Is TRPC6 c.2485del pathogenic?

TRPC6 c.2485del is classified Uncertain significance in TRPC6 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-17). Very rare (popmax 0.00272%, nfe); Associated with focal segmental glomerulosclerosis 2.

What condition is associated with TRPC6 c.2485del?

TRPC6 c.2485del is associated with focal segmental glomerulosclerosis 2 (ClinVar).

How common is TRPC6 c.2485del in the general population?

TRPC6 c.2485del is very rare (popmax 0.00272%, nfe) (gnomAD).

TRPC6 c.2485del

VCV4531661

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00272%, nfe)

Conditions

focal segmental glomerulosclerosis 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.5	GERP -1.3, phastCons 1
Non-coding constraint	Z 0.50	1 kb window · o/e 0.96 · regional · uncalibrated

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00272% European (non-Finnish) · 32/1,178,072 alleles

Filtering AF 0.00197% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00168%

Overall 0.00199% 32/1,611,336 alleles · very rare exomes 32/1,459,078 · genomes 0/152,258 · 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: TRPC6
Coding: c.2485del
MANE Select: NM_004621
Type: Deletion
Location: chr11:101455101 (GRCh38)
Gene constraint: LOEUF 0.708 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.98 · 6 PDB

Full TRPC6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

focal segmental glomerulosclerosis 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TRPC6 p.Asn805fs Likely pathogenic ★ same condition
TRPC6 p.Asp873fs Likely pathogenic ★ same condition
TRPC6 p.Gln889fs Likely pathogenic ★ same condition
TRPC6 p.Gly794fs Likely pathogenic ★ same condition
TRPC6 p.Leu454fs Likely pathogenic ★ same condition
TRPC6 p.Leu614fs Likely pathogenic ★ same condition
TRPC6 p.Lys585fs Likely pathogenic ★ same condition
TRPC6 p.Trp514fs Likely pathogenic ★ 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/trpc6-c-2485del (accessed [today's date]).

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