NM_174878.3(CLRN1):c.189C>A (p.Tyr63Ter) AND CLRN1-related disorder

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 21, 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:: RCV003407275.4

Allele description [Variation Report for NM_174878.3(CLRN1):c.189C>A (p.Tyr63Ter)]

NM_174878.3(CLRN1):c.189C>A (p.Tyr63Ter)

Gene:

CLRN1:clarin 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q25.1

Genomic location:

Preferred name:

NM_174878.3(CLRN1):c.189C>A (p.Tyr63Ter)

HGVS:

NC_000003.12:g.150972520G>T
NG_009168.1:g.5480C>A
NM_001195794.1:c.189C>A
NM_001256819.2:c.189C>A
NM_174878.3:c.189C>AMANE SELECT
NP_001182723.1:p.Tyr63Ter
NP_001243748.1:p.Tyr63Ter
NP_777367.1:p.Tyr63Ter
LRG_700t1:c.189C>A
LRG_700:g.5480C>A
LRG_700p1:p.Tyr63Ter
NC_000003.11:g.150690307G>T
NM_174878.3:c.189C>A
NR_046380.3:n.208C>A
c.189C>A
p.Tyr63X

Protein change:

Y63*; TYR63TER

Links:

OMIM: 606397.0006; dbSNP: rs111033267

NCBI 1000 Genomes Browser:

rs111033267

Molecular consequence:

NR_046380.3:n.208C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001195794.1:c.189C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001256819.2:c.189C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_174878.3:c.189C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: CLRN1-related disorder
Synonyms:: CLRN1-related condition
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004114993	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 21, 2023)	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

SCV004114993

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jun 21, 2023)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 PreventionGenetics, part of Exact Sciences, SCV004114993.1

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

Description

The CLRN1 c.189C>A variant is predicted to result in premature protein termination (p.Tyr63*). This variant has been reported to be causative for autosomal recessive Usher syndrome or retinitis pigmentosa (Adato et al. 2002. PubMed ID: 12080385; Melo et al. 2014. PubMed ID: 24596593; Carss et al. 2016. PubMed ID: 28041643). This variant is reported in 0.0056% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/3-150690307-G-T). Nonsense variants in CLRN1 are expected to be pathogenic. Given the evidence, we interpret c.189C>A (p.Tyr63*) 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: Jun 17, 2024

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