MTMR6

myotubularin related protein 6, the group of Myotubularins|Phosphoinositide phosphatases

Basic information

Region (hg38): 13:25246221-25287510

Links

ENSG00000139505 ∙ NCBI:9107 ∙ OMIM:603561 ∙ HGNC:7453 ∙ Uniprot:Q9Y217 ∙ 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 MTMR6 gene.

• Inborn genetic diseases (17 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTMR6 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						0
missense			12	5		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	5	0

Variants in MTMR6

This is a list of pathogenic ClinVar variants found in the MTMR6 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-25249320-T-C		not specified	Uncertain significance (May 10, 2022)
13-25249329-G-A		not specified	Likely benign (Apr 19, 2023)
13-25249398-G-A		not specified	Uncertain significance (Dec 26, 2023)
13-25249458-C-T		not specified	Uncertain significance (Mar 30, 2022)
13-25249479-C-T		not specified	Likely benign (Jan 06, 2023)
13-25251689-T-C		not specified	Uncertain significance (Dec 18, 2023)
13-25251878-G-A		not specified	Uncertain significance (May 25, 2022)
13-25251895-C-T		not specified	Likely benign (Jul 11, 2023)
13-25251905-C-T		not specified	Likely benign (Dec 14, 2022)
13-25251911-T-A		not specified	Uncertain significance (Aug 22, 2023)
13-25253774-C-T		not specified	Uncertain significance (Jan 21, 2022)
13-25253821-T-C		not specified	Uncertain significance (Jan 07, 2022)
13-25253852-C-G		not specified	Uncertain significance (Mar 21, 2023)
13-25253885-C-T		not specified	Uncertain significance (Jun 26, 2023)
13-25253891-A-C		not specified	Uncertain significance (Dec 26, 2023)
13-25257779-C-T		not specified	Uncertain significance (Aug 30, 2022)
13-25261685-T-C		not specified	Likely benign (Jul 26, 2021)
13-25266140-G-A		not specified	Uncertain significance (Oct 29, 2021)
13-25267822-A-C		not specified	Uncertain significance (Mar 16, 2022)
13-25267842-T-C		not specified	Uncertain significance (Jan 08, 2024)
13-25274147-T-C		not specified	Uncertain significance (Aug 04, 2021)
13-25287234-C-T		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTMR6	protein_coding	protein_coding	ENST00000381801	14	59841

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.86e-8	0.997	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.871	276	320	0.863	0.0000157	4104
Missense in Polyphen		63	110.27	0.57132		1405
Synonymous	0.910	102	114	0.892	0.00000571	1097
Loss of Function	2.70	18	35.3	0.510	0.00000185	427

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000404	0.000397
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000239	0.000237
Middle Eastern	0.0000546	0.0000544
South Asian	0.000140	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phosphatase that acts on lipids with a phosphoinositol headgroup. Acts as a negative regulator of KCNN4/KCa3.1 channel activity in CD4+ T-cells possibly by decreasing intracellular levels of phosphatidylinositol 3 phosphatase. Negatively regulates proliferation of reactivated CD4+ T-cells. {ECO:0000269|PubMed:15831468, ECO:0000269|PubMed:16847315}.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Metabolism of lipids;Metabolism;Nicotinate Nicotinamide metabolism;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.157

Intolerance Scores

• loftool: 0.247
• rvis_EVS: 0.95
• rvis_percentile_EVS: 90.09

Haploinsufficiency Scores

• pHI: 0.310
• hipred: N
• hipred_score: 0.441
• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.989

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mtmr6

Gene ontology

• Biological process: protein dephosphorylation;phosphatidylinositol biosynthetic process;peptidyl-tyrosine dephosphorylation;phosphatidylinositol dephosphorylation;potassium ion transmembrane transport
• Cellular component: nuclear envelope;cytoplasm;cytosol
• Molecular function: phosphatidylinositol-3-phosphatase activity;protein serine/threonine phosphatase activity;protein tyrosine phosphatase activity;protein binding;calcium-activated potassium channel activity;phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity;phosphatidylinositol-3,5-bisphosphate phosphatase activity