chrX-150641297-C-T

Variant names:

• chrX-150641297-C-T
• rs587783836
• NM_000252.3:c.557C>T

Variant summary

Our verdict is Pathogenic. The variant received 16 ACMG points: 16P and 0B. PM1 PM2 PP3_Strong PP5_Very_Strong

The NM_000252.3(MTM1):​c.557C>T​(p.Thr186Ile) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency: Genomes: not found (cov: 23)
• Consequence: MTM1 NM_000252.3 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:2
• Conservation: PhyloP100: 3.82
• Publications: 3 publications found

Genes affected

MTM1 (HGNC:7448): (myotubularin 1) This gene encodes a dual-specificity phosphatase that acts on both phosphotyrosine and phosphoserine. It is required for muscle cell differentiation and mutations in this gene have been identified as being responsible for X-linked myotubular myopathy. [provided by RefSeq, Jul 2008]

MTM1 Gene-Disease associations (from GenCC):

• X-linked myotubular myopathy

  Inheritance: XL Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), ClinGen, Myriad Women’s Health, Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 16 ACMG points.

• PM1: In a hotspot region, there are 6 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 7 uncertain in NM_000252.3
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.978
• PP5: Variant X-150641297-C-T is Pathogenic according to our data. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-150641297-C-T is described in CliVar as Pathogenic/Likely_pathogenic. Clinvar id is 158982.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTM1	NM_000252.3	c.557C>T	p.Thr186Ile	missense_variant	Exon 8 of 15	ENST00000370396.7	NP_000243.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTM1	ENST00000370396.7	c.557C>T	p.Thr186Ile	missense_variant	Exon 8 of 15	1	NM_000252.3	ENSP00000359423.3

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 23

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Severe X-linked myotubular myopathy Pathogenic:1

Feb 08, 2013

Genetic Services Laboratory, University of Chicago

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Pathogenic:1

Nov 07, 2022

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Identified in a patient with a myotubular myopathy confirmed by biopsy in the published literature, however zygosity of the variant was not provided (Herman et al., 2002); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 11793470, 30047259, 31324802, 26338224) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.84
BayesDel_addAF	Pathogenic	0.52	D
BayesDel_noAF	Pathogenic	0.50
CADD	Benign	21
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.94	D
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.86	D
M_CAP	Pathogenic	0.78	D
MetaRNN	Pathogenic	0.98	D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Pathogenic	3.1	M
PhyloP100		3.8
PrimateAI	Uncertain	0.58	T
PROVEAN	Pathogenic	-4.5	D
REVEL	Pathogenic	0.82
Sift	Uncertain	0.0020	D
Sift4G	Uncertain	0.0040	D
Polyphen		0.88	P
Vest4		0.94
MutPred		0.78		Gain of ubiquitination at K190 (P = 0.0872);
MVP		1.0
MPC		1.5
ClinPred		0.99	D
GERP RS		4.5
Varity_R		0.70
gMVP		0.97
Mutation Taster		=3/97	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs587783836; hg19: chrX-149809770;