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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:
RCV002273029.3

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_001145308.4:c.-74delC
  • 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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002557583Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(May 25, 2020) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV002557583.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 1, 2024