dbSNP rs782703141: MTMR1:p.Ala93Asp (chrX-150718626-C-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001306144.3(MTMR1):c.278C>A(p.Ala93Asp) variant causes a missense, splice region change. 2/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A93G) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 13)

Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )

Failed GnomAD Quality Control

Consequence

MTMR1
NM_001306144.3 missense, splice_region

Scores

Splicing: ADA: 0.9583

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.08

Publications

0 publications found

Variant links:

Genes affected

MTMR1 (HGNC:7449): (myotubularin related protein 1) This gene encodes a member of the myotubularin related family of proteins. Members of this family contain the consensus sequence for the active site of protein tyrosine phosphatases. Alternatively spliced variants have been described but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

MTMR1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001306144.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MTMR1	NM_001306144.3	MANE Select	c.278C>A	p.Ala93Asp	missense splice_region	Exon 4 of 16	NP_001293073.1	F8WA39
MTMR1	NM_001353990.2		c.305C>A	p.Ala102Asp	missense splice_region	Exon 4 of 16	NP_001340919.1	E9PPP8
MTMR1	NM_003828.5		c.254C>A	p.Ala85Asp	missense splice_region	Exon 3 of 16	NP_003819.1	Q13613-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MTMR1	ENST00000445323.7	TSL:1 MANE Select	c.278C>A	p.Ala93Asp	missense splice_region	Exon 4 of 16	ENSP00000414178.2	F8WA39
MTMR1	ENST00000370390.7	TSL:1	c.254C>A	p.Ala85Asp	missense splice_region	Exon 3 of 16	ENSP00000359417.3	Q13613-1
MTMR1	ENST00000542156.5	TSL:1	c.254C>A	p.Ala85Asp	missense splice_region	Exon 3 of 10	ENSP00000445281.1	Q8NEC6

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

300724

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

102704

African (AFR)

AF:

0.00

AC:

AN:

8020

American (AMR)

AF:

0.00

AC:

AN:

21965

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

8026

East Asian (EAS)

AF:

0.00

AC:

AN:

12100

South Asian (SAS)

AF:

0.00

AC:

AN:

31385

European-Finnish (FIN)

AF:

0.00

AC:

AN:

21970

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1092

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

182822

Other (OTH)

AF:

0.00

AC:

AN:

13344

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.66

BayesDel_addAF

Pathogenic

0.58

BayesDel_noAF

Pathogenic

0.60

CADD

Uncertain

(source)

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.43

FATHMM_MKL

Uncertain

0.94

LIST_S2

Benign

0.70

M_CAP

Pathogenic

0.80

MetaRNN

Uncertain

0.60

MetaSVM

Uncertain

0.37

MutationAssessor

Benign

1.6

PhyloP100

4.1

PrimateAI

Uncertain

0.77

PROVEAN

Benign

-1.0

REVEL

Uncertain

0.56

Sift

Benign

0.37

Sift4G

Benign

0.19

Polyphen

0.017

Vest4

0.72

MutPred

0.39

Loss of MoRF binding (P = 0.0256)

MVP

1.0

ClinPred

0.60

GERP RS

5.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.45

gMVP

0.90

Mutation Taster

=33/67

disease causing

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Pathogenic

0.96

dbscSNV1_RF

Benign

0.72

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

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over