X-150619115-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_000252.3(MTM1):c.420C>T(p.Tyr140Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000083 in 1,204,489 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0000090 ( 0 hom., 0 hem., cov: 22)

Exomes 𝑓: 0.0000082 ( 0 hom. 2 hem. )

Consequence

MTM1
NM_000252.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.467

Publications

1 publications found

Variant links:

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

MTM1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

Variant X-150619115-C-T is Benign according to our data. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-150619115-C-T is described in CliVar as Likely_benign. Clinvar id is 730278.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.467 with no splicing effect.

BS2

High Hemizygotes in GnomAdExome4 at 2 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTM1	NM_000252.3 link	c.420C>T	p.Tyr140Tyr	synonymous_variant	Exon 6 of 15	ENST00000370396.7	NP_000243.1	Q13496-1A0A024RC06

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTM1	ENST00000370396.7 link	c.420C>T	p.Tyr140Tyr	synonymous_variant	Exon 6 of 15	1	NM_000252.3	ENSP00000359423.3		Q13496-1

Frequencies

GnomAD3 genomes

AF:

0.00000897

AC:

AN:

111474

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000188

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00000546

AC:

AN:

183224

AF XY:

0.00

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000122

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000823

AC:

AN:

1093015

Hom.:

Cov.:

AF XY:

0.00000558

AC XY:

AN XY:

358531

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

26317

American (AMR)

AF:

0.00

AC:

AN:

35200

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19359

East Asian (EAS)

AF:

0.00

AC:

AN:

30174

South Asian (SAS)

AF:

0.0000185

AC:

AN:

54032

European-Finnish (FIN)

AF:

0.00

AC:

AN:

40528

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4127

European-Non Finnish (NFE)

AF:

0.00000955

AC:

AN:

837338

Other (OTH)

AF:

0.00

AC:

AN:

45940

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00000897

AC:

AN:

111474

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

33682

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

30604

American (AMR)

AF:

0.00

AC:

AN:

10507

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2639

East Asian (EAS)

AF:

0.00

AC:

AN:

3547

South Asian (SAS)

AF:

0.00

AC:

AN:

2645

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5993

Middle Eastern (MID)

AF:

0.00

AC:

AN:

238

European-Non Finnish (NFE)

AF:

0.0000188

AC:

AN:

53133

Other (OTH)

AF:

0.00

AC:

AN:

1481

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Severe X-linked myotubular myopathy

Benign:1

Feb 01, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

2.1

(source)

DANN

Benign

0.58

PhyloP100

0.47

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over