NM_174878.3(CLRN1):c.301_305del (p.Val101fs) AND Rare genetic deafness

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 8, 2011
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:: RCV000844625.4

Allele description [Variation Report for NM_174878.3(CLRN1):c.301_305del (p.Val101fs)]

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]

Observations:

Condition(s)

Name:: Rare genetic deafness
Identifiers:: MedGen: C5680250; Orphanet: 96210

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000065130	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Pathogenic (Nov 8, 2011)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 21675857, 24033266

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000065130

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Pathogenic
(Nov 8, 2011)

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	not provided	2	1	not provided	not provided	not provided	clinical testing

Citations

PubMed

A novel 5-bp deletion in Clarin 1 in a family with Usher syndrome.

Akoury E, El Zir E, Mansour A, Mégarbané A, Majewski J, Slim R.

Ophthalmic Genet. 2011 Nov;32(4):245-9. doi: 10.3109/13816810.2011.587083. Epub 2011 Jun 15.

PubMed [citation]

PMID:: 21675857

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000065130.5

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

Description

The Val101fs variant in CLRN1 has been identified in the homozygous state in two Lebanese siblings with Usher syndrome (Akoury 2011). This variant results in a frameshift at position 101 leading to a premature stop 27 codons downstream, whi ch is predicted to lead to a truncated or absent protein. In summary, this varia nt meets our criteria to be classified as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		2	not provided	1	not provided

Last Updated: Feb 14, 2024

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