The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_005422.2(TECTA):c.4004G>A (p.Gly1335Glu)

CA6327326

287165 (ClinVar)

Gene: TECTA
Condition: nonsyndromic genetic deafness
Inheritance Mode: Autosomal recessive inheritance
UUID: 3ceeb535-2184-4cff-8232-0aca43c9220e
Approved on: 2025-05-21
Published on: 2025-06-30

HGVS expressions

NM_005422.2:c.4004G>A
NM_005422.2(TECTA):c.4004G>A (p.Gly1335Glu)
NC_000011.10:g.121146015G>A
CM000673.2:g.121146015G>A
NC_000011.9:g.121016724G>A
CM000673.1:g.121016724G>A
NC_000011.8:g.120521934G>A
NG_011633.1:g.48350G>A
ENST00000392793.6:c.4004G>A
ENST00000642222.1:c.4004G>A
ENST00000645008.1:c.1311G>A
ENST00000264037.2:c.4004G>A
ENST00000392793.5:c.4004G>A
ENST00000478058.1:n.569G>A
NM_001378761.1:c.4961G>A
NM_005422.4:c.4004G>A
More

Likely Benign

Met criteria codes 1
BS1
Not Met criteria codes 2
BP4 PP3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Hearing Loss Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for CDH23, COCH, GJB2, KCNQ4, MYO6, MYO7A, SLC26A4, TECTA and USH2A Version 2

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Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The c.4004G>A variant in TECTA is a missense variant predicted to cause substitution of glycine by glutamic acid at amino acid 1335. The filtering allele frequency of this variant in gnomAD v4.1 is 0.2865% in the African/African American population, and there was agreement to apply BS1, which has a threshold of 0.3% for the ClinGen Hearing Loss group. The computational predictor REVEL gives a score of 0.35, which is neither above nor below the thresholds predicting a damaging or benign impact on TECTA function (BP4 and PP3 not met). The variant has been detected in heterozygosity in 1 individual with sloping moderately-severe sensorineural hearing loss, but no variant on the other allele was identified (Partners LMM internal data, SCV000711207.2). This variant has been observed in the heterozygous state and in combination with a second variant (phase unknown) in individuals undergoing testing for hearing loss (GeneDx internal data, SCV001770060.3). The variant has also been detected with another TECTA variant of uncertain significance in phase unknown in a patient with bilateral sensorineural hearing loss, and in the homozygous state in a patient with sensorineural hearing loss (Labcorp internal data, SCV001051355.5). In summary, this variant meets criteria to be classified as likely benign for autosomal recessive nonsyndromic hearing loss based on the ACMG/AMP criteria applied as specified by the Hearing Loss Expert Panel: BS1 (ClinGen Hearing Loss VCEP specifications version 2; 5/21/2025).
Met criteria codes
BS1
The filtering allele frequency of this variant in gnomAD v4.1 is 0.2865% in the African/African American population, and there was agreement to apply BS1, which has a threshold of 0.03% for the ClinGen Hearing Loss group.
Not Met criteria codes
BP4
The computational predictor REVEL gives a score of 0.35, so BP4 is not met because the REVEL score is not below 0.15.
PP3
The computational predictor REVEL gives a score of 0.35 which does not meet PP3 as the REVEL score is not ≥ 0.7.
Curation History
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