PTPMT1

protein tyrosine phosphatase mitochondrial 1, the group of Phosphoinositide phosphatases|Atypical dual specificity phosphatases

Basic information

Region (hg38): 11:47565430-47573461

Links

ENSG00000110536

∙ NCBI:114971 ∙ OMIM:609538 ∙ HGNC:26965 ∙ Uniprot:Q8WUK0 ∙ 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 PTPMT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPMT1 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			8 clinvar	1 clinvar		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			6 clinvar			6
Total	0	0	14	1	0

Variants in PTPMT1

This is a list of pathogenic ClinVar variants found in the PTPMT1 region.

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

Position	Phenotype	Significance	ClinVar
11-47565644-G-C	not specified	Uncertain significance (Jun 22, 2023)	2599822
11-47565953-G-C	not specified	Uncertain significance (Dec 27, 2023)	3149054
11-47569721-G-A	not specified	Uncertain significance (Nov 30, 2021)	2211762
11-47569730-C-T	not specified	Uncertain significance (Jul 08, 2022)	2372688
11-47569851-G-A	not specified	Uncertain significance (May 30, 2022)	2293070
11-47571486-C-A	not specified	Uncertain significance (Feb 13, 2024)	3149055
11-47571510-G-A	not specified	Likely benign (Jan 26, 2022)	2360508
11-47571585-G-A	not specified	Uncertain significance (Oct 29, 2021)	2257912
11-47571588-C-T	not specified	Uncertain significance (Jan 09, 2024)	3149056
11-47571628-G-C		Benign (Aug 22, 2018)	720436
11-47573018-G-A	not specified	Uncertain significance (Oct 17, 2023)	3112970
11-47573102-G-C	not specified	Uncertain significance (Aug 22, 2022)	2308799
11-47573163-C-A	not specified	Uncertain significance (Jul 27, 2021)	2396111
11-47573243-T-G	not specified	Uncertain significance (Apr 19, 2023)	2538772
11-47573329-C-A	not specified	Uncertain significance (Aug 12, 2021)	2394727
11-47573355-C-T	not specified	Uncertain significance (Apr 20, 2023)	2539391

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPMT1	protein_coding	protein_coding	ENST00000326674	4	8032

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0127	0.868	124775	0	14	124789	0.0000561

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.489	94	108	0.868	0.00000573	1264
Missense in Polyphen		43	50.455	0.85225		551
Synonymous	-0.400	50	46.5	1.07	0.00000233	427
Loss of Function	1.28	4	7.89	0.507	3.38e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000179	0.000179
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000470	0.0000464
European (Non-Finnish)	0.0000532	0.0000530
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Lipid phosphatase which dephosphorylates phosphatidylglycerophosphate (PGP) to phosphatidylglycerol (PG) (By similarity). PGP is an essential intermediate in the biosynthetic pathway of cardiolipin, a mitochondrial-specific phospholipid regulating the membrane integrity and activities of the organelle (By similarity). Has also been shown to display phosphatase activity toward phosphoprotein substrates, specifically mediates dephosphorylation of mitochondrial proteins, thereby playing an essential role in ATP production (By similarity). Has probably a preference for proteins phosphorylated on Ser and/or Thr residues compared to proteins phosphorylated on Tyr residues (By similarity). Probably involved in regulation of insulin secretion in pancreatic beta cells (By similarity). May prevent intrinsic apoptosis, probably by regulating mitochondrial membrane integrity (PubMed:24709986). {ECO:0000250|UniProtKB:P0C089, ECO:0000250|UniProtKB:Q66GT5, ECO:0000269|PubMed:24709986}.;
Pathway: Inositol Metabolism;Phospholipid Biosynthesis;Metabolism of lipids;cardiolipin biosynthesis;Metabolism;Phosphatidylinositol phosphate metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PG (Consensus)

Recessive Scores

pRec: 0.124

Haploinsufficiency Scores

pHI: 0.201
hipred: N
hipred_score: 0.291
ghis: 0.414

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.653

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ptpmt1
Phenotype: immune system phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype; hematopoietic system phenotype; cellular phenotype; endocrine/exocrine gland phenotype;

Zebrafish Information Network

Gene name: ptpmt1
Affected structure: skeletal muscle
Phenotype tag: abnormal
Phenotype quality: disorganized

Gene ontology

Biological process: cardiolipin biosynthetic process;peptidyl-tyrosine dephosphorylation;regulation of intrinsic apoptotic signaling pathway
Cellular component: nucleus;mitochondrial inner membrane
Molecular function: phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity;protein tyrosine phosphatase activity;protein binding;protein tyrosine/serine/threonine phosphatase activity;phosphatidylglycerophosphatase activity