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NM_001128228.3(TPRN):c.943dup (p.Leu315fs) AND Autosomal recessive nonsyndromic hearing loss 79

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 28, 2019
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:
RCV002470583.1

Allele description [Variation Report for NM_001128228.3(TPRN):c.943dup (p.Leu315fs)]

NM_001128228.3(TPRN):c.943dup (p.Leu315fs)

Gene:
TPRN:taperin [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
9q34.3
Genomic location:
Preferred name:
NM_001128228.3(TPRN):c.943dup (p.Leu315fs)
HGVS:
  • NC_000009.12:g.137199770dup
  • NG_027801.2:g.9425dup
  • NM_001128228.2:c.943dup
  • NM_001128228.3:c.943dupMANE SELECT
  • NP_001121700.2:p.Leu315fs
  • LRG_1360t1:c.943dup
  • LRG_1360:g.9425dup
  • LRG_1360p1:p.Leu315fs
  • NC_000009.11:g.140094220_140094221insG
  • NC_000009.11:g.140094222dup
  • NM_001128228.2:c.943dupC
Protein change:
L315fs
Molecular consequence:
  • NM_001128228.3:c.943dup - frameshift variant - [Sequence Ontology: SO:0001589]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002768780Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Aug 28, 2019) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002768780.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

A heterozygous duplication variant was identified, NM_001128228.2(TPRN):c.943dup in exon 1 of 4 of the TPRN gene. This duplication is predicted to cause a frameshift from amino acid position 315 introducing a stop codon 32 residues downstream, NP_001121700.2(TPRN):p.(Leu315Profs*32), resulting in loss of normal protein function through nonsense-mediated decay (NMD). The variant is present in the gnomAD population database at a frequency of 0.003% (3 heterozygotes, 0 homozygotes) in the non-Finnish European population. It is not present in other subpopulations in gnomAD. It has been previously reported in a compound heterozygous state in a patient with autosomal recessive non-syndromic hearing loss (Sloan-Heggen, C. et al. (2016)); and has been reported as pathogenic in the Deafness Variation Database (http://deafnessvariationdatabase.org/). Other variants predicted to cause NMD have been reported as pathogenic in individuals with autosomal recessive deafness 79 (ClinVar). Based on information available at the time of curation, this variant has been classified as PATHOGENIC.

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

Last Updated: Feb 14, 2024