MTMR3

myotubularin related protein 3, the group of Myotubularins|Phosphoinositide phosphatases|MicroRNA protein coding host genes|Zinc fingers FYVE-type

Basic information

Region (hg38): 22:29883169-30030868

Links

ENSG00000100330

∙ NCBI:8897 ∙ OMIM:603558 ∙ HGNC:7451 ∙ Uniprot:Q13615 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MTMR3 gene.

not_specified (131 variants)
not_provided (2 variants)
Myopathy,_proximal,_and_ophthalmoplegia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTMR3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021090.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			128 clinvar	3 clinvar		131
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	128	5	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTMR3	protein_coding	protein_coding	ENST00000401950	18	147712

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000627	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.00	524	669	0.783	0.0000373	7858
Missense in Polyphen		198	320.55	0.6177		3761
Synonymous	0.0182	253	253	0.999	0.0000144	2335
Loss of Function	6.17	9	61.0	0.148	0.00000336	656

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000146	0.000146
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000571	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.0000571	0.0000544
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Phosphatase that acts on lipids with a phosphoinositol headgroup. Has phosphatase activity towards phosphatidylinositol 3-phosphate and phosphatidylinositol 3,5-bisphosphate. May also dephosphorylate proteins phosphorylated on Ser, Thr, and Tyr residues (PubMed:10733931). {ECO:0000269|PubMed:10733931, ECO:0000269|PubMed:11676921}.;
Pathway: Inositol phosphate metabolism - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Metabolism of lipids;3-phosphoinositide degradation;Metabolism;D-<i>myo</i>-inositol-5-phosphate metabolism;superpathway of inositol phosphate compounds;Macroautophagy;Cellular responses to external stimuli;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism (Consensus)

Recessive Scores

pRec: 0.120

Intolerance Scores

loftool: 0.0122
rvis_EVS: -0.9
rvis_percentile_EVS: 10.16

Haploinsufficiency Scores

pHI: 0.241
hipred: Y
hipred_score: 0.553
ghis: 0.566

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: K
gene_indispensability_pred: N
gene_indispensability_score: 0.102

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Mtmr3
Phenotype: homeostasis/metabolism phenotype;

Gene ontology

Biological process: protein dephosphorylation;phosphatidylinositol biosynthetic process;macroautophagy;peptidyl-tyrosine dephosphorylation;cellular response to glucose starvation;phosphatidylinositol dephosphorylation;regulation of phosphatidylinositol dephosphorylation;phosphatidylinositol 5-phosphate metabolic process;regulation of autophagosome assembly
Cellular component: cytoplasm;cytosol;membrane;extrinsic component of membrane
Molecular function: phosphatidylinositol-3-phosphatase activity;protein serine/threonine phosphatase activity;protein tyrosine phosphatase activity;protein binding;protein phosphatase binding;metal ion binding;phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity