Genetic Variant NM_000252.3:c.1052A>G (chrX-150649900-A-G) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 1P and 9B. PP3BP6BS1BS2

The NM_000252.3(MTM1):c.1052A>G(p.Lys351Arg) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000392 in 1,192,902 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 152 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). The gene MTM1 is included in the ClinGen Criteria Specification Registry.

Frequency

Genomes: 𝑓 0.00020 ( 0 hom., 7 hem., cov: 24)

Exomes 𝑓: 0.00041 ( 0 hom. 145 hem. )

Consequence

MTM1
NM_000252.3 missense, splice_region

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:3B:3

Conservation

PhyloP100: 9.24

Publications

0 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: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Orphanet, ClinGen, G2P, Myriad Women’s Health, Ambry Genetics

MTM1 links:

Genome browser will be placed here

ACMG classification

Specifications for MTM1 are available in the ClinGen Criteria Specification Registry and recommended for reference when assigning criteria.

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

PP3

MetaRNN computational evidence supports a deleterious effect, 0.747

BP6

Variant X-150649900-A-G is Benign according to our data. Variant chrX-150649900-A-G is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 500885.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.000196 (22/112354) while in subpopulation NFE AF = 0.000338 (18/53276). AF 95% confidence interval is 0.000218. There are 0 homozygotes in GnomAd4. There are 7 alleles in the male GnomAd4 subpopulation. Median coverage is 24. This position passed quality control check.

BS2

High Hemizygotes in GnomAd4 at 7 XL gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000252.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MTM1	NM_000252.3	MANE Select	c.1052A>G	p.Lys351Arg	missense splice_region	Exon 10 of 15	NP_000243.1	Q13496-1
MTM1	NM_001376908.1		c.1052A>G	p.Lys351Arg	missense splice_region	Exon 10 of 15	NP_001363837.1	Q13496-1
MTM1	NM_001376906.1		c.1052A>G	p.Lys351Arg	missense splice_region	Exon 10 of 15	NP_001363835.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MTM1	ENST00000370396.7	TSL:1 MANE Select	c.1052A>G	p.Lys351Arg	missense splice_region	Exon 10 of 15	ENSP00000359423.3	Q13496-1
MTM1	ENST00000689314.1		c.1097A>G	p.Lys366Arg	missense splice_region	Exon 11 of 16	ENSP00000510607.1	A0A8I5KZ76
MTM1	ENST00000866458.1		c.1097A>G	p.Lys366Arg	missense splice_region	Exon 11 of 16	ENSP00000536517.1

Frequencies

GnomAD3 genomes

AF:

0.000196

AC:

AN:

112354

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000323

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000188

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:

0.000338

Gnomad OTH

AF:

0.000668

GnomAD2 exomes

AF:

0.000199

AC:

AN:

175656

AF XY:

0.000163

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000778

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000401

Gnomad OTH exome

AF:

0.000233

GnomAD4 exome

AF:

0.000413

AC:

446

AN:

1080548

Hom.:

Cov.:

AF XY:

0.000418

AC XY:

145

AN XY:

347190

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

26030

American (AMR)

AF:

0.000117

AC:

AN:

34293

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19140

East Asian (EAS)

AF:

0.00

AC:

AN:

29989

South Asian (SAS)

AF:

0.00

AC:

AN:

51934

European-Finnish (FIN)

AF:

0.0000247

AC:

AN:

40431

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4005

European-Non Finnish (NFE)

AF:

0.000523

AC:

434

AN:

829255

Other (OTH)

AF:

0.000154

AC:

AN:

45471

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.000196

AC:

AN:

112354

Hom.:

Cov.:

AF XY:

0.000203

AC XY:

AN XY:

34500

show subpopulations

African (AFR)

AF:

0.0000323

AC:

AN:

30929

American (AMR)

AF:

0.000188

AC:

AN:

10628

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2659

East Asian (EAS)

AF:

0.00

AC:

AN:

3615

South Asian (SAS)

AF:

0.00

AC:

AN:

2730

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6097

Middle Eastern (MID)

AF:

0.00

AC:

AN:

239

European-Non Finnish (NFE)

AF:

0.000338

AC:

AN:

53276

Other (OTH)

AF:

0.000668

AC:

AN:

1496

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

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:

0.000433

Hom.:

Bravo

AF:

0.000215

TwinsUK

AF:

0.000539

AC:

ALSPAC

AF:

0.00

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000298

AC:

ExAC

AF:

0.000140

AC:

ClinVar

ClinVar submissions

Significance:Conflicting classifications of pathogenicity

Revision:criteria provided, conflicting classifications

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

Severe X-linked myotubular myopathy (2)

Inborn genetic diseases (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Uncertain

0.063

BayesDel_noAF

Pathogenic

0.17

CADD

Benign

(source)

DANN

Uncertain

0.99

DEOGEN2

Uncertain

0.74

FATHMM_MKL

Pathogenic

1.0

LIST_S2

Benign

0.80

M_CAP

Pathogenic

0.49

MetaRNN

Pathogenic

0.75

MetaSVM

Uncertain

-0.15

MutationAssessor

Benign

0.57

PhyloP100

9.2

PrimateAI

Uncertain

0.65

PROVEAN

Benign

-1.7

REVEL

Uncertain

0.43

Sift

Benign

0.42

Sift4G

Benign

0.47

Polyphen

0.019

Vest4

0.77

MVP

0.99

MPC

1.5

ClinPred

0.19

GERP RS

5.7

Varity_R

0.54

gMVP

0.70

Mutation Taster

=90/10

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.12

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over