NM_000252.3(MTM1):c.145G>A (p.Val49Ile) AND Severe X-linked myotubular myopathy

Germline classification:: Conflicting classifications of pathogenicity (2 submissions)
Last evaluated:: Aug 30, 2021
Review status:: criteria provided, conflicting classifications

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:: RCV000146418.10

Allele description [Variation Report for NM_000252.3(MTM1):c.145G>A (p.Val49Ile)]

NM_000252.3(MTM1):c.145G>A (p.Val49Ile)

Gene:

MTM1:myotubularin 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq28

Genomic location:

Preferred name:

NM_000252.3(MTM1):c.145G>A (p.Val49Ile)

HGVS:

NC_000023.11:g.150598600G>A
NG_008199.1:g.35018G>A
NM_000252.3:c.145G>AMANE SELECT
NM_001376906.1:c.145G>A
NM_001376907.1:c.145G>A
NM_001376908.1:c.145G>A
NP_000243.1:p.Val49Ile
NP_000243.1:p.Val49Ile
NP_001363835.1:p.Val49Ile
NP_001363836.1:p.Val49Ile
NP_001363837.1:p.Val49Ile
LRG_839t1:c.145G>A
LRG_839:g.35018G>A
LRG_839p1:p.Val49Ile
NC_000023.10:g.149767064G>A
NM_000252.2:c.145G>A

Protein change:

V49I

Links:

dbSNP: rs587783796

NCBI 1000 Genomes Browser:

rs587783796

Molecular consequence:

NM_000252.3:c.145G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001376906.1:c.145G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001376907.1:c.145G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001376908.1:c.145G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Severe X-linked myotubular myopathy (CNMX)
Synonyms:: X-linked centronuclear myopathy; MYOTUBULAR MYOPATHY 1; Myotubular myopathy, X-linked
Identifiers:: MONDO: MONDO:0010683; MedGen: C0410203; Orphanet: 596; OMIM: 310400

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000193704	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2007)	Pathogenic (Feb 8, 2013)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002580385	MGZ Medical Genetics Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Aug 30, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000193704

Genetic Services Laboratory, University of Chicago

criteria provided, single submitter

(ACMG Guidelines, 2007)

Pathogenic
(Feb 8, 2013)

germline

clinical testing

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

SCV002580385

MGZ Medical Genetics Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Aug 30, 2021)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.

Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee.

Genet Med. 2008 Apr;10(4):294-300. doi: 10.1097/GIM.0b013e31816b5cae.

PubMed [citation]

PMID:: 18414213

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 Genetic Services Laboratory, University of Chicago, SCV000193704.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From MGZ Medical Genetics Center, SCV002580385.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Jan 19, 2025

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