PTPRT

protein-coding

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

Gene summary

The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP possesses an extracellular region, a single transmembrane region, and two tandem intracellular catalytic domains, and thus represents a receptor-type PTP. The extracellular region contains a meprin-A5 antigen-PTP (MAM) domain, Ig-like and fibronectin type III-like repeats. The protein domain structure and the expression pattern of the mouse counterpart of this PTP suggest its roles in both signal transduction and cellular adhesion in the central nervous system. Two alternatively spliced transcript variants of this gene, which encode distinct proteins, have been reported. [provided by RefSeq, Jul 2008]

MANE transcript

NM_007050.6

Inheritance

—

ClinVar variants

P:1U:179B:47

Top phenotype

PTPRT-related disorder

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr20:42,072,752-43,189,970

External References & Databases

Ensembl (ENSG00000196090)

Transcript & Mutation Effects

hg38 • Region Span ~1,117.2 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 PTPRT variants in ClinVar

9 Conditions Cataloged

not specifiedTotal: 155

PTPRT-related disorderTotal: 47

not providedTotal: 44

Abnormal brain morphologyTotal: 2

PTPRT-associated neurodevelopmental disorderTotal: 1

Abnormality of neuronal migrationTotal: 1

Autism spectrum disorderTotal: 1

PTPRT-associated neurodevelopmentaldisorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007050.6. 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			3 clinvar	18 clinvar	19 clinvar	40
missense		1 clinvar	163 clinvar	6 clinvar	4 clinvar	174
nonsense			6 clinvar			6
start loss						0
frameshift			5 clinvar			5
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	1	179	24	23	227

Highest pathogenic variant AF is 0.0000024902197

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007050.6	RefSeq	NP_008981.4	31	MANE Select
ENST00000373187.6	Ensembl	ENSP00000362283.1	31	MANE Select
NM_001394024.1	RefSeq	NP_001380953.1	32	Standard
NM_001394025.1	RefSeq	NP_001380954.1	31	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein dephosphorylation
cell adhesion
homophilic cell adhesion via plasma membrane adhesion molecules
signal transduction
transmembrane receptor protein tyrosine kinase signaling pathway

Molecular Function

protein tyrosine phosphatase activity
transmembrane receptor protein tyrosine phosphatase activity
protein binding
beta-catenin binding
protein phosphatase binding

Cellular Component

plasma membrane
integral component of plasma membrane
cell surface
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373187
Coding exons: 31
Length: 1117219
Individuals with no LoFs: 124791
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 124802
p: 0.0000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.14	612	873	0.701	0.0000539	9387
Missense (PolyPhen)		213	381.02	0.55902		4044
Synonymous	-0.355	353	345	1.02	0.0000225	2827
Loss of Function	7.48	8	80.3	0.0996	0.00000460	816

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000030	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000059	0.000056	rare
Finnish	0.000093	0.000093	rare
European (Non-Finnish)	0.000055	0.000053	rare
South Asian	0	0.0	absent
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in both signal transduction and cellular adhesion in the CNS.;

Recessive Scores

pRec: 0.110

Intolerance Scores

LoFtool: 0.0898
RVIS EVS: -1.03
RVIS percentile EVS: 7.87

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.268

Gene Damage Prediction

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