Is TRPC5 p.Thr47= (c.141T>G) pathogenic?

TRPC5 p.Thr47= (c.141T>G) is classified Likely benign in TRPC5 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-06-14). Very rare (popmax 0.00826%, nfe); Associated with TRPC5-related disorder.

What condition is associated with TRPC5 p.Thr47= (c.141T>G)?

TRPC5 p.Thr47= (c.141T>G) is associated with TRPC5-related disorder (ClinVar).

How common is TRPC5 p.Thr47= (c.141T>G) in the general population?

TRPC5 p.Thr47= (c.141T>G) is very rare (popmax 0.00826%, nfe) (gnomAD).

TRPC5 p.Thr47=

c.141T>G · rs368534615 · VCV3032167

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00826%, nfe)

Conditions

TRPC5-related disorder

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 -1.8	GERP -3.5
Overall
CADD	1.081	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00826% European (non-Finnish) · 74/895,386 alleles

Filtering AF 0.00673% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00617%

Overall 0.0062% 75/1,210,396 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00826%	12,100
Remaining individualsnot grpmax-eligible	0.0021%	47,616

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: TRPC5
Protein: p.Thr47=
Coding: c.141T>G
MANE Select: NM_012471
dbSNP: rs368534615
Type: single nucleotide variant
Location: chrX:111952280 (GRCh38)
Structure: AlphaFold pLDDT 73.82 · 30 PDB
Residue 47: an α-helix

Full TRPC5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

TRPC5-related disorder

Similar variants

TRPC5 p.Arg222Cys Uncertain significance ★ ⚠ same condition
TRPC5 p.Gln914Glu Uncertain significance ★ ⚠ same condition
TRPC5 p.Lys7Gln Uncertain significance ★ ⚠ same condition
TRPC5 p.Ala912Thr Uncertain significance ⚠ same condition
TRPC5 p.Arg120Trp Uncertain significance ⚠ same condition
TRPC5 p.Arg191His Uncertain significance ⚠ same condition
TRPC5 p.Arg260Trp Uncertain significance ⚠ same condition
TRPC5 p.Arg324Gln 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/trpc5-p-thr47 (accessed [today's date]).

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