NM_153676.4(USH1C):c.1099G>T (p.Glu367Ter) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jan 6, 2020
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001388636.6

Allele description [Variation Report for NM_153676.4(USH1C):c.1099G>T (p.Glu367Ter)]

NM_153676.4(USH1C):c.1099G>T (p.Glu367Ter)

Gene:

USH1C:USH1 protein network component harmonin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11p15.1

Genomic location:

Preferred name:

NM_153676.4(USH1C):c.1099G>T (p.Glu367Ter)

HGVS:

NC_000011.10:g.17520981C>A
NG_011883.2:g.28436G>T
NM_001297764.2:c.1042G>T
NM_005709.4:c.1099G>T
NM_153676.4:c.1099G>TMANE SELECT
NP_001284693.1:p.Glu348Ter
NP_005700.2:p.Glu367Ter
NP_710142.1:p.Glu367Ter
NC_000011.9:g.17542528C>A
NR_123738.2:n.1208G>T

Protein change:

E348*

Links:

dbSNP: rs2133868490

NCBI 1000 Genomes Browser:

rs2133868490

Molecular consequence:

NR_123738.2:n.1208G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001297764.2:c.1042G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_005709.4:c.1099G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_153676.4:c.1099G>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV001589708	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 6, 2020)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 10973247, 17407589, 20301442, 21203349, 28492532
SCV002568848	Laboratoire de Génétique Moléculaire, CHU Bordeaux	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001589708

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 6, 2020)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

SCV002568848

Laboratoire de Génétique Moléculaire, CHU Bordeaux

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

A defect in harmonin, a PDZ domain-containing protein expressed in the inner ear sensory hair cells, underlies Usher syndrome type 1C.

Verpy E, Leibovici M, Zwaenepoel I, Liu XZ, Gal A, Salem N, Mansour A, Blanchard S, Kobayashi I, Keats BJ, Slim R, Petit C.

Nat Genet. 2000 Sep;26(1):51-5.

PubMed [citation]

PMID:: 10973247

Deafblindness in French Canadians from Quebec: a predominant founder mutation in the USH1C gene provides the first genetic link with the Acadian population.

Ebermann I, Lopez I, Bitner-Glindzicz M, Brown C, Koenekoop RK, Bolz HJ.

Genome Biol. 2007;8(4):R47.

PubMed [citation]

PMID:: 17407589
PMCID:: PMC1895989

See all PubMed Citations (6)

Details of each submission

From Invitae, SCV001589708.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

Loss-of-function variants in USH1C are known to be pathogenic (PMID: 10973247, 17407589, 20301442, 21203349). For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. This variant has not been reported in the literature in individuals with USH1C-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Glu367*) in the USH1C gene. It is expected to result in an absent or disrupted protein product.

#	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

From Laboratoire de Génétique Moléculaire, CHU Bordeaux, SCV002568848.1

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

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

Last Updated: Feb 20, 2024

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