Is TMC6 p.Ala615= (c.1845C>T) pathogenic?

TMC6 p.Ala615= (c.1845C>T) is classified Likely benign in TMC6 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-28). Very rare (popmax 0.00781%, sas); Associated with epidermodysplasia verruciformis.

What condition is associated with TMC6 p.Ala615= (c.1845C>T)?

TMC6 p.Ala615= (c.1845C>T) is associated with epidermodysplasia verruciformis (ClinVar).

How common is TMC6 p.Ala615= (c.1845C>T) in the general population?

TMC6 p.Ala615= (c.1845C>T) is very rare (popmax 0.00781%, sas) (gnomAD).

How is Inherited epidermodysplasia verruciformis inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

TMC6 p.Ala615=

c.1845C>T · rs745633089 · VCV2900144

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00781%, sas)

Conditions

epidermodysplasia verruciformis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.75 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.76	GERP -2.3
Overall
CADD	6.507	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00781% South Asian · 7/89,592 alleles

Filtering AF 0.00364% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00258%

Overall 0.00193% 31/1,604,200 alleles · very rare exomes 30/1,452,044 · genomes 1/152,156 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00781%	12,799
Admixed American	0.0034%	29,394
European (non-Finnish)	0.0017%	58,793
Remaining individualsnot grpmax-eligible	0.00161%	62,038
African / African-American	0.00134%	74,736

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: TMC6
Protein: p.Ala615=
Coding: c.1845C>T
MANE Select: NM_001127198
dbSNP: rs745633089
Type: single nucleotide variant
Location: chr17:78119013 (GRCh38)
Gene constraint: LOEUF 1.019 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 72.56

Full TMC6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

epidermodysplasia verruciformis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Inherited epidermodysplasia verruciformis (Orphanet):

Inheritance: Autosomal recessive
Onset: All ages

Similar variants

TMC6 p.Ala615Thr Uncertain significance ★ ⚠ same residue
TMC6 p.Arg94Ter Pathogenic ★★ same condition
TMC6 c.1383+4C>T Uncertain significance ★★ same condition
TMC6 p.Ala124Pro Uncertain significance ★★ ⚠ same condition
TMC6 p.Ala212Val Uncertain significance ★★ ⚠ same condition
TMC6 p.Ala233Thr Uncertain significance ★★ ⚠ same condition
TMC6 p.Ala380Thr Uncertain significance ★★ ⚠ same condition
TMC6 p.Ala432Val 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/tmc6-p-ala615 (accessed [today's date]).

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