NM_145309.6(LRRC51):c.330del (p.His110fs) AND Autosomal recessive nonsyndromic hearing loss 63

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 25, 2020
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:: RCV002273029.2

Allele description [Variation Report for NM_145309.6(LRRC51):c.330del (p.His110fs)]

NM_145309.6(LRRC51):c.330del (p.His110fs)

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.330del (p.His110fs)

HGVS:

NC_000011.10:g.72094989del
NG_021423.1:g.19654del
NM_001145307.5:c.330del
NM_001145308.5:c.-74del
NM_001145309.4:c.-74del
NM_001145310.4:c.-74del
NM_001205138.4:c.276del
NM_001271471.3:c.330del
NM_001318803.2:c.330del
NM_145309.6:c.330delMANE SELECT
NP_001138779.1:p.His110fs
NP_001192067.1:p.His92fs
NP_001258400.1:p.His110fs
NP_001305732.1:p.His110fs
NP_660352.1:p.His110fs
NC_000011.9:g.71806035del
NM_001318803.1:c.330delC
NR_026886.4:n.685del
NR_134858.2:n.284del

Protein change:

H110fs

Links:

dbSNP: rs2136541413

NCBI 1000 Genomes Browser:

rs2136541413

Molecular consequence:

NM_001145308.5:c.-74del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001145309.4:c.-74del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001145310.4:c.-74del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001145307.5:c.330del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001205138.4:c.276del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001271471.3:c.330del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001318803.2:c.330del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_145309.6:c.330del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_026886.4:n.685del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_134858.2:n.284del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002557583	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute See additional submitters Shariant Australia, Australian Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (May 25, 2020)	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

SCV002557583

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(May 25, 2020)

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	unknown	not provided	not provided	not provided	not provided	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 Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002557583.1

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

Description

Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as 3B-VUS. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene. (N) 0106 - This gene is known to be associated with autosomal recessive disease. (N) 0202 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein but is located in an exon that may undergo alternative splicing (exon 5 of 6). (P) 0251 - Variant is heterozygous. (N) 0301 - Variant is absent from gnomAD. (P) 0705 - No comparable variants in this transcript have been reported in the literature. (N) 0807 - Variant has not previously been reported in a clinical context. (N) 0905 - No segregation evidence has been identified for this variant. (N) 1007 - No published functional evidence has been identified for this variant. (N) 1208 - Inheritance information for this variant is not currently available. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign

#	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: Dec 24, 2023

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