NM_001145308.5(LRTOMT):c.754C>T (p.Arg252Cys) AND Deafness, autosomal recessive 63

Clinical significance:Uncertain significance (Last evaluated: Jan 12, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_001145308.5(LRTOMT):c.754C>T (p.Arg252Cys)]

NM_001145308.5(LRTOMT):c.754C>T (p.Arg252Cys)

ANAPC15:anaphase promoting complex subunit 15 [Gene - OMIM - HGNC]
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:
Genomic location:
Preferred name:
NM_001145308.5(LRTOMT):c.754C>T (p.Arg252Cys)
  • NC_000011.10:g.72108803C>T
  • NG_021423.1:g.33468C>T
  • NM_001145308.5:c.754C>T
  • NM_001145309.4:c.754C>T
  • NM_001145310.4:c.634C>T
  • NM_001330321.2:c.319-1198G>A
  • NM_001393427.1:c.319-1198G>A
  • NM_001393428.1:c.319-1198G>A
  • NM_001393429.1:c.319-1198G>A
  • NM_001393430.1:c.319-1198G>A
  • NM_001393431.1:c.319-1198G>A
  • NM_001393443.1:c.*16G>A
  • NM_001393444.1:c.*16G>A
  • NM_001393445.1:c.*16G>A
  • NM_001393459.1:c.64-1198G>A
  • NP_001138780.1:p.Arg252Cys
  • NP_001138781.1:p.Arg252Cys
  • NP_001138782.1:p.Arg212Cys
  • NP_001380429.1:p.Arg219Cys
  • NC_000011.9:g.71819849C>T
  • NM_001145308.4:c.754C>T
  • NM_001393500.1:c.655C>T
  • NR_171687.1:n.640G>A
Protein change:
dbSNP: rs370168246
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001393443.1:c.*16G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001393444.1:c.*16G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001393445.1:c.*16G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001330321.2:c.319-1198G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001393427.1:c.319-1198G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001393428.1:c.319-1198G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001393429.1:c.319-1198G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001393430.1:c.319-1198G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001393431.1:c.319-1198G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001393459.1:c.64-1198G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001145308.5:c.754C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001145309.4:c.754C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001145310.4:c.634C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_171687.1:n.640G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]


Deafness, autosomal recessive 63 (DFNB63)
Autosomal recessive nonsyndromic hearing loss 63
MONDO: MONDO:0012670; MedGen: C1969621; Orphanet: 90636; OMIM: 611451

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV001272256Illumina Laboratory Services,Illuminacriteria provided, single submitter
Uncertain significance
(Jan 12, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Illumina Laboratory Services,Illumina, SCV001272256.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided


This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

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

Last Updated: Jan 15, 2022

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