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.

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.

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				1		1
missense			54	1		55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					1	1
Total	0	0	54	2	1

Variants in MTMR3

This is a list of pathogenic ClinVar variants found in the MTMR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-29978987-G-A		not specified	Uncertain significance (Feb 21, 2024)
22-29979012-A-G		not specified	Uncertain significance (Apr 11, 2023)
22-29979047-G-C		not specified	Uncertain significance (Oct 06, 2022)
22-29991557-A-G		not specified	Uncertain significance (Jun 17, 2024)
22-29991559-G-C		not specified	Uncertain significance (Nov 22, 2022)
22-30007207-G-T		not specified	Uncertain significance (Sep 01, 2021)
22-30007233-A-G		not specified	Uncertain significance (Feb 16, 2023)
22-30007239-G-T		not specified	Uncertain significance (Jan 26, 2022)
22-30007242-C-T		not specified	Uncertain significance (Jan 16, 2024)
22-30007267-G-T		not specified	Uncertain significance (Jun 29, 2022)
22-30007290-A-G		not specified	Uncertain significance (Apr 08, 2024)
22-30007315-G-T		not specified	Uncertain significance (Feb 16, 2023)
22-30007318-C-T			Likely benign (Feb 01, 2023)
22-30007949-C-T		not specified	Uncertain significance (Jul 12, 2023)
22-30007952-A-G		not specified	Uncertain significance (Jun 11, 2021)
22-30013528-A-G		not specified	Uncertain significance (Jan 23, 2024)
22-30016534-C-T			Likely benign (Feb 01, 2023)
22-30016646-G-A		not specified	Uncertain significance (Feb 12, 2024)
22-30017981-C-G		not specified	Uncertain significance (Jun 17, 2024)
22-30017999-A-G		not specified	Uncertain significance (Sep 29, 2023)
22-30018065-C-G		not specified	Uncertain significance (Mar 19, 2024)
22-30018071-C-T		Myopathy, proximal, and ophthalmoplegia	Uncertain significance (Dec 17, 2024)
22-30019542-C-T		not specified	Uncertain significance (Feb 28, 2023)
22-30019582-G-T		not specified	Uncertain significance (May 08, 2023)
22-30019592-C-T		not specified	Uncertain significance (Aug 30, 2021)

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