NM_016156.6(MTMR2):c.8A>C (p.Lys3Thr) AND Charcot-Marie-Tooth disease, type 4B1

Clinical significance:Benign (Last evaluated: Sep 5, 2021)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
4 submissions [Details]
Record status:
current
Accession:
RCV000576747.4

Allele description [Variation Report for NM_016156.6(MTMR2):c.8A>C (p.Lys3Thr)]

NM_016156.6(MTMR2):c.8A>C (p.Lys3Thr)

Gene:
MTMR2:myotubularin related protein 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q21
Genomic location:
Preferred name:
NM_016156.6(MTMR2):c.8A>C (p.Lys3Thr)
HGVS:
  • NC_000011.10:g.95923947T>G
  • NG_008333.1:g.5261A>C
  • NM_001243571.2:c.-476A>C
  • NM_016156.6:c.8A>CMANE SELECT
  • NM_201278.3:c.-403A>C
  • NM_201281.3:c.-280A>C
  • NP_057240.3:p.Lys3Thr
  • NP_057240.3:p.Lys3Thr
  • LRG_257t1:c.8A>C
  • LRG_257:g.5261A>C
  • LRG_257p1:p.Lys3Thr
  • NC_000011.9:g.95657111T>G
  • NM_016156.5:c.8A>C
  • NM_016156.6:c.8A>C
  • Q13614:p.Lys3Thr
Protein change:
K3T
Links:
UniProtKB: Q13614#VAR_047255; dbSNP: rs3824874
NCBI 1000 Genomes Browser:
rs3824874
Molecular consequence:
  • NM_001243571.2:c.-476A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_201278.3:c.-403A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_201281.3:c.-280A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_016156.6:c.8A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Charcot-Marie-Tooth disease, type 4B1 (CMT4B1)
Synonyms:
CHARCOT-MARIE-TOOTH DISEASE, AUTOSOMAL RECESSIVE, WITH FOCALLY FOLDED MYELIN SHEATHS, AUTOSOMAL RECESSIVE, TYPE 4B1; CMT 4B1; Charcot-Marie-Tooth disease, Type 4B; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0011066; MedGen: C1832399; Orphanet: 99955; OMIM: 601382

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000375003Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Benign
(Jan 13, 2018)
germlineclinical testing

Citation Link,

SCV000677363Athena Diagnostics Inccriteria provided, single submitter
Benign
(Jun 2, 2017)
germlineclinical testing

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

SCV001138410Mendelicscriteria provided, single submitter
Benign
(May 28, 2019)
unknownclinical testing

Citation Link,

SCV002014271Nilou-Genome Labcriteria provided, single submitter
Benign
(Sep 5, 2021)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

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 Illumina Clinical Services Laboratory,Illumina, SCV000375003.3

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

Description

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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

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

From Athena Diagnostics Inc, SCV000677363.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Mendelics, SCV001138410.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Nilou-Genome Lab, SCV002014271.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

Last Updated: Dec 4, 2021

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