Is TRPM4 p.Phe1027= (c.3081C>T) pathogenic?

TRPM4 p.Phe1027= (c.3081C>T) is classified Likely benign in TRPM4 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-23). Very rare (popmax 0.004%, afr); Associated with Cardiovascular phenotype.

What condition is associated with TRPM4 p.Phe1027= (c.3081C>T)?

TRPM4 p.Phe1027= (c.3081C>T) is associated with Cardiovascular phenotype (ClinVar).

How common is TRPM4 p.Phe1027= (c.3081C>T) in the general population?

TRPM4 p.Phe1027= (c.3081C>T) is very rare (popmax 0.004%, afr) (gnomAD).

TRPM4 p.Phe1027=

c.3081C>T · rs753938906 · VCV2448593

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.004%, afr)

Conditions

Cardiovascular phenotype

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 0.43	phastCons 0.99
Overall
CADD	7.462	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.004% African / African-American · 3/75,050 alleles

Filtering AF 0.00106% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000494%

Overall 0.000186% 3/1,614,110 alleles · very rare exomes 3/1,461,824 · genomes 0/152,286 · joint denominator

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: TRPM4
Protein: p.Phe1027=
Coding: c.3081C>T
MANE Select: NM_017636
dbSNP: rs753938906
Type: single nucleotide variant
Location: chr19:49202091 (GRCh38)
Gene constraint: LOEUF 1.084 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.51 · 42 PDB
Residue 1027: 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.Phe1027Ile 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
TRPM4 c.2645+1G>A Uncertain significance ★★ same condition
TRPM4 c.2953+1G>A Uncertain significance ★★ same condition
TRPM4 c.2953+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-phe1027 (accessed [today's date]).

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