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NM_144672.4(OTOA):c.1560_1563del (p.Phe521fs) AND Autosomal recessive nonsyndromic hearing loss 22

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 28, 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:
RCV003155417.1

Allele description [Variation Report for NM_144672.4(OTOA):c.1560_1563del (p.Phe521fs)]

NM_144672.4(OTOA):c.1560_1563del (p.Phe521fs)

Gene:
OTOA:otoancorin [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
16p12.2
Genomic location:
Preferred name:
NM_144672.4(OTOA):c.1560_1563del (p.Phe521fs)
HGVS:
  • NC_000016.10:g.21716978_21716981del
  • NG_012973.2:g.57846_57849del
  • NM_001161683.2:c.1323_1326del
  • NM_144672.4:c.1560_1563delMANE SELECT
  • NM_170664.3:c.588_591del
  • NP_001155155.1:p.Phe442fs
  • NP_653273.3:p.Phe521fs
  • NP_733764.1:p.Phe197fs
  • NC_000016.9:g.21728299_21728302del
  • NM_144672.4:c.1559_1562delTCTTMANE SELECT
Protein change:
F197fs
Links:
dbSNP: rs2141700836
NCBI 1000 Genomes Browser:
rs2141700836
Molecular consequence:
  • NM_001161683.2:c.1323_1326del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_144672.4:c.1560_1563del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_170664.3:c.588_591del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Autosomal recessive nonsyndromic hearing loss 22
Synonyms:
Deafness, autosomal recessive 22
Identifiers:
MONDO: MONDO:0011762; MedGen: C1846896; Orphanet: 90636; OMIM: 607039

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003844160King Laboratory, University of Washington
criteria provided, single submitter

(Li et al. (Genet Med. 2022))		Pathogenic
(Feb 28, 2023) 		unknownresearch

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedresearch

Citations

PubMed

Association of Genetic Diagnoses for Childhood-Onset Hearing Loss With Cochlear Implant Outcomes.

Carlson RJ, Walsh T, Mandell JB, Aburayyan A, Lee MK, Gulsuner S, Horn DL, Ou HC, Sie KCY, Mancl L, Rubinstein J, King MC.

JAMA Otolaryngol Head Neck Surg. 2023 Mar 1;149(3):212-222. doi: 10.1001/jamaoto.2022.4463.

PubMed [citation]
PMID:
36633841
PMCID:
PMC9857764

Clinical evaluation and etiologic diagnosis of hearing loss: A clinical practice resource of the American College of Medical Genetics and Genomics (ACMG).

Li MM, Tayoun AA, DiStefano M, Pandya A, Rehm HL, Robin NH, Schaefer AM, Yoshinaga-Itano C; ACMG Professional Practice and Guidelines Committee. Electronic address: documents@acmg.net..

Genet Med. 2022 Jul;24(7):1392-1406. doi: 10.1016/j.gim.2022.03.018. Epub 2022 May 10.

PubMed [citation]
PMID:
35802133

Details of each submission

From King Laboratory, University of Washington, SCV003844160.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (2)

Description

This variant occurred in compound heterozygosity with an OTOA missense variant in a patient with bilateral sensorineural hearing loss of onset <18 years, in a study of pediatric hearing loss conducted by the King Laboratory (Carlson RJ et al. JAMA-OtoHNS 2023). This patient’s family has no other history of hearing loss. This variant is a frameshift that is predicted to lead to the addition of 1 incorrect amino acid and a premature stop codon at position 522 of the otherwise 1139 amino acid protein. As of January 2023, this variant has been reported to ClinVar as likely pathogenic and is not found on gnomAD. Based on the prediction that this variant leads to a truncated protein and goodness of fit of genotype to phenotype, we conclude that this variant is pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Dec 24, 2023