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NM_001128228.3(TPRN):c.1725+5G>A AND Autosomal recessive nonsyndromic hearing loss 79

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 30, 2021
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:
RCV001803363.7

Allele description [Variation Report for NM_001128228.3(TPRN):c.1725+5G>A]

NM_001128228.3(TPRN):c.1725+5G>A

Gene:
TPRN:taperin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q34.3
Genomic location:
Preferred name:
NM_001128228.3(TPRN):c.1725+5G>A
HGVS:
  • NC_000009.12:g.137198982C>T
  • NG_027801.2:g.10212G>A
  • NM_001128228.3:c.1725+5G>AMANE SELECT
  • LRG_1360t1:c.1725+5G>A
  • LRG_1360:g.10212G>A
  • NC_000009.11:g.140093434C>T
Links:
dbSNP: rs373827566
NCBI 1000 Genomes Browser:
rs373827566
Molecular consequence:
  • NM_001128228.3:c.1725+5G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Autosomal recessive nonsyndromic hearing loss 79
Synonyms:
Deafness, autosomal recessive 79
Identifiers:
MONDO: MONDO:0013215; MedGen: C2750082; Orphanet: 90636; OMIM: 613307

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002048902ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2021)		Uncertain significance
(Nov 30, 2021) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV002048902.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.1725+5G>A variant has been previously reported in an individual with propound congenital hearing loss who also carried an additional pathogenic variant in TPRN. However, segregation, allele phase, and other evidence of causality was not presented. This is an intronic variant in a moderately conserved nucleotide in intron 1, and computational analyses (Alamut v.2.11) predict that this variant may impact splicing. However, in the absence of functional data, such predictions are not sufficient to assign pathogenicity. Due to limited information, the clinical significance of this variant is uncertain at this time. References: Sloan-Heggen et al. Comprehensive genetic testing in the clinical evaluation of 1119 patients with hearing loss. Hum Genet. 2016 Apr;135(4):441-450. PMID: 26969326

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

Last Updated: Dec 24, 2023