Is TECTA p.Cys2045= (c.6135C>T) pathogenic?

TECTA p.Cys2045= (c.6135C>T) is classified Conflicting classifications of pathogenicity in TECTA (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2025-11-10). Ultra-rare (popmax 0.0223%, eas); Associated with autosomal recessive nonsyndromic hearing loss 21.

What condition is associated with TECTA p.Cys2045= (c.6135C>T)?

TECTA p.Cys2045= (c.6135C>T) is associated with autosomal recessive nonsyndromic hearing loss 21, autosomal dominant nonsyndromic hearing loss 12 (ClinVar).

How common is TECTA p.Cys2045= (c.6135C>T) in the general population?

TECTA p.Cys2045= (c.6135C>T) is ultra-rare (popmax 0.0223%, eas) (gnomAD).

TECTA p.Cys2045=

c.6135C>T · rs139552118 · VCV303043

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0223%, eas)

Conditions

autosomal recessive nonsyndromic hearing loss 21

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -8.6	GERP -3.7
Overall
CADD	1.279	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0223% East Asian · 10/44,882 alleles

Filtering AF 0.012% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00916%

Overall 0.00997% 161/1,614,172 alleles · ultra-rare exomes 150/1,461,872 · genomes 11/152,300 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0223%	4,488
Middle Eastern	0.0165%	6,062
Remaining individualsnot grpmax-eligible	0.0144%	6,945
Admixed American	0.0117%	8,575
European (non-Finnish)	0.0108%	9,219
South Asian	0.00329%	30,360
Finnishnot grpmax-eligible	0.00312%	32,010
African / African-American	0.00133%	75,050

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.Cys2045=
Coding: c.6135C>T
MANE Select: NM_005422
dbSNP: rs139552118
Type: single nucleotide variant
Location: chr11:121187967 (GRCh38)

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

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-cys2045 (accessed [today's date]).

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