38)
Gene constraint: LOEUF 0.974 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.65

Full CAPN15 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CAPN15-related disorder

Similar variants

CAPN15 p.Val195Ile Uncertain significance ★ ⚠ same residue
CAPN15 p.Val195Phe Uncertain significance ★ ⚠ same residue
CAPN15 p.Pro494Ser Uncertain significance ★ ⚠ same condition
CAPN15 p.Ser613Leu Conflicting classifications of pathogenicity ★ ⚠ same condition
CAPN15 p.Thr950Ala Uncertain significance ⚠ same condition
CAPN15 p.Ala559= Likely benign same condition
CAPN15 p.Ala817= Likely benign same condition
CAPN15 p.Arg428Gln 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/capn15-p-val195 (accessed [today's date]).

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