Is TRPC3 p.Leu656Pro (c.1967T>C) pathogenic?

TRPC3 p.Leu656Pro (c.1967T>C) is classified Uncertain significance in TRPC3 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-12). Absent from gnomAD v4.1.

How common is TRPC3 p.Leu656Pro (c.1967T>C) in the general population?

TRPC3 p.Leu656Pro (c.1967T>C) is absent from gnomAD v4.1 (gnomAD).

TRPC3 p.Leu656Pro

c.1967T>C · rs2476798624 · VCV2089874

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.957	strongly pathogenic-leaning
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · A>C here scores Δ0.35 · evaluated, not missing
Constraint at this position
Conservation	phyloP 8.1	GERP 2.2, phastCons 1
Regional constraint	o/e 0.56	unconstrained · MANE · 6,020 bp · p 7.1e-13 · regional, not allelic
Overall
CADD	32.0	PHRED · no single calibrated threshold — expert panels disagree

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: TRPC3
Protein: p.Leu656Pro
Coding: c.1967T>C
MANE Select: NM_001130698
dbSNP: rs2476798624
Type: single nucleotide variant
Location: chr4:121907393 (GRCh38)
Gene constraint: LOEUF 0.751 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.42 · 19 PDB
Residue 656: an α-helix

Full TRPC3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

TRPC3 p.Arg381Cys Uncertain significance ★★ same type
TRPC3 p.Arg795Gln Uncertain significance ★★ same type
TRPC3 p.Asn728Ser Uncertain significance ★★ same type
TRPC3 p.Glu901Lys Uncertain significance ★★ same type
TRPC3 p.Ile629Val Uncertain significance ★★ same type
TRPC3 p.Leu905Val Uncertain significance ★★ same type
TRPC3 p.Lys710Arg Uncertain significance ★★ same type
TRPC3 p.Pro444Ser Uncertain significance ★★ same type

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/trpc3-p-leu656pro (accessed [today's date]).

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