PTPRZ1

protein tyrosine phosphatase receptor type Z1, the group of Fibronectin type III domain containing|Protein tyrosine phosphatases receptor type

Basic information

Region (hg38): 7:121873089-122062036

Previous symbols: [ "PTPZ", "PTPRZ" ]

Links

ENSG00000106278 ∙ NCBI:5803 ∙ OMIM:176891 ∙ HGNC:9685 ∙ Uniprot:P23471 ∙ 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 PTPRZ1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPRZ1 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				3	4	7
missense			98	6	2	106
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	0	0	99	10	6

Variants in PTPRZ1

This is a list of pathogenic ClinVar variants found in the PTPRZ1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-121968054-T-A		not specified	Uncertain significance (Jun 05, 2024)
7-121968055-C-A		not specified	Uncertain significance (May 02, 2024)
7-121968055-C-T		not specified	Uncertain significance (Jul 16, 2021)
7-121968064-C-A		not specified	Uncertain significance (Dec 02, 2022)
7-121972594-G-A		not specified	Uncertain significance (Oct 26, 2022)
7-121972670-A-C		not specified	Uncertain significance (Aug 20, 2024)
7-121976195-C-T		not specified	Uncertain significance (Oct 02, 2023)
7-121976220-A-C		not specified	Uncertain significance (Feb 21, 2024)
7-121976266-G-A		not specified	Uncertain significance (Mar 06, 2023)
7-121976277-T-C			Likely benign (Dec 31, 2019)
7-121976791-A-G		not specified	Uncertain significance (Jun 26, 2024)
7-121976833-G-A		not specified	Uncertain significance (Dec 03, 2021)
7-121983708-G-T			Uncertain significance (-)
7-121984017-G-A		not specified	Uncertain significance (Feb 22, 2023)
7-121984068-T-C			Benign (Nov 26, 2018)
7-121996396-C-G		not specified	Uncertain significance (Apr 18, 2023)
7-121996478-T-C		not specified	Uncertain significance (Oct 10, 2023)
7-121996492-G-A		not specified	Uncertain significance (Sep 14, 2023)
7-121996535-A-G		not specified	Uncertain significance (Oct 05, 2021)
7-121996551-T-C			Likely benign (Apr 06, 2018)
7-121997893-A-G		not specified	Uncertain significance (Feb 05, 2024)
7-121997985-G-A		not specified	Uncertain significance (Feb 22, 2023)
7-121997991-C-A		not specified	Uncertain significance (Jul 09, 2024)
7-122004612-AGAACTT-A		Spastic paraparesis	Uncertain significance (Jan 19, 2018)
7-122004617-T-A		not specified	Uncertain significance (May 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPRZ1	protein_coding	protein_coding	ENST00000393386	30	188948

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.990	0.0100	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.853	1103	1.19e+3	0.930	0.0000578	15222
Missense in Polyphen		224	305.24	0.73384		4004
Synonymous	1.05	417	445	0.937	0.0000235	4534
Loss of Function	7.22	18	93.2	0.193	0.00000442	1227

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.00	0.00
Finnish	0.0000930	0.0000924
European (Non-Finnish)	0.0000798	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein tyrosine phosphatase that negatively regulates oligodendrocyte precursor proliferation in the embryonic spinal cord. Required for normal differentiation of the precursor cells into mature, fully myelinating oligodendrocytes. May play a role in protecting oligondendrocytes against apoptosis. May play a role in the establishment of contextual memory, probably via the dephosphorylation of proteins that are part of important signaling cascades (By similarity). {ECO:0000250}.
• Pathway: Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human);Spinal Cord Injury;VEGFA-VEGFR2 Signaling Pathway;Other interleukin signaling;Signaling by Interleukins;Cytokine Signaling in Immune system;Immune System (Consensus)

Recessive Scores

• pRec: 0.274

Intolerance Scores

• loftool: 0.535
• rvis_EVS: -2.22
• rvis_percentile_EVS: 1.35

Haploinsufficiency Scores

• pHI: 0.418
• hipred: Y
• hipred_score: 0.651
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.584

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Ptprz1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: hematopoietic progenitor cell differentiation;protein dephosphorylation;axonogenesis;central nervous system development;learning or memory;cytokine-mediated signaling pathway;peptidyl-tyrosine dephosphorylation;oligodendrocyte differentiation;regulation of oligodendrocyte progenitor proliferation
• Cellular component: plasma membrane;integral component of plasma membrane;intrinsic component of plasma membrane;synapse;perineuronal net
• Molecular function: protein tyrosine phosphatase activity;transmembrane receptor protein tyrosine phosphatase activity;protein binding