NM_145309.6(LRRC51):c.115C>T (p.Arg39Ter) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 10, 2015
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:: RCV000215650.4

Allele description [Variation Report for NM_145309.6(LRRC51):c.115C>T (p.Arg39Ter)]

NM_145309.6(LRRC51):c.115C>T (p.Arg39Ter)

Genes:

LRRC51:leucine rich repeat containing 51 [Gene - HGNC]
LRTOMT:leucine rich transmembrane and O-methyltransferase domain containing [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q13.4

Genomic location:

Preferred name:

NM_145309.6(LRRC51):c.115C>T (p.Arg39Ter)

HGVS:

NC_000011.10:g.72093528C>T
NG_021423.1:g.18193C>T
NM_001145307.5:c.115C>T
NM_001145308.5:c.-289C>T
NM_001145309.4:c.-289C>T
NM_001145310.4:c.-289C>T
NM_001205138.4:c.61C>T
NM_001271471.3:c.115C>T
NM_001318803.2:c.115C>T
NM_145309.6:c.115C>TMANE SELECT
NP_001138779.1:p.Arg39Ter
NP_001192067.1:p.Arg21Ter
NP_001258400.1:p.Arg39Ter
NP_001305732.1:p.Arg39Ter
NP_660352.1:p.Arg39Ter
NC_000011.9:g.71804574C>T
NM_001145307.1:c.115C>T
NR_026886.4:n.470C>T
NR_134858.2:n.69C>T
p.Arg39X

Protein change:

R21*

Links:

dbSNP: rs780299621

NCBI 1000 Genomes Browser:

rs780299621

Molecular consequence:

NM_001145308.5:c.-289C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001145309.4:c.-289C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001145310.4:c.-289C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NR_026886.4:n.470C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_134858.2:n.69C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001145307.5:c.115C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001205138.4:c.61C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001271471.3:c.115C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001318803.2:c.115C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_145309.6:c.115C>T - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000271958	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Uncertain significance (Oct 10, 2015)	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

SCV000271958

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Uncertain significance
(Oct 10, 2015)

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

Citations

PubMed

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, SCV000271958.2

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

Description

The p.Arg39X variant in LRTOMT (NM_001145307.1) has not been previously reported in individuals with hearing loss, but has been identified in 0.15% (16/10440) o f Latino chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broa dinstitute.org; dbSNP rs780299621). This variant leads to a premature terminatio n codon at position 39 in the NM_001145307.1 transcript of LRTOMT. However, in s everal alternate transcripts of the LRTOMT gene, the variant lies in the 5'UTR a nd its impact on these transcripts is unknown. In addition, the majority of repo rted pathogenic LRTOMT variants are located in the coding exons of these alterna te transcripts, which correspond to noncoding regions in the NM_001145307.1 tran script. Therefore, there is insufficient evidence to determine whether loss of f unction variants affecting the NM_001145307.1 transcript of LRTOMT are causative for hearing loss, and the impact of this variant on alternate transcripts of LR TOMT is not known. In summary, the clinical significance of the p.Arg39X variant in the NM_001145307.1 transcript of LRTOMT is uncertain.

#	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		1	not provided	1	not provided

Last Updated: Mar 4, 2023

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