MTMR6

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

Basic information

Region (hg38): 13:25246222-25287510

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.

not_specified (73 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. These statistics are base on transcript: NM_000004685.5. 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						0
missense			67 clinvar	6 clinvar		73
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	67	6	0

Loading clinvar variants...

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
Phenotype

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