MTMR12

myotubularin related protein 12, the group of Myotubularins

Basic information

Region (hg38): 5:32226994-32312987

Previous symbols: [ "PIP3AP" ]

Links

ENSG00000150712 ∙ NCBI:54545 ∙ OMIM:606501 ∙ HGNC:18191 ∙ Uniprot:Q9C0I1 ∙ 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 MTMR12 gene.

• not_specified (67 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTMR12 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001040446.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			65	2	1	68
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	65	2	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTMR12	protein_coding	protein_coding	ENST00000382142	16	86016

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00362	125720	0	26	125746	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.30	268	397	0.676	0.0000206	4953
Missense in Polyphen		66	122.25	0.53988		1550
Synonymous	1.13	134	152	0.883	0.00000837	1354
Loss of Function	5.23	6	43.0	0.139	0.00000224	488

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000673	0.000673
Ashkenazi Jewish	0.000202	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000624	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000656	0.0000653
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalytically inactive phosphatase that plays a role as an adapter for the phosphatase myotubularin to regulate myotubularin intracellular location. {ECO:0000269|PubMed:11504939, ECO:0000269|PubMed:12847286}.
• Pathway: Metabolism of lipids;Metabolism;Synthesis of PIPs at the early endosome membrane;PI Metabolism;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.112
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.57

Haploinsufficiency Scores

• pHI: 0.188
• hipred: Y
• hipred_score: 0.688
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.333

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mtmr12
• 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); vision/eye phenotype

Zebrafish Information Network

• Gene name: mtmr12
• Affected structure: muscle cell
• Phenotype tag: abnormal
• Phenotype quality: displaced to

Gene ontology

• Biological process: phosphatidylinositol biosynthetic process;regulation of catalytic activity;toxin transport
• Cellular component: cytoplasm;cytosol
• Molecular function: protein binding;phosphatase regulator activity