Is TRPC3 p.Lys204= (c.612G>A) pathogenic?

TRPC3 p.Lys204= (c.612G>A) is classified Likely benign in TRPC3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-11). Absent from gnomAD v4.1.

How common is TRPC3 p.Lys204= (c.612G>A) in the general population?

TRPC3 p.Lys204= (c.612G>A) is absent from gnomAD v4.1 (gnomAD).

TRPC3 p.Lys204=

c.612G>A · rs1364096894 · VCV2890157

Likely benign Single submitter

Classification

Likely benign

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.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.83	GERP -1.8, phastCons 0.3
Overall
CADD	11.02	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.Lys204=
Coding: c.612G>A
MANE Select: NM_001130698
dbSNP: rs1364096894
Type: single nucleotide variant
Location: chr4:121932646 (GRCh38)
Gene constraint: LOEUF 0.751 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.42 · 19 PDB
Residue 204: a β-strand

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-lys204 (accessed [today's date]).

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