Is CAPN1 p.Val162Met (c.484G>A) pathogenic?

CAPN1 p.Val162Met (c.484G>A) is classified Uncertain significance in CAPN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-19). AlphaMissense: likely pathogenic (0.8727); Ultra-rare (popmax 0.0218%, sas); Associated with Inborn genetic diseases.

What condition is associated with CAPN1 p.Val162Met (c.484G>A)?

CAPN1 p.Val162Met (c.484G>A) is associated with Inborn genetic diseases (ClinVar).

How common is CAPN1 p.Val162Met (c.484G>A) in the general population?

CAPN1 p.Val162Met (c.484G>A) is ultra-rare (popmax 0.0218%, sas) (gnomAD).

What do computational predictors say about CAPN1 p.Val162Met (c.484G>A)?

AlphaMissense predicts likely pathogenic (score 0.8727) — an in-silico prediction, not a clinical call.

CAPN1 p.Val162Met

c.484G>A · VCV4218729

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8727 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0218%, sas)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.8727	likely pathogenic
REVEL	0.529	indeterminate
SaProt	LLR -15.83	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.4, phastCons 1
Regional constraint	o/e 0.85	unconstrained · MANE · 29 kb · p 4.3e-06 · regional, not allelic
Overall
CADD	33.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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 0.0218% South Asian · 19/87,344 alleles

Filtering AF 0.0142% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0118%

Overall 0.00188% 27/1,437,918 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0218%	4,597
Ashkenazi Jewishnot grpmax-eligible	0.00344%	29,074
Remaining individualsnot grpmax-eligible	0.00162%	61,724
European (non-Finnish)	0.000514%	194,680

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: CAPN1
Protein: p.Val162Met
Coding: c.484G>A
MANE Select: NM_005186
Type: single nucleotide variant
Location: chr11:65185944 (GRCh38)
Gene constraint: LOEUF 0.977 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.03 · 5 PDB
Residue 162: the calpain catalytic domain; a β-strand

Full CAPN1 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

CAPN1 p.Val162Leu Uncertain significance ★★ ⚠ same residue
CAPN1 p.Arg104His Uncertain significance ★★ ⚠ same condition
CAPN1 p.Arg293Gln Uncertain significance ★★ ⚠ same condition
CAPN1 p.Arg293Trp Uncertain significance ★★ ⚠ same condition
CAPN1 p.Arg347Cys Uncertain significance ★★ ⚠ same condition
CAPN1 p.Arg347His Uncertain significance ★★ ⚠ same condition
CAPN1 p.Arg48Gln Uncertain significance ★★ ⚠ same condition
CAPN1 p.Arg581Gln 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/capn1-p-val162met (accessed [today's date]).

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