NM_174878.3(CLRN1):c.301_305del (p.Val101fs) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 13, 2022
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:: RCV002513586.2

Allele description

NM_174878.3(CLRN1):c.301_305del (p.Val101fs)

Gene:

CLRN1:clarin 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

3q25.1

Genomic location:

Preferred name:

NM_174878.3(CLRN1):c.301_305del (p.Val101fs)

Other names:

p.(Val101SerfsTer27)

HGVS:

NC_000003.11:g.150659497_150659501del
NC_000003.12:g.150941712_150941716del
NG_009168.1:g.36286_36290del
NM_001195794.1:c.301_305del
NM_001256819.2:c.473_477del
NM_052995.2:c.73_77del
NM_174878.3:c.301_305delMANE SELECT
NP_001182723.1:p.Val101fs
NP_001243748.1:p.Cys158fs
NP_443721.1:p.Val25fs
NP_777367.1:p.Val101fs
LRG_700t1:c.301_305del
LRG_700t2:c.73_77del
LRG_700:g.36286_36290del
LRG_700p1:p.Val101fs
LRG_700p2:p.Val25fs
NC_000003.11:g.150659497_150659501del
NC_000003.11:g.150659497_150659501delATGAC
NC_000003.11:g.150659499_150659503del
NM_001195794.1:c.301_305delGTCAT
NM_174878.2:c.301_305delGTCAT
NR_046380.3:n.471_475del
c.301_305delGTCAT
p.Val101SerfsX27

Protein change:

C158fs

Links:

dbSNP: rs397517932

NCBI 1000 Genomes Browser:

rs397517932

Molecular consequence:

NM_001195794.1:c.301_305del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001256819.2:c.473_477del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_052995.2:c.73_77del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_174878.3:c.301_305del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_046380.3:n.471_475del - 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
SCV003525371	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 13, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 11524702, 24498627, 21675857, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003525371

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 13, 2022)

germline

clinical testing

PubMed (4)
[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 (4)

Details of each submission

From Invitae, SCV003525371.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Val101Serfs*27) 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). This variant is present in population databases (rs397517932, gnomAD 0.002%). This premature translational stop signal has been observed in individual(s) with Usher syndrome (PMID: 21675857). ClinVar contains an entry for this variant (Variation ID: 48145). For these reasons, this variant has been classified as Pathogenic.

#	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: Feb 14, 2024

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