Is CALM2 p.Asp134= (c.402T>C) pathogenic?

CALM2 p.Asp134= (c.402T>C) is classified Likely benign in CALM2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-27). Very rare (popmax 0.0011%, sas); Associated with long QT syndrome 1.

What condition is associated with CALM2 p.Asp134= (c.402T>C)?

CALM2 p.Asp134= (c.402T>C) is associated with long QT syndrome 1 (ClinVar).

How common is CALM2 p.Asp134= (c.402T>C) in the general population?

CALM2 p.Asp134= (c.402T>C) is very rare (popmax 0.0011%, sas) (gnomAD).

How is Romano-Ward syndrome inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

CALM2 p.Asp134=

c.402T>C · VCV4702567

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Conditions

long QT syndrome 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · A>C here scores Δ0.56 · evaluated, not missing
Constraint at this position
Conservation	phyloP 3	GERP -1.5, phastCons 1
Overall
CADD	7.609	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/90,774 alleles

Overall 0.000657% 1/152,200 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: CALM2
Protein: p.Asp134=
Coding: c.402T>C
MANE Select: NM_001743
Type: single nucleotide variant
Location: chr2:47161742 (GRCh38)
Gene constraint: LOEUF 0.262 · pLI 0.99 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 85.82 · 21 PDB
Residue 134: a binding site; a UniProt-annotated variant site (in lqt15; reduction in calcium affinity); the ef-hand 4 domain; the 'necessary and sufficient for interaction with pcp4' region; a β-strand

Full CALM2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

long QT syndrome 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Romano-Ward syndrome (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive
Onset: All ages
Prevalence: 1-5 / 10 000 (Europe)

Similar variants

CALM2 p.Asp134Asn Likely pathogenic ★★ same residue
CALM2 p.Asp134His Pathogenic/Likely pathogenic same residue
CALM2 p.Asn98Ser Pathogenic ★★ same condition
CALM2 p.Asp96Tyr Pathogenic/Likely pathogenic ★★ same condition
CALM2 p.Asp96Val Pathogenic ★★ same condition
CALM2 c.285+5G>A Uncertain significance ★★ same condition
CALM2 p.Ala58Pro Uncertain significance ★★ same condition
CALM2 p.Arg107Cys 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/calm2-p-asp134 (accessed [today's date]).

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