Is TMC8 p.Cys562= (c.1686C>T) pathogenic?

TMC8 p.Cys562= (c.1686C>T) is classified Benign in TMC8 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-02-01). Low-frequency (popmax 3.37%, afr); Associated with epidermodysplasia verruciformis.

What condition is associated with TMC8 p.Cys562= (c.1686C>T)?

TMC8 p.Cys562= (c.1686C>T) is associated with epidermodysplasia verruciformis (ClinVar).

How common is TMC8 p.Cys562= (c.1686C>T) in the general population?

TMC8 p.Cys562= (c.1686C>T) is low-frequency (popmax 3.37%, afr) (gnomAD).

How is Inherited epidermodysplasia verruciformis inherited?

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

TMC8 p.Cys562=

c.1686C>T · rs142857824 · VCV526262

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

low-frequency (popmax 3.37%, afr)

Conditions

epidermodysplasia verruciformis

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 -3.7	GERP -3.1
Overall
CADD	1.434	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.37% African / African-American · 2,527/75,076 alleles

Filtering AF 3.26% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.21%

Overall 0.185% 2,990/1,613,962 alleles · low-frequency exomes 1,500/1,461,582 · genomes 1,490/152,380 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	3.37%	30
Remaining individualsnot grpmax-eligible	0.28%	357
Admixed American	0.272%	368
Ashkenazi Jewishnot grpmax-eligible	0.169%	592
Middle Eastern	0.132%	758
South Asian	0.00878%	11,386
European (non-Finnish)	0.00483%	20,702
East Asian	0.00446%	22,441

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: TMC8
Protein: p.Cys562=
Coding: c.1686C>T
MANE Select: NM_152468
dbSNP: rs142857824
Type: single nucleotide variant
Location: chr17:78138595 (GRCh38)
Gene constraint: LOEUF 1.201 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 76.77
Residue 562: a UniProt-annotated variant site (in ev2)

Full TMC8 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

TMC8 c.1824-1G>C Pathogenic/Likely pathogenic ★★ same condition
TMC8 c.449-1G>T Likely pathogenic ★★ same condition
TMC8 p.Arg190Ter Pathogenic ★★ same condition
TMC8 p.Ala188Val Uncertain significance ★★ ⚠ same condition
TMC8 p.Ala290Thr Uncertain significance ★★ ⚠ same condition
TMC8 p.Ala313Val Uncertain significance ★★ ⚠ same condition
TMC8 p.Ala316Thr Uncertain significance ★★ ⚠ same condition
TMC8 p.Ala345Thr 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/tmc8-p-cys562 (accessed [today's date]).

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