Is TRPC5 p.Pro13= (c.39G>T) pathogenic?

TRPC5 p.Pro13= (c.39G>T) is classified Benign in TRPC5 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-04-05). Low-frequency (popmax 1.46%, sas); Associated with TRPC5-related disorder.

What condition is associated with TRPC5 p.Pro13= (c.39G>T)?

TRPC5 p.Pro13= (c.39G>T) is associated with TRPC5-related disorder (ClinVar).

How common is TRPC5 p.Pro13= (c.39G>T) in the general population?

TRPC5 p.Pro13= (c.39G>T) is low-frequency (popmax 1.46%, sas) (gnomAD).

TRPC5 p.Pro13=

c.39G>T · rs150908311 · VCV3043005

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 1.46%, sas)

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 -6.9	GERP -3.5
Overall
CADD	0.471	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.46% South Asian · 822/56,319 alleles

Filtering AF 1.38% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.34%

Overall 0.0731% 883/1,208,132 alleles · low-frequency

Ancestry group	Frequency	1 in
South Asiangrpmax	1.46%	69
Remaining individualsnot grpmax-eligible	0.107%	932
Middle Eastern	0.0461%	2,167
African / African-American	0.0035%	28,572
East Asian	0.00296%	33,735
European (non-Finnish)	0.000559%	178,886

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.Pro13=
Coding: c.39G>T
MANE Select: NM_012471
dbSNP: rs150908311
Type: single nucleotide variant
Location: chrX:111952382 (GRCh38)
Structure: AlphaFold pLDDT 73.82 · 30 PDB

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-pro13 (accessed [today's date]).

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