PTPMT1

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

Basic information

Region (hg38): 11:47565429-47573461

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.

• Inborn genetic diseases (11 variants)
• not provided (1 variants)

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			5	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5			5
Total	0	0	10	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	Type	Phenotype	Significance	ClinVar
11-47565644-G-C		not specified	Uncertain significance (Jun 22, 2023)
11-47565953-G-C		not specified	Uncertain significance (Dec 27, 2023)
11-47569721-G-A		not specified	Uncertain significance (Nov 30, 2021)
11-47569730-C-T		not specified	Uncertain significance (Jul 08, 2022)
11-47569851-G-A		not specified	Uncertain significance (May 30, 2022)
11-47571486-C-A		not specified	Uncertain significance (Feb 13, 2024)
11-47571510-G-A		not specified	Likely benign (Jan 26, 2022)
11-47571585-G-A		not specified	Uncertain significance (Oct 29, 2021)
11-47571588-C-T		not specified	Uncertain significance (Jan 09, 2024)
11-47571628-G-C			Benign (Aug 22, 2018)
11-47573018-G-A		not specified	Uncertain significance (Oct 17, 2023)
11-47573102-G-C		not specified	Uncertain significance (Aug 22, 2022)
11-47573163-C-A		not specified	Uncertain significance (Jul 27, 2021)
11-47573243-T-G		not specified	Uncertain significance (Apr 19, 2023)
11-47573329-C-A		not specified	Uncertain significance (Aug 12, 2021)
11-47573355-C-T		not specified	Uncertain significance (Apr 20, 2023)

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