MTMR4

myotubularin related protein 4, the group of Zinc fingers FYVE-type|Myotubularins|Phosphoinositide phosphatases

Basic information

Region (hg38): 17:58489529-58517905

Links

ENSG00000108389 ∙ NCBI:9110 ∙ OMIM:603559 ∙ HGNC:7452 ∙ Uniprot:Q9NYA4 ∙ 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 MTMR4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTMR4 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					3	3
missense			48	3		51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	3	3

Variants in MTMR4

This is a list of pathogenic ClinVar variants found in the MTMR4 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-58492593-G-A		not specified	Uncertain significance (Jun 24, 2022)
17-58492898-T-C		not specified	Uncertain significance (Jan 31, 2024)
17-58492916-C-T		not specified	Uncertain significance (May 25, 2022)
17-58494951-A-G		not specified	Uncertain significance (Jan 03, 2024)
17-58494984-C-T		not specified	Uncertain significance (Apr 07, 2022)
17-58495011-C-T		not specified	Uncertain significance (Sep 29, 2022)
17-58495012-G-A		not specified	Uncertain significance (Jan 23, 2024)
17-58495020-C-T		not specified	Uncertain significance (May 16, 2023)
17-58495063-G-T		not specified	Uncertain significance (Mar 25, 2024)
17-58495103-T-A			Benign (Aug 15, 2018)
17-58495106-A-C		not specified	Uncertain significance (Oct 18, 2021)
17-58495156-C-T		not specified	Uncertain significance (Jun 12, 2023)
17-58495173-A-T		not specified	Uncertain significance (Oct 20, 2023)
17-58495245-C-T		not specified	Uncertain significance (May 31, 2023)
17-58495252-A-G		not specified	Uncertain significance (May 26, 2024)
17-58495314-C-T		not specified	Uncertain significance (Aug 13, 2021)
17-58495384-C-A		not specified	Uncertain significance (Dec 22, 2023)
17-58495454-C-G		not specified	Uncertain significance (Jul 11, 2023)
17-58495482-A-C		not specified	Uncertain significance (Feb 16, 2023)
17-58495488-A-G		not specified	Uncertain significance (Nov 10, 2022)
17-58495491-G-A		not specified	Uncertain significance (Aug 10, 2021)
17-58495629-G-A		not specified	Uncertain significance (May 07, 2024)
17-58495645-G-A		not specified	Uncertain significance (Jul 14, 2023)
17-58495665-A-G		not specified	Likely benign (Aug 10, 2021)
17-58495683-G-A		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTMR4	protein_coding	protein_coding	ENST00000323456	18	28369

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000407	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.49	424	680	0.623	0.0000390	7877
Missense in Polyphen		139	323.85	0.42921		3580
Synonymous	0.730	246	261	0.943	0.0000145	2339
Loss of Function	6.06	8	57.7	0.139	0.00000314	632

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000307	0.000307
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dephosphorylates proteins phosphorylated on Ser, Thr, and Tyr residues and low molecular weight phosphatase substrate para-nitrophenylphosphate. Phosphorylates phosphatidylinositol 3,4,5-trisphosphate (PIP3). {ECO:0000269|PubMed:11302699}.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Signal Transduction;Metabolism of lipids;Metabolism;Synthesis of PIPs at the early endosome membrane;Synthesis of PIPs at the late endosome membrane;PI Metabolism;Phospholipid metabolism;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;Downregulation of TGF-beta receptor signaling;TGF-beta receptor signaling activates SMADs (Consensus)

Intolerance Scores

• loftool: 0.0342
• rvis_EVS: -0.55
• rvis_percentile_EVS: 19.93

Haploinsufficiency Scores

• pHI: 0.586
• hipred: Y
• hipred_score: 0.575
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.926

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Mtmr4
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: protein dephosphorylation;phosphatidylinositol biosynthetic process;transforming growth factor beta receptor signaling pathway;response to denervation involved in regulation of muscle adaptation;negative regulation of transforming growth factor beta receptor signaling pathway;peptidyl-tyrosine dephosphorylation;regulation of phosphatidylinositol dephosphorylation
• Cellular component: extracellular space;endosome;cytosol;early endosome 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