NM_005422.4(TECTA):c.4085G>A (p.Trp1362Ter) AND Nonsyndromic genetic hearing loss

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 21, 2020
Review status:: 3 stars out of maximum of 4 stars
reviewed by expert panel

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001089678.1

Allele description [Variation Report for NM_005422.4(TECTA):c.4085G>A (p.Trp1362Ter)]

NM_005422.4(TECTA):c.4085G>A (p.Trp1362Ter)

Genes:

TBCEL-TECTA:TBCEL-TECTA readthrough [Gene - HGNC]
TECTA:tectorin alpha [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q23.3

Genomic location:

Preferred name:

NM_005422.4(TECTA):c.4085G>A (p.Trp1362Ter)

HGVS:

NC_000011.10:g.121146096G>A
NG_011633.1:g.48431G>A
NM_001378761.1:c.5042G>A
NM_005422.4:c.4085G>AMANE SELECT
NP_001365690.1:p.Trp1681Ter
NP_005413.2:p.Trp1362Ter
NP_005413.2:p.Trp1362Ter
NC_000011.9:g.121016805G>A
NM_005422.2(TECTA):c.4085G>A
NM_005422.2:c.4085G>A
p.Trp1362Ter
p.Trp1362X

Protein change:

W1362*

Links:

dbSNP: rs199638531

NCBI 1000 Genomes Browser:

rs199638531

Molecular consequence:

NM_001378761.1:c.5042G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_005422.4:c.4085G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Nonsyndromic genetic hearing loss
Synonyms:: Nonsyndromic hearing loss and deafness; Non-syndromic genetic deafness; Nonsyndromic genetic deafness
Identifiers:: MONDO: MONDO:0019497; MedGen: C5680182; Orphanet: 87884

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001245162	ClinGen Hearing Loss Variant Curation Expert Panel	reviewed by expert panel (ClinGen HL ACMG Specifications v1)	Pathogenic (Jan 21, 2020)	germline	curation	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001245162

ClinGen Hearing Loss Variant Curation Expert Panel

reviewed by expert panel

(ClinGen HL ACMG Specifications v1)

Pathogenic
(Jan 21, 2020)

germline

curation

PubMed (1)
[See all records that cite this PMID]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	curation

Citations

PubMed

Genetic testing for congenital non-syndromic sensorineural hearing loss.

Raymond M, Walker E, Dave I, Dedhia K.

Int J Pediatr Otorhinolaryngol. 2019 Sep;124:68-75. doi: 10.1016/j.ijporl.2019.05.038. Epub 2019 May 29.

PubMed [citation]

PMID:: 31163360

Details of each submission

From ClinGen Hearing Loss Variant Curation Expert Panel, SCV001245162.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (1)

Description

The c.4085G>A (p.Trp1362Ter) nonsense variant in TECTA is predicted to cause a premature stop codon in biologically-relevant exon 11 of 23 total exons, leading to a truncated or absent protein in a gene in which loss of function is an established mechanism of autosomal recessive nonsyndromic hearing loss (PVS1; PMID: 30192042). This variant is present in 0.01121% (14/124864) of non-Finnish European chromosomes in gnomAD v2 (PM2_Supporting). It has been observed in at least two probands presenting with nonsyndromic hearing loss (PMID: 31163360; LMM internal data SCV000711208.2). One individual harbored another nonsense variant in TECTA, which was suspected to be pathogenic (PM3_Supporting). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive nonsyndromic hearing loss. ACMG/AMP Criteria applied as specified by the Hearing Loss Expert Panel: PVS1, PM2_Supporting, PM3_Supporting.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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