NM_144672.4(OTOA):c.1765del (p.Gln589fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 15, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003558608.2

Allele description [Variation Report for NM_144672.4(OTOA):c.1765del (p.Gln589fs)]

NM_144672.4(OTOA):c.1765del (p.Gln589fs)

Gene:

OTOA:otoancorin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16p12.2

Genomic location:

Preferred name:

NM_144672.4(OTOA):c.1765del (p.Gln589fs)

HGVS:

NC_000016.10:g.21719463del
NG_012973.2:g.60331del
NM_001161683.2:c.1528del
NM_144672.4:c.1765delMANE SELECT
NM_170664.3:c.793del
NP_001155155.1:p.Gln510fs
NP_653273.3:p.Gln589fs
NP_733764.1:p.Gln265fs
NC_000016.9:g.21730783del
NC_000016.9:g.21730784del
NC_000016.9:g.21730784delC
NG_012973.1:g.45950del
NM_144672.3:c.1764delC
NM_144672.4:c.1765delCMANE SELECT

Protein change:

Q265fs

Links:

dbSNP: rs775776282

NCBI 1000 Genomes Browser:

rs775776282

Molecular consequence:

NM_001161683.2:c.1528del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_144672.4:c.1765del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_170664.3:c.793del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004297685	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 15, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 11972037, 25373420, 30740825, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004297685

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 15, 2023)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

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	clinical testing

Citations

PubMed

Otoancorin, an inner ear protein restricted to the interface between the apical surface of sensory epithelia and their overlying acellular gels, is defective in autosomal recessive deafness DFNB22.

Zwaenepoel I, Mustapha M, Leibovici M, Verpy E, Goodyear R, Liu XZ, Nouaille S, Nance WE, Kanaan M, Avraham KB, Tekaia F, Loiselet J, Lathrop M, Richardson G, Petit C.

Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):6240-5. Epub 2002 Apr 23.

PubMed [citation]

PMID:: 11972037
PMCID:: PMC122933

Exploration of molecular genetic etiology for Korean cochlear implantees with severe to profound hearing loss and its implication.

Park JH, Kim NK, Kim AR, Rhee J, Oh SH, Koo JW, Nam JY, Park WY, Choi BY.

Orphanet J Rare Dis. 2014 Nov 6;9:167. doi: 10.1186/s13023-014-0167-8.

PubMed [citation]

PMID:: 25373420
PMCID:: PMC4243193

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004297685.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Gln589Argfs*55) in the OTOA gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in OTOA are known to be pathogenic (PMID: 11972037). This variant is present in population databases (rs775776282, gnomAD 0.02%). This premature translational stop signal has been observed in individual(s) with deafness (PMID: 25373420, 30740825). ClinVar contains an entry for this variant (Variation ID: 684616). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

#	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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