Is TRPM4 p.Arg442Ser (c.1324C>A) pathogenic?

TRPM4 p.Arg442Ser (c.1324C>A) is classified Uncertain significance in TRPM4 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-28). AlphaMissense: likely pathogenic (0.6032); Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with TRPM4 p.Arg442Ser (c.1324C>A)?

TRPM4 p.Arg442Ser (c.1324C>A) is associated with Cardiovascular phenotype (ClinVar).

How common is TRPM4 p.Arg442Ser (c.1324C>A) in the general population?

TRPM4 p.Arg442Ser (c.1324C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about TRPM4 p.Arg442Ser (c.1324C>A)?

AlphaMissense predicts likely pathogenic (score 0.6032) — an in-silico prediction, not a clinical call.

TRPM4 p.Arg442Ser

c.1324C>A · VCV4615266

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6032 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.6032	likely pathogenic
REVEL	0.326	indeterminate
SaProt	LLR -8.95	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.5	phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 43 kb · p 0.93 · regional, not allelic
Overall
CADD	26.3	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: TRPM4
Protein: p.Arg442Ser
Coding: c.1324C>A
MANE Select: NM_017636
Type: single nucleotide variant
Location: chr19:49182638 (GRCh38)
Gene constraint: LOEUF 1.084 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.51 · 42 PDB
Residue 442: an α-helix

Full TRPM4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TRPM4 p.Arg442Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
TRPM4 p.Arg442His Uncertain significance ★★ ⚠ same residue
TRPM4 p.Arg442Leu Uncertain significance ★ same residue
TRPM4 p.Arg442Pro Uncertain significance ★ ⚠ same residue
TRPM4 p.Ile376Thr Pathogenic/Likely pathogenic ★★ ⚠ same condition
TRPM4 c.1050+1G>A Uncertain significance ★★ same condition
TRPM4 c.1150+5A>T Uncertain significance ★★ same condition
TRPM4 c.2019+5G>A 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/trpm4-p-arg442ser (accessed [today's date]).

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