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.

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.

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	1
missense			41	2	1	44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	2	2

Variants in MTMR12

This is a list of pathogenic ClinVar variants found in the MTMR12 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-32229798-C-T		not specified	Uncertain significance (Dec 20, 2023)
5-32229807-C-A		not specified	Uncertain significance (Sep 20, 2023)
5-32229825-C-T		not specified	Uncertain significance (Jun 13, 2024)
5-32229843-C-T		not specified	Uncertain significance (Aug 10, 2024)
5-32229849-A-G		not specified	Uncertain significance (Mar 15, 2024)
5-32229867-C-T		not specified	Uncertain significance (Jan 17, 2025)
5-32229878-G-C		not specified	Uncertain significance (Nov 08, 2024)
5-32229893-A-G		not specified	Uncertain significance (Sep 15, 2021)
5-32229924-C-T		not specified	Uncertain significance (Apr 16, 2024)
5-32229947-G-C		not specified	Uncertain significance (May 08, 2023)
5-32230027-C-G		not specified	Uncertain significance (Dec 02, 2024)
5-32230169-C-G		not specified	Uncertain significance (Mar 19, 2024)
5-32230196-A-G			Benign (Dec 31, 2019)
5-32230269-G-T		not specified	Uncertain significance (Dec 06, 2021)
5-32233778-A-G		not specified	Uncertain significance (Jun 17, 2022)
5-32233780-C-T		not specified	Likely benign (Apr 25, 2022)
5-32233781-G-A		not specified	Uncertain significance (Feb 20, 2025)
5-32233846-G-C		not specified	Uncertain significance (Jul 25, 2023)
5-32233858-G-A		not specified	Uncertain significance (Aug 12, 2024)
5-32233933-C-T		not specified	Uncertain significance (Jun 06, 2023)
5-32234970-T-C		not specified	Uncertain significance (Feb 19, 2025)
5-32235002-G-A		not specified	Uncertain significance (Jan 29, 2025)
5-32235002-G-T		not specified	Uncertain significance (Dec 20, 2023)
5-32235018-T-C		not specified	Uncertain significance (Jun 23, 2021)
5-32235026-C-T		not specified	Uncertain significance (Jul 10, 2024)

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