PTPRD

protein tyrosine phosphatase receptor type D, the group of Fibronectin type III domain containing|I-set domain containing|Protein tyrosine phosphatases receptor type

Basic information

Region (hg38): 9:8314245-10613002

Links

ENSG00000153707 ∙ NCBI:5789 ∙ OMIM:601598 ∙ HGNC:9668 ∙ Uniprot:P23468 ∙ 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 PTPRD gene.

• Inborn genetic diseases (58 variants)
• not provided (37 variants)
• not specified (2 variants)
• Intellectual disability (1 variants)
• PTPRD-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPRD 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				14	8	22
missense			60	1	4	65
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	5	2	8
non coding				1	3	4
Total	0	0	60	16	15

Variants in PTPRD

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

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

Position	Type	Phenotype	Significance	ClinVar
9-8317921-G-A		Malignant tumor of prostate	Uncertain significance (-)
9-8319833-C-G		not specified	Uncertain significance (Aug 08, 2023)
9-8319890-C-G		not specified	Uncertain significance (Aug 21, 2023)
9-8319964-G-A		not specified	Uncertain significance (Jun 03, 2022)
9-8331548-C-T			Benign (Mar 29, 2019)
9-8331574-A-AAACTTACCATTCTTGAACTGT			Likely benign (Jun 23, 2021)
9-8331574-A-AAACTTACCATTCTTGAACTGTAACT		not specified	Benign (Apr 03, 2015)
9-8331574-A-AAACTTACCCTTCTTGAACTGTAACT		not specified	Uncertain significance (Oct 31, 2013)
9-8331574-A-AAACTTACTTACCATTCTTGAACTGT			Likely benign (Jun 07, 2023)
9-8331644-G-A		PTPRD-related disorder	Benign/Likely benign (Nov 01, 2022)
9-8331660-C-A		not specified	Uncertain significance (Feb 28, 2023)
9-8340356-C-A		not specified	Uncertain significance (Oct 26, 2021)
9-8341114-T-C		not specified	Uncertain significance (-)
9-8341140-A-C			Likely benign (Feb 01, 2024)
9-8341184-T-C		not specified	Uncertain significance (Jan 13, 2023)
9-8341185-A-G		PTPRD-related disorder	Benign (Dec 31, 2019)
9-8341220-G-C		not specified	Uncertain significance (Dec 17, 2021)
9-8341267-C-T		not specified	Uncertain significance (Feb 28, 2023)
9-8341818-C-T		not specified	Uncertain significance (Jan 30, 2024)
9-8376609-T-G		not specified	Uncertain significance (Oct 26, 2022)
9-8376669-C-G		not specified	Uncertain significance (Mar 04, 2024)
9-8376681-C-T		not specified	Uncertain significance (Aug 10, 2021)
9-8376686-G-T		not specified	Uncertain significance (Nov 17, 2022)
9-8389328-T-A		PTPRD-related disorder	Likely benign (May 03, 2019)
9-8389343-A-G		PTPRD-related disorder	Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPRD	protein_coding	protein_coding	ENST00000381196	35	2298478

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	3.38e-12	125730	0	17	125747	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.273	1058	1.08e+3	0.977	0.0000604	12469
Missense in Polyphen		605	718.29	0.84228		8268
Synonymous	-5.58	536	395	1.36	0.0000229	3744
Loss of Function	8.52	5	94.2	0.0531	0.00000483	1139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000326	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000618	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000725	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Can bidirectionally induce pre- and post-synaptic differentiation of neurons by mediating interaction with IL1RAP and IL1RAPL1 trans-synaptically. Involved in pre-synaptic differentiation through interaction with SLITRK2. {ECO:0000250|UniProtKB:Q64487}.
• Pathway: Neuronal System;Synaptic adhesion-like molecules;Receptor-type tyrosine-protein phosphatases;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.174

Intolerance Scores

• loftool: 0.0868
• rvis_EVS: -3.08
• rvis_percentile_EVS: 0.48

Haploinsufficiency Scores

• pHI: 0.897
• hipred: Y
• hipred_score: 0.749
• ghis: 0.617

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.773

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptprd
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system 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); 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); skeleton phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region 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); muscle phenotype

Gene ontology

• Biological process: protein dephosphorylation;phosphate-containing compound metabolic process;heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;transmembrane receptor protein tyrosine phosphatase signaling pathway;neuron differentiation;peptidyl-tyrosine dephosphorylation;positive regulation of dendrite morphogenesis;positive regulation of synapse assembly;presynaptic membrane assembly;regulation of postsynaptic density assembly;trans-synaptic signaling by trans-synaptic complex;synaptic membrane adhesion;regulation of presynapse assembly
• Cellular component: plasma membrane;integral component of plasma membrane;extracellular exosome;glutamatergic synapse
• Molecular function: transmembrane receptor protein tyrosine phosphatase activity;signaling receptor binding;protein binding;cell adhesion molecule binding