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NM_001145308.5(LRTOMT):c.154C>T (p.Arg52Trp) AND Autosomal recessive nonsyndromic hearing loss 63

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 3, 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:
RCV001808875.2

Allele description [Variation Report for NM_001145308.5(LRTOMT):c.154C>T (p.Arg52Trp)]

NM_001145308.5(LRTOMT):c.154C>T (p.Arg52Trp)

Genes:
LRTOMT:leucine rich transmembrane and O-methyltransferase domain containing [Gene - OMIM - HGNC]
TOMT:transmembrane O-methyltransferase [Gene - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q13.4
Genomic location:
Preferred name:
NM_001145308.5(LRTOMT):c.154C>T (p.Arg52Trp)
HGVS:
  • NC_000011.10:g.72106006C>T
  • NG_021423.1:g.30671C>T
  • NM_001145308.5:c.154C>T
  • NM_001145309.4:c.154C>T
  • NM_001145310.4:c.84-50C>T
  • NM_001393500.2:c.55C>TMANE SELECT
  • NP_001138780.1:p.Arg52Trp
  • NP_001138780.1:p.Arg52Trp
  • NP_001138781.1:p.Arg52Trp
  • NP_001380429.1:p.Arg19Trp
  • NC_000011.9:g.71817052C>T
  • NM_001145308.4:c.154C>T
Protein change:
R19W
Links:
dbSNP: rs1372399805
NCBI 1000 Genomes Browser:
rs1372399805
Molecular consequence:
  • NM_001145310.4:c.84-50C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001145308.5:c.154C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001145309.4:c.154C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001393500.2:c.55C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

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
SCV0020590853billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Jan 3, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not 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 3billion, SCV002059085.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000013, PM2_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.635, PP3_P). Therefore, this variant is classified as uncertain significance according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Oct 8, 2024