Is CALR3 p.Ile93Val (c.277A>G) pathogenic?

CALR3 p.Ile93Val (c.277A>G) is classified Uncertain significance in CALR3 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-16). AlphaMissense: likely benign (0.1061); Very rare (popmax 8.47e-05%, nfe); Associated with hypertrophic cardiomyopathy 19.

What condition is associated with CALR3 p.Ile93Val (c.277A>G)?

CALR3 p.Ile93Val (c.277A>G) is associated with hypertrophic cardiomyopathy 19 (ClinVar).

How common is CALR3 p.Ile93Val (c.277A>G) in the general population?

CALR3 p.Ile93Val (c.277A>G) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

What do computational predictors say about CALR3 p.Ile93Val (c.277A>G)?

AlphaMissense predicts likely benign (score 0.1061) — an in-silico prediction, not a clinical call.

CALR3 p.Ile93Val

c.277A>G · rs2093396133 · VCV1505764

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1061 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hypertrophic cardiomyopathy 19

Computational evidence

Protein change
AlphaMissense	0.1061	likely benign
REVEL	0.1	moderately benign-leaning
SaProt	LLR -5.86	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · T>A here scores Δ0.55 · evaluated, not missing
Constraint at this position
Conservation	phyloP -4.7	GERP -4.6
Regional constraint	o/e 0.95	unconstrained · MANE · 17 kb · p 0.24 · regional, not allelic
Overall
CADD	7.386	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 8.47e-05% European (non-Finnish) · 1/1,180,042 alleles

Overall 0.000657% 1/152,172 alleles · very rare

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: CALR3
Protein: p.Ile93Val
Coding: c.277A>G
MANE Select: NM_145046
dbSNP: rs2093396133
Type: single nucleotide variant
Location: chr19:16490487 (GRCh38)
Gene constraint: LOEUF 1.028 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.43
Residue 93: the 'n-domain' region

Full CALR3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hypertrophic cardiomyopathy 19 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CALR3 p.Ala331Val Uncertain significance ★★ ⚠ same condition
CALR3 p.Ala348Val Uncertain significance ★★ ⚠ same condition
CALR3 p.Arg278Cys Uncertain significance ★★ ⚠ same condition
CALR3 p.Arg278His Uncertain significance ★★ ⚠ same condition
CALR3 p.Arg278Leu Uncertain significance ★★ ⚠ same condition
CALR3 p.Arg308Ile Uncertain significance ★★ ⚠ same condition
CALR3 p.Arg80Cys Uncertain significance ★★ ⚠ same condition
CALR3 p.Asp242His 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/calr3-p-ile93val (accessed [today's date]).

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