Is TECTA p.Val932Ala (c.2795T>C) pathogenic?

TECTA p.Val932Ala (c.2795T>C) is classified Benign/Likely benign in TECTA (ClinVar, Multiple submitters, 9 submitters; last evaluated 2026-02-04). AlphaMissense: likely benign (0.2347); Common (popmax 26.4%, eas) — too common for a highly-penetrant pathogenic allele; Associated with autosomal recessive nonsyndromic hearing loss 21.

What condition is associated with TECTA p.Val932Ala (c.2795T>C)?

TECTA p.Val932Ala (c.2795T>C) is associated with autosomal recessive nonsyndromic hearing loss 21, autosomal dominant nonsyndromic hearing loss 12 (ClinVar).

What do computational predictors say about TECTA p.Val932Ala (c.2795T>C)?

AlphaMissense predicts likely benign (score 0.2347) — an in-silico prediction, not a clinical call.

TECTA p.Val932Ala

Q: How common is TECTA p.Val932Ala (c.2795T>C) in the general population?

TECTA p.Val932Ala (c.2795T>C) is common (popmax 26.4%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.2795T>C · rs520805 · VCV45322

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 9 submitters

AlphaMissense

likely benign

0.2347 · ACMG-weighted

gnomAD v4.1

Common

common (popmax 26.4%, eas) — too common for a highly-penetrant pathogenic allele

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

autosomal recessive nonsyndromic hearing loss 21

Computational evidence

Protein change
AlphaMissense	0.2347	likely benign
REVEL	0.122	moderately benign-leaning
SaProt	LLR -5.89	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.5	GERP -0.54, phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 66 kb · p 0.00019 · regional, not allelic
Overall
CADD	17.1	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 26.4% East Asian · 11,846/44,874 alleles

Filtering AF 26% ClinGen BA1/BS1 input FAF95, joint · FAF99 25.8%

Overall 21.9% 353,358/1,613,878 alleles · common exomes 322,267/1,461,748 · genomes 31,091/152,130 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	26.4%	4
Finnishnot grpmax-eligible	24.6%	4
Admixed American	22.3%	4
European (non-Finnish)	22.1%	5
Ashkenazi Jewishnot grpmax-eligible	21.5%	5
Remaining individualsnot grpmax-eligible	21%	5
South Asian	20%	5
Middle Eastern	17.6%	6
African / African-American	17.2%	6
Amishnot grpmax-eligible	10.7%	9

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: TECTA
Protein: p.Val932Ala
Coding: c.2795T>C
MANE Select: NM_005422
dbSNP: rs520805
Type: single nucleotide variant
Location: chr11:121130065 (GRCh38)
Gene constraint: LOEUF 0.661 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.64
Residue 932: a UniProt-annotated variant site (in)

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

Disease context

autosomal recessive nonsyndromic hearing loss 21 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: autosomal dominant nonsyndromic hearing loss 12

Similar variants

TECTA p.Arg371Gly Benign ★★★ same condition
TECTA c.2367+2T>C Likely pathogenic ★★ same condition
TECTA c.4690-1G>A Pathogenic/Likely pathogenic ★★ same condition
TECTA p.Arg1174Ter Pathogenic ★★ same condition
TECTA p.Ala567Thr Uncertain significance ★★ ⚠ same condition
TECTA p.Arg284Cys Uncertain significance ★★ ⚠ same condition
TECTA p.Arg474Cys Uncertain significance ★★ ⚠ same condition
TECTA p.Cys1072= 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/tecta-p-val932ala (accessed [today's date]).

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