NM_174878.3(CLRN1):c.488_492del (p.His163fs) AND not provided

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

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 14, 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:: RCV003017994.2

Allele description

NM_174878.3(CLRN1):c.488_492del (p.His163fs)

Gene:

CLRN1:clarin 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

3q25.1

Genomic location:

Preferred name:

NM_174878.3(CLRN1):c.488_492del (p.His163fs)

HGVS:

NC_000003.12:g.150928145_150928149del
NG_009168.1:g.49853_49857del
NM_001195794.1:c.527_531del
NM_001256819.2:c.*102_*106del
NM_052995.2:c.260_264del
NM_174878.3:c.488_492delMANE SELECT
NP_001182723.1:p.His176fs
NP_443721.1:p.His87fs
NP_777367.1:p.His163fs
LRG_700t1:c.527_531del
LRG_700t2:c.260_264del
LRG_700:g.49853_49857del
LRG_700p1:p.His176fs
LRG_700p2:p.His87fs
NC_000003.11:g.150645930_150645934del
NC_000003.11:g.150645932_150645936del
NR_046380.3:n.697_701del

Protein change:

H163fs

Molecular consequence:

NM_001256819.2:c.*102_*106del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001195794.1:c.527_531del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_052995.2:c.260_264del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_174878.3:c.488_492del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_046380.3:n.697_701del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Suillus sp. RZ-2017a voucher HKAS:57630 translation elongation factor 1-alpha (T...
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gi|1180720505|gb|KU721622.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003302169	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 14, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 22952768, 23304067, 26338283, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003302169

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 14, 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

Molecular diagnosis of Usher syndrome: application of two different next generation sequencing-based procedures.

Licastro D, Mutarelli M, Peluso I, Neveling K, Wieskamp N, Rispoli R, Vozzi D, Athanasakis E, D'Eustacchio A, Pizzo M, D'Amico F, Ziviello C, Simonelli F, Fabretto A, Scheffer H, Gasparini P, Banfi S, Nigro V.

PLoS One. 2012;7(8):e43799. doi: 10.1371/journal.pone.0043799. Epub 2012 Aug 29.

PubMed [citation]

PMID:: 22952768
PMCID:: PMC3430670

Two novel disease-causing mutations in the CLRN1 gene in patients with Usher syndrome type 3.

García-García G, Aparisi MJ, Rodrigo R, Sequedo MD, Espinós C, Rosell J, Olea JL, Mendívil MP, Ramos-Arroyo MA, Ayuso C, Jaijo T, Aller E, Millán JM.

Mol Vis. 2012;18:3070-8. Epub 2012 Dec 29.

PubMed [citation]

PMID:: 23304067
PMCID:: PMC3538041

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV003302169.2

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the CLRN1 protein in which other variant(s) (p.Arg207*) have been determined to be pathogenic (PMID: 22952768, 23304067, 26338283). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. 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.His163Leufs*8) in the CLRN1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 70 amino acid(s) of the CLRN1 protein.

#	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 1, 2024

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