MTMR1

myotubularin related protein 1, the group of Myotubularins|Phosphoinositide phosphatases

Basic information

Region (hg38): X:150692971-150765108

Links

ENSG00000063601NCBI:8776OMIM:300171HGNC:7449Uniprot:Q13613AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MTMR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTMR1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
2
clinvar
1
clinvar
3
missense
25
clinvar
1
clinvar
26
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
9
clinvar
9
Total 0 0 25 3 10

Variants in MTMR1

This is a list of pathogenic ClinVar variants found in the MTMR1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
X-150693550-C-A not specified Uncertain significance (Aug 02, 2021)2377371
X-150693570-G-A not specified Uncertain significance (Oct 12, 2021)2205657
X-150693582-C-G not specified Uncertain significance (Apr 19, 2024)3296662
X-150693596-G-C Likely benign (Sep 01, 2022)2661635
X-150693651-C-A not specified Uncertain significance (Dec 27, 2022)2339655
X-150693741-A-C Benign (Jun 19, 2021)1257576
X-150698971-CTTTG-C Benign (Jun 20, 2021)1233021
X-150699265-T-A not specified Uncertain significance (Aug 10, 2021)2352598
X-150718584-C-T Benign (Jun 19, 2021)1231508
X-150718626-C-G not specified Uncertain significance (Aug 16, 2022)2307445
X-150718858-C-T Benign (Nov 12, 2018)1181836
X-150727244-A-T not specified Uncertain significance (Apr 06, 2022)2281308
X-150727547-G-A Benign (Nov 12, 2018)1279285
X-150727727-G-A not specified Uncertain significance (Jul 19, 2022)2302155
X-150730140-A-G not specified Uncertain significance (Dec 14, 2021)2267411
X-150730534-G-T not specified Uncertain significance (Feb 27, 2023)2489146
X-150730566-T-A not specified Uncertain significance (Dec 28, 2022)2340021
X-150730573-A-C not specified Uncertain significance (Dec 28, 2023)3215704
X-150731555-C-T not specified Uncertain significance (May 14, 2024)3296665
X-150731569-G-T not specified Uncertain significance (Jan 08, 2024)3215709
X-150731603-C-T not specified Uncertain significance (Mar 06, 2023)2454774
X-150731781-A-G Benign (Jun 19, 2021)1232751
X-150731903-T-G Benign (Nov 12, 2018)1252234
X-150732542-G-C not specified Uncertain significance (May 17, 2023)2518161
X-150732620-C-T not specified Uncertain significance (Jun 29, 2023)2601650

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
MTMR1protein_codingprotein_codingENST00000544228 1572142
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9980.00240123989021239910.00000807
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.021502380.6310.00001894364
Missense in Polyphen2364.0830.358911054
Synonymous0.005869494.10.9990.000008051280
Loss of Function4.41226.50.07550.00000223420

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00006280.0000462
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.00005660.0000345
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Lipid phosphatase that has high specificity for phosphatidylinositol 3-phosphate and has no activity with phosphatidylinositol 4-phosphate, phosphatidylinositol (4,5)- bisphosphate and phosphatidylinositol (3,4,5)-trisphosphate (PubMed:11733541, PubMed:27018598). Activity with phosphatidylinositol (3,5)-bisphosphate is controversial; it has been shown by PubMed:27018598, while PubMed:11733541 find no activity with this substrate. {ECO:0000269|PubMed:11733541, ECO:0000269|PubMed:27018598}.;
Pathway
Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Metabolism of lipids;Metabolism;Nicotinate Nicotinamide metabolism;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism (Consensus)

Recessive Scores

pRec
0.176

Intolerance Scores

loftool
0.175
rvis_EVS
-0.09
rvis_percentile_EVS
46.74

Haploinsufficiency Scores

pHI
0.400
hipred
Y
hipred_score
0.696
ghis
0.520

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.469

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Mtmr1
Phenotype
normal phenotype;

Gene ontology

Biological process
phosphatidylinositol biosynthetic process;peptidyl-tyrosine dephosphorylation;phosphatidylinositol dephosphorylation;regulation of phosphatidylinositol dephosphorylation
Cellular component
cytoplasm;cytosol;plasma membrane
Molecular function
phosphatidylinositol-3-phosphatase activity;protein tyrosine phosphatase activity;protein homodimerization activity;phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity