NM_174878.3(CLRN1):c.292del (p.His98fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 7, 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:: RCV001386767.5

Allele description [Variation Report for NM_174878.3(CLRN1):c.292del (p.His98fs)]

NM_174878.3(CLRN1):c.292del (p.His98fs)

Gene:

CLRN1:clarin 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

3q25.1

Genomic location:

Preferred name:

NM_174878.3(CLRN1):c.292del (p.His98fs)

HGVS:

NC_000003.12:g.150941724del
NG_009168.1:g.36277del
NM_001195794.1:c.292del
NM_001256819.2:c.464del
NM_052995.2:c.64del
NM_174878.3:c.292delMANE SELECT
NP_001182723.1:p.His98fs
NP_001243748.1:p.Pro155fs
NP_443721.1:p.His22fs
NP_777367.1:p.His98fs
LRG_700t1:c.292del
LRG_700t2:c.64del
LRG_700:g.36277del
LRG_700p1:p.His98fs
LRG_700p2:p.His22fs
NC_000003.11:g.150659510del
NC_000003.11:g.150659511del
NR_046380.3:n.462del

Protein change:

H22fs

Links:

dbSNP: rs2107951359

NCBI 1000 Genomes Browser:

rs2107951359

Molecular consequence:

NM_001195794.1:c.292del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001256819.2:c.464del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_052995.2:c.64del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_174878.3:c.292del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_046380.3:n.462del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV001587115	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 7, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 11524702, 24498627, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001587115

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 7, 2023)

germline

clinical testing

PubMed (3)
[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

Mutations in a novel gene with transmembrane domains underlie Usher syndrome type 3.

Joensuu T, Hämäläinen R, Yuan B, Johnson C, Tegelberg S, Gasparini P, Zelante L, Pirvola U, Pakarinen L, Lehesjoki AE, de la Chapelle A, Sankila EM.

Am J Hum Genet. 2001 Oct;69(4):673-84. Epub 2001 Aug 27. Erratum in: Am J Hum Genet 2001 Nov;69(5):1160.

PubMed [citation]

PMID:: 11524702
PMCID:: PMC1226054

Experience of targeted Usher exome sequencing as a clinical test.

Besnard T, García-García G, Baux D, Vaché C, Faugère V, Larrieu L, Léonard S, Millan JM, Malcolm S, Claustres M, Roux AF.

Mol Genet Genomic Med. 2014 Jan;2(1):30-43. doi: 10.1002/mgg3.25. Epub 2013 Jul 10.

PubMed [citation]

PMID:: 24498627
PMCID:: PMC3907913

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001587115.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1073695). This variant has not been reported in the literature in individuals affected with CLRN1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.His98Thrfs*14) in the CLRN1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CLRN1 are known to be pathogenic (PMID: 11524702, 24498627).

#	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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