rs782703141

Variant names:

• chrX-150718626-C-A
• rs782703141
• NM_001306144.3:c.278C>A

Your query was ambiguous. Multiple possible variants found:

• chrX-150718626-C-A
• chrX-150718626-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 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

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTMR1	NM_001306144.3	c.278C>A	p.Ala93Asp	missense_variant, splice_region_variant	Exon 4 of 16	ENST00000445323.7	NP_001293073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTMR1	ENST00000445323.7	c.278C>A	p.Ala93Asp	missense_variant, splice_region_variant	Exon 4 of 16	1	NM_001306144.3	ENSP00000414178.2

Frequencies

GnomAD3 genomes Cov.: 13

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 300724 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 102704

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 13

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.66
BayesDel_addAF	Pathogenic	0.58	D
BayesDel_noAF	Pathogenic	0.60
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.43	T;.;.;T;T;T
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Benign	0.70	T;T;T;T;T;T
M_CAP	Pathogenic	0.80	D
MetaRNN	Uncertain	0.60	D;D;D;D;D;D
MetaSVM	Uncertain	0.37	D
MutationAssessor	Benign	1.6	L;.;.;.;.;.
PrimateAI	Uncertain	0.77	T
PROVEAN	Benign	-1.0	N;N;N;N;N;N
REVEL	Uncertain	0.56
Sift	Benign	0.37	T;D;D;D;D;D
Sift4G	Benign	0.19	T;D;T;T;D;D
Polyphen		0.017	B;.;D;B;.;.
Vest4		0.72
MutPred		0.39		.;.;.;Loss of MoRF binding (P = 0.0256);.;.;
MVP		1.0
ClinPred		0.60	D
GERP RS		5.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.45
gMVP		0.90

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

LitVar

Other links and lift over

dbSNP: rs782703141; hg19: chrX-149887098; COSMIC: COSV100954008; COSMIC: COSV100954008;