NM_174878.3(CLRN1):c.606T>G (p.Asn202Lys) AND not provided

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

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 29, 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:: RCV001246907.7

Allele description

NM_174878.3(CLRN1):c.606T>G (p.Asn202Lys)

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.606T>G (p.Asn202Lys)

HGVS:

NC_000003.12:g.150928029A>C
NG_009168.1:g.49971T>G
NM_001195794.1:c.645T>G
NM_001256819.2:c.*220T>G
NM_052995.2:c.342+36T>G
NM_174878.3:c.606T>GMANE SELECT
NP_001182723.1:p.Asn215Lys
NP_777367.1:p.Asn202Lys
LRG_700t1:c.645T>G
LRG_700t2:c.342+36T>G
LRG_700:g.49971T>G
LRG_700p1:p.Asn215Lys
NC_000003.11:g.150645816A>C
NM_174878.2:c.606T>G
NM_174878.3:c.606T>G
NR_046380.3:n.815T>G

Protein change:

N202K

Links:

dbSNP: rs746128095

NCBI 1000 Genomes Browser:

rs746128095

Molecular consequence:

NM_001256819.2:c.*220T>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_052995.2:c.342+36T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001195794.1:c.645T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_174878.3:c.606T>G - missense variant - [Sequence Ontology: SO:0001583]
NR_046380.3:n.815T>G - 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
SCV001420299	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 29, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25743179, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001420299

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 29, 2023)

germline

clinical testing

PubMed (2)
[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

Identification of a novel CLRN1 gene mutation in Usher syndrome type 3: two case reports.

Yoshimura H, Oshikawa C, Nakayama J, Moteki H, Usami S.

Ann Otol Rhinol Laryngol. 2015 May;124 Suppl 1:94S-9S. doi: 10.1177/0003489415574069. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25743179

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001420299.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change replaces asparagine, which is neutral and polar, with lysine, which is basic and polar, at codon 202 of the CLRN1 protein (p.Asn202Lys). This variant is present in population databases (rs746128095, gnomAD 0.01%). This missense change has been observed in individual(s) with Usher syndrome (PMID: 25743179). ClinVar contains an entry for this variant (Variation ID: 971183). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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: Aug 18, 2024

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