MTMR7

myotubularin related protein 7, the group of Myotubularins|Phosphoinositide phosphatases

Basic information

Region (hg38): 8:17296794-17413528

Links

ENSG00000003987NCBI:9108OMIM:603562HGNC:7454Uniprot:Q9Y216AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MTMR7 gene.

  • not_specified (120 variants)
  • MTMR7-related_disorder (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTMR7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004686.5. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
119
clinvar
4
clinvar
123
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 119 5 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
MTMR7protein_codingprotein_codingENST00000180173 14115499
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.21e-140.5971256851621257480.000251
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.614653771.230.00002134378
Missense in Polyphen1681601.051916
Synonymous-2.711791381.290.000007971201
Loss of Function1.642737.90.7120.00000213419

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003880.000388
Ashkenazi Jewish0.000.00
East Asian0.0002190.000217
Finnish0.0006970.000647
European (Non-Finnish)0.0002820.000281
Middle Eastern0.0002190.000217
South Asian0.00006530.0000653
Other0.0001650.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Phosphatase that acts on lipids with a phosphoinositol headgroup. {ECO:0000305}.;
Pathway
Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Metabolism of lipids;Metabolism;Inositol phosphate metabolism;Synthesis of PIPs at the late endosome membrane;PI Metabolism;Phospholipid metabolism;Synthesis of IP2, IP, and Ins in the cytosol (Consensus)

Recessive Scores

pRec
0.121

Intolerance Scores

loftool
0.171
rvis_EVS
-1.13
rvis_percentile_EVS
6.56

Haploinsufficiency Scores

pHI
0.181
hipred
N
hipred_score
0.445
ghis
0.591

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.404

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Mtmr7
Phenotype

Gene ontology

Biological process
protein dephosphorylation;phosphatidylinositol biosynthetic process;peptidyl-tyrosine dephosphorylation;inositol phosphate dephosphorylation;phosphatidylinositol dephosphorylation
Cellular component
cytoplasm;cytosol;membrane
Molecular function
phosphatidylinositol-3-phosphatase activity;protein tyrosine phosphatase activity;protein binding;phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity