Is TMPRSS3 p.Tyr77= (c.231C>T) pathogenic?

TMPRSS3 p.Tyr77= (c.231C>T) is classified Benign/Likely benign in TMPRSS3 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-06). Rare (popmax 0.456%, afr); Associated with autosomal recessive nonsyndromic hearing loss 8.

What condition is associated with TMPRSS3 p.Tyr77= (c.231C>T)?

TMPRSS3 p.Tyr77= (c.231C>T) is associated with autosomal recessive nonsyndromic hearing loss 8 (ClinVar).

How common is TMPRSS3 p.Tyr77= (c.231C>T) in the general population?

TMPRSS3 p.Tyr77= (c.231C>T) is rare (popmax 0.456%, afr) (gnomAD).

TMPRSS3 p.Tyr77=

c.231C>T · rs139934512 · VCV810901

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

rare (popmax 0.456%, afr)

Conditions

autosomal recessive nonsyndromic hearing loss 8

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 5.3	GERP 1.1, phastCons 1
Overall
CADD	6.968	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.456% African / African-American · 342/75,056 alleles

Filtering AF 0.416% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.4%

Overall 0.0232% 374/1,614,188 alleles · rare exomes 202/1,461,824 · genomes 172/152,364 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.456%	219
Admixed American	0.0316%	3,160
Middle Eastern	0.0165%	6,062
Remaining individualsnot grpmax-eligible	0.0112%	8,930
South Asian	0.0022%	45,544
European (non-Finnish)	0.000254%	393,338

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: TMPRSS3
Protein: p.Tyr77=
Coding: c.231C>T
MANE Select: NM_001256317
dbSNP: rs139934512
Type: single nucleotide variant
Location: chr21:42389020 (GRCh38)
Gene constraint: LOEUF 1.106 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 87.09
Residue 77: the ldl-receptor class a domain

Full TMPRSS3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

autosomal recessive nonsyndromic hearing loss 8 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TMPRSS3 c.1049-4G>A Likely pathogenic ★★ same condition
TMPRSS3 c.206-2A>G Likely pathogenic ★★ same condition
TMPRSS3 c.323-6G>A Pathogenic/Likely pathogenic ★★ same condition
TMPRSS3 c.446+1G>T Likely pathogenic ★★ same condition
TMPRSS3 c.573-1G>A Likely pathogenic ★★ same condition
TMPRSS3 p.Ala138Glu Pathogenic/Likely pathogenic ★★ same condition
TMPRSS3 p.Ala306Thr Pathogenic/Likely pathogenic ★★ same condition
TMPRSS3 p.Ala306Val 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/tmprss3-p-tyr77 (accessed [today's date]).

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