NM_016156.6(MTMR2):c.1233G>A (p.Thr411=) AND Charcot-Marie-Tooth disease type 4B1

Germline classification:: Benign (3 submissions)
Last evaluated:: Oct 13, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000576743.17

Allele description [Variation Report for NM_016156.6(MTMR2):c.1233G>A (p.Thr411=)]

NM_016156.6(MTMR2):c.1233G>A (p.Thr411=)

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.1233G>A (p.Thr411=)

Other names:

p.T411T:ACG>ACA

HGVS:

NC_000011.10:g.95845106C>T
NG_008333.1:g.84102G>A
NM_001243571.2:c.1017G>A
NM_003912.1:c.1233G>A
NM_016156.6:c.1233G>AMANE SELECT
NM_201278.3:c.1017G>A
NM_201281.3:c.1017G>A
NP_001230500.1:p.Thr339=
NP_057240.3:p.Thr411=
NP_057240.3:p.Thr411=
NP_958435.1:p.Thr339=
NP_958438.1:p.Thr339=
LRG_257t1:c.1233G>A
LRG_257:g.84102G>A
LRG_257p1:p.Thr411=
NC_000011.9:g.95578270C>T
NM_016156.5:c.1233G>A
p.Thr411Thr

Links:

dbSNP: rs113897932

NCBI 1000 Genomes Browser:

rs113897932

Molecular consequence:

NM_001243571.2:c.1017G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_016156.6:c.1233G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_201278.3:c.1017G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_201281.3:c.1017G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Charcot-Marie-Tooth disease type 4B1
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

Recent activity

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RecName: Full=RNA pseudouridylate synthase domain-containing protein 1
RecName: Full=RNA pseudouridylate synthase domain-containing protein 1
gi|123908280|sp|Q08C69.1|RUSD1_DANR

Protein
JUN, partial [Homo sapiens]
JUN, partial [Homo sapiens]
gi|49456463|emb|CAG46552.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000374994	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Jan 13, 2018)	germline	clinical testing	Citation Link,
SCV000677360	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (Jun 2, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 11354824, 26467025
SCV001156816	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Benign (Oct 13, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000374994

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Jan 13, 2018)

germline

clinical testing

Citation Link,

SCV000677360

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Benign
(Jun 2, 2017)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV001156816

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)

Benign
(Oct 13, 2023)

germline

clinical testing

Citation Link

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

Denaturing high-performance liquid chromatography of the myotubularin-related 2 gene (MTMR2) in unrelated patients with Charcot-Marie-Tooth disease suggests a low frequency of mutation in inherited neuropathy.

Bolino A, Lonie LJ, Zimmer M, Boerkoel CF, Takashima H, Monaco AP, Lupski JR.

Neurogenetics. 2001 Mar;3(2):107-9.

PubMed [citation]

PMID:: 11354824

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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000374994.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not 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.

#	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

From Athena Diagnostics, SCV000677360.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

#	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

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV001156816.6

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

#	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: Sep 29, 2024

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