NM_174878.3(CLRN1):c.368C>A (p.Ala123Asp) AND Usher syndrome type 3

Germline classification:: Likely pathogenic (3 submissions)
Last evaluated:: Jun 27, 2014
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000041436.9

Allele description [Variation Report for NM_174878.3(CLRN1):c.368C>A (p.Ala123Asp)]

NM_174878.3(CLRN1):c.368C>A (p.Ala123Asp)

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.368C>A (p.Ala123Asp)

HGVS:

NC_000003.12:g.150941647G>T
NG_009168.1:g.36353C>A
NM_001195794.1:c.368C>A
NM_001256819.2:c.540C>A
NM_052995.2:c.140C>A
NM_174878.3:c.368C>AMANE SELECT
NP_001182723.1:p.Ala123Asp
NP_001243748.1:p.Cys180Ter
NP_443721.1:p.Ala47Asp
NP_777367.1:p.Ala123Asp
LRG_700t1:c.368C>A
LRG_700t2:c.140C>A
LRG_700:g.36353C>A
LRG_700p1:p.Ala123Asp
LRG_700p2:p.Ala47Asp
NC_000003.11:g.150659434G>T
NM_174878.2:c.368C>A
NR_046380.3:n.538C>A
c.368C>A

Protein change:

A123D

Links:

dbSNP: rs374963432

NCBI 1000 Genomes Browser:

rs374963432

Molecular consequence:

NM_001195794.1:c.368C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_052995.2:c.140C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_174878.3:c.368C>A - missense variant - [Sequence Ontology: SO:0001583]
NR_046380.3:n.538C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001256819.2:c.540C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Usher syndrome type 3
Synonyms:: Usher Syndrome, Type III
Identifiers:: MONDO: MONDO:0016485; MedGen: C1568248

Recent activity

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hydroxymethylbilane synthase [Azospirillum sp. B510]
hydroxymethylbilane synthase [Azospirillum sp. B510]
gi|502738046|ref|WP_012973030.1|

Protein
Croton socotranus voucher Lavranos & James 31042 (RSA), cultivated in California...
Croton socotranus voucher Lavranos & James 31042 (RSA), cultivated in California internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence
gi|64474301|gb|AY971250.1|

Nucleotide
da26h05.x1 Xenla 13LiCl Xenopus laevis cDNA clone IMAGE:2942265 3' similar to gb...
da26h05.x1 Xenla 13LiCl Xenopus laevis cDNA clone IMAGE:2942265 3' similar to gb:M29551 PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT 2 (HUMAN); gb:J04134 Mouse brain calmodulin-dependent phosphatase (MOUSE); gb:gb|AF019569.1|AF019569 Xenopus laevis calcineurin A mRNA, complete (XENOPUS), mRNA sequence
gi|7030829|gnl|dbEST|3871390|gb|AW4 .1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000220455	Counsyl	criteria provided, single submitter (Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015))	Likely pathogenic (Jun 27, 2014)	unknown	literature only	PubMed (3) [See all records that cite these PMIDs] 23304067, 19753315, 17407589 Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015), Citation Link,
SCV001162963	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002081534	Natera, Inc.	no assertion criteria provided	Pathogenic (Jan 13, 2021)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000220455

Counsyl

criteria provided, single submitter

(Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015))

Likely pathogenic
(Jun 27, 2014)

unknown

literature only

PubMed (3)
[See all records that cite these PMIDs]

Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015),

Citation Link,

SCV001162963

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002081534

Natera, Inc.

no assertion criteria provided

Pathogenic
(Jan 13, 2021)

germline

clinical testing

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
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

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

Disease-causing mutations in the CLRN1 gene alter normal CLRN1 protein trafficking to the plasma membrane.

Isosomppi J, Västinsalo H, Geller SF, Heon E, Flannery JG, Sankila EM.

Mol Vis. 2009 Sep 8;15:1806-18.

PubMed [citation]

PMID:: 19753315
PMCID:: PMC2742642

See all PubMed Citations (4)

Details of each submission

From Counsyl, SCV000220455.2

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV001162963.1

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

#	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

From Natera, Inc., SCV002081534.1

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

#	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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