PTPRZ1

protein-coding

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

Gene summary

This gene encodes a member of the receptor protein tyrosine phosphatase family. Expression of this gene is restricted to the central nervous system (CNS), and it may be involved in the regulation of specific developmental processes in the CNS. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, May 2011]

Previous symbols:

PTPZ
PTPRZ

MANE transcript

NM_002851.3

Inheritance

—

ClinVar variants

U:297B:21

Top phenotype

High myopia

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr7:121,873,089-122,062,036

External References & Databases

Ensembl (ENSG00000106278)

Transcript & Mutation Effects

hg38 • Region Span ~188.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PTPRZ1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 286

not providedTotal: 18

High myopiaTotal: 1

Spastic paraparesisTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002851.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	4 clinvar	4 clinvar	10
missense			286 clinvar	11 clinvar	2 clinvar	299
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	297	15	6	318

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 42 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002851.3	RefSeq	NP_002842.2	30	MANE Select
ENST00000393386.7	Ensembl	ENSP00000377047.2	30	MANE Select
NM_001206838.2	RefSeq	NP_001193767.1	30	Standard
NM_001206839.2	RefSeq	NP_001193768.1	29	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human)
Spinal Cord Injury
VEGFA-VEGFR2 Signaling Pathway
Other interleukin signaling
Signaling by Interleukins

Biological Process

hematopoietic progenitor cell differentiation
protein dephosphorylation
axonogenesis
central nervous system development
learning or memory

Molecular Function

protein tyrosine phosphatase activity
transmembrane receptor protein tyrosine phosphatase activity
protein binding

Cellular Component

plasma membrane
integral component of plasma membrane
intrinsic component of plasma membrane
synapse
perineuronal net

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000393386
Coding exons: 30
Length: 188948
Individuals with no LoFs: 125734
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125748
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.853	1103	1.19e+3	0.930	0.0000578	15222
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.000080	0.000079	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.274

Intolerance Scores

LoFtool: 0.535
RVIS EVS: -2.22
RVIS percentile EVS: 1.35

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.584

Gene Damage Prediction

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