NM_145309.6(LRRC51):c.340_346del (p.Ile114fs) AND Autosomal recessive nonsyndromic hearing loss 63

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 22, 2022
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:: RCV002251284.1

Allele description [Variation Report for NM_145309.6(LRRC51):c.340_346del (p.Ile114fs)]

NM_145309.6(LRRC51):c.340_346del (p.Ile114fs)

Genes:

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

Variant type:

Deletion

Cytogenetic location:

11q13.4

Genomic location:

Preferred name:

NM_145309.6(LRRC51):c.340_346del (p.Ile114fs)

HGVS:

NC_000011.10:g.72094999_72095005del
NG_021423.1:g.19664_19670del
NM_001145307.5:c.340_346del
NM_001145308.5:c.-64_-58del
NM_001145309.4:c.-64_-58del
NM_001145310.4:c.-64_-58del
NM_001205138.4:c.286_292del
NM_001271471.3:c.340_346del
NM_001318803.2:c.340_346del
NM_145309.6:c.340_346delMANE SELECT
NP_001138779.1:p.Ile114fs
NP_001192067.1:p.Ile96fs
NP_001258400.1:p.Ile114fs
NP_001305732.1:p.Ile114fs
NP_660352.1:p.Ile114fs
NC_000011.9:g.71806045_71806051del
NM_001145308.4:c.-64_-58delATCCAGC
NR_026886.4:n.695_701del
NR_134858.2:n.294_300del

Protein change:

I114fs

Links:

dbSNP: rs759544282

NCBI 1000 Genomes Browser:

rs759544282

Molecular consequence:

NM_001145308.5:c.-64_-58del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001145309.4:c.-64_-58del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001145310.4:c.-64_-58del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001145307.5:c.340_346del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001205138.4:c.286_292del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001271471.3:c.340_346del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001318803.2:c.340_346del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_145309.6:c.340_346del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_026886.4:n.695_701del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_134858.2:n.294_300del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Name:: Autosomal recessive nonsyndromic hearing loss 63
Synonyms:: Deafness, autosomal recessive 63
Identifiers:: MONDO: MONDO:0012670; MedGen: C1969621; Orphanet: 90636; OMIM: 611451

Recent activity

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PREDICTED: homeobox-leucine zipper protein ATHB-15 isoform X1 [Tarenaya hassleri...
PREDICTED: homeobox-leucine zipper protein ATHB-15 isoform X1 [Tarenaya hassleriana]
gi|729357759|ref|XP_010545672.1|

Protein
PREDICTED: Homo sapiens histone deacetylase 2 (HDAC2), transcript variant X1, mR...
PREDICTED: Homo sapiens histone deacetylase 2 (HDAC2), transcript variant X1, mRNA
gi|2217361202|ref|XM_047418692.1|

Nucleotide
Taxonomy Links for Nucleotide (Select 2217361202) (1)
Taxonomy
PubChem Substance Links for Gene (Select 445347) (53)
PubChem Substance
RefSeq Protein Links for Gene (Select 445347) (2)
Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002521871	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 22, 2022)	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

SCV002521871

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(May 22, 2022)

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	yes	1	not provided	not provided	1	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 3billion, SCV002521871.1

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

Description

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: <0.001%). Frameshift: predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

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

Last Updated: Sep 1, 2024

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