MTMR14

myotubularin related protein 14, the group of Myotubularins|Phosphoinositide phosphatases

Basic information

Region (hg38): 3:9649432-9702393

Previous symbols: [ "C3orf29" ]

Links

ENSG00000163719 ∙ NCBI:64419 ∙ OMIM:611089 ∙ HGNC:26190 ∙ Uniprot:Q8NCE2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal dominant centronuclear myopathy (Limited), mode of inheritance: Digenic inheritance HP:0010984

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MTMR14 gene.

• not provided (193 variants)
• Inborn genetic diseases (24 variants)
• Autosomal dominant centronuclear myopathy (6 variants)
• not specified (3 variants)
• MYOPATHY, CENTRONUCLEAR, AUTOSOMAL DOMINANT, MODIFIER OF (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTMR14 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	42	2	45
missense			94	2	1	97
nonsense		1	2			3
start loss						0
frameshift			2			2
inframe indel			3			3
splice donor/acceptor (+/-2bp)			2			2
splice region			8	6	1	15
non coding			5	25	4	34
Total	0	1	109	69	7

Variants in MTMR14

This is a list of pathogenic ClinVar variants found in the MTMR14 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-9649589-C-T			Likely benign (Jul 10, 2023)
3-9649593-G-A		not specified	Uncertain significance (Nov 09, 2021)
3-9649606-C-T			Uncertain significance (Jul 21, 2023)
3-9649607-CGCCGCT-C			Uncertain significance (Dec 01, 2023)
3-9649610-C-T			Likely benign (Jun 01, 2022)
3-9649613-T-G			Likely benign (Oct 22, 2023)
3-9649614-GCCTCGGCGGGGT-G			Uncertain significance (Sep 03, 2023)
3-9649622-G-A			Likely benign (Jul 25, 2022)
3-9649624-G-A			Uncertain significance (Jun 30, 2022)
3-9649631-G-A			Likely benign (Nov 04, 2022)
3-9649637-T-C			Likely benign (Nov 25, 2023)
3-9649641-G-T		not specified	Uncertain significance (Feb 28, 2023)
3-9649649-G-A		MTMR14-related disorder	Benign (Jan 29, 2024)
3-9649657-A-G			Uncertain significance (Aug 09, 2022)
3-9649660-A-AGCTGGGGCTTGGGGAGCT			Uncertain significance (Jan 31, 2020)
3-9649666-G-A			Uncertain significance (Feb 20, 2020)
3-9649668-C-G		not specified	Uncertain significance (Mar 01, 2024)
3-9649669-T-C			Uncertain significance (Nov 04, 2023)
3-9649675-A-T			Uncertain significance (May 21, 2022)
3-9649680-C-T			Likely benign (Nov 14, 2023)
3-9649681-TGGA-T			Uncertain significance (Oct 10, 2022)
3-9649683-G-C		not specified	Uncertain significance (Jun 18, 2021)
3-9649693-C-T			Uncertain significance (Dec 24, 2021)
3-9649715-G-T		not specified	Uncertain significance (Jun 24, 2022)
3-9649716-G-T			Uncertain significance (Dec 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTMR14	protein_coding	protein_coding	ENST00000296003	19	52961

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.36e-7	1.00	124704	1	129	124834	0.000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.298	352	368	0.956	0.0000231	4226
Missense in Polyphen		198	217.46	0.9105		2576
Synonymous	-2.18	183	149	1.23	0.00000898	1282
Loss of Function	3.08	18	38.6	0.466	0.00000210	433

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000290	0.000290
Ashkenazi Jewish	0.000894	0.000894
East Asian	0.00161	0.00156
Finnish	0.0000995	0.0000928
European (Non-Finnish)	0.000558	0.000556
Middle Eastern	0.00161	0.00156
South Asian	0.000490	0.000490
Other	0.000496	0.000494

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lipid phosphatase which efficiently dephosphorylates phosphatidylinositol 3-phosphate (PtdIns3P) and PtdIns(3,5)P2; inactive toward PtdIns4P, PtdIns(3,4)P2, PtdIns(4,5)P2 and PtdIns(3,4,5)P3. {ECO:0000269|PubMed:17008356}.
• 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: 0.113

Intolerance Scores

• loftool: 0.119
• rvis_EVS: -0.91
• rvis_percentile_EVS: 9.96

Haploinsufficiency Scores

• pHI: 0.310
• hipred: N
• hipred_score: 0.492
• ghis: 0.596

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0943

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mtmr14
• Phenotype: homeostasis/metabolism phenotype; muscle phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: mtmr14
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: phosphatidylinositol biosynthetic process;macroautophagy;peptidyl-tyrosine dephosphorylation
• Cellular component: ruffle;cytosol;perinuclear region of cytoplasm
• Molecular function: phosphatidylinositol-3-phosphatase activity;protein serine/threonine phosphatase activity;protein tyrosine phosphatase activity;protein binding;phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity