PTPRA

protein tyrosine phosphatase receptor type A, the group of Protein tyrosine phosphatases receptor type

Basic information

Region (hg38): 20:2873419-3039076

Previous symbols: [ "PTPRL2", "PTPA" ]

Links

ENSG00000132670 ∙ ∙ OMIM:176884 ∙ HGNC:9664 ∙ Uniprot:P18433 ∙ 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 PTPRA gene.

• Inborn genetic diseases (27 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPRA 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					1	1
missense			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	1

Variants in PTPRA

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

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

Position	Type	Phenotype	Significance	ClinVar
20-2964282-A-T		not specified	Uncertain significance (Jun 11, 2021)
20-2964309-G-T		not specified	Uncertain significance (Oct 05, 2021)
20-2965026-A-G		not specified	Uncertain significance (Feb 17, 2022)
20-2965090-T-G		not specified	Uncertain significance (Jun 11, 2021)
20-2965104-C-T		not specified	Uncertain significance (May 26, 2023)
20-2965116-A-G		not specified	Uncertain significance (Apr 22, 2022)
20-2965145-C-A		not specified	Uncertain significance (Dec 17, 2023)
20-2965151-G-A		not specified	Uncertain significance (Dec 19, 2022)
20-2986783-C-T		not specified	Uncertain significance (Jan 08, 2024)
20-2986784-G-A			Benign (Aug 14, 2018)
20-2986818-G-A		not specified	Uncertain significance (Mar 04, 2024)
20-2988067-A-G		not specified	Uncertain significance (Jul 26, 2022)
20-2988347-G-A		not specified	Uncertain significance (Dec 13, 2021)
20-2988349-G-A		not specified	Uncertain significance (Jul 20, 2022)
20-3007404-A-G		not specified	Uncertain significance (Dec 05, 2022)
20-3021318-G-A		not specified	Uncertain significance (Dec 06, 2023)
20-3021363-C-T		not specified	Uncertain significance (Apr 12, 2022)
20-3021405-G-A		not specified	Uncertain significance (Dec 06, 2022)
20-3022071-C-A		not specified	Uncertain significance (Dec 05, 2022)
20-3022171-G-A		not specified	Uncertain significance (May 11, 2022)
20-3022768-G-C		not specified	Uncertain significance (Nov 09, 2023)
20-3022822-G-A		not specified	Uncertain significance (Feb 27, 2023)
20-3024596-A-G		not specified	Uncertain significance (Nov 13, 2023)
20-3027731-A-G		not specified	Uncertain significance (May 17, 2023)
20-3027761-A-G		not specified	Uncertain significance (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPRA	protein_coding	protein_coding	ENST00000380393	21	174893

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000230	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.67	307	470	0.654	0.0000271	5281
Missense in Polyphen		150	263.99	0.5682		2950
Synonymous	0.741	165	178	0.929	0.0000105	1534
Loss of Function	5.87	4	47.7	0.0838	0.00000247	535

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000356	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Regulation of Microtubule Cytoskeleton;Spinal Cord Injury;Developmental Biology;Signal Transduction;TCR;EGFR1;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;NCAM signaling for neurite out-growth;Axon guidance;Insulin Pathway;Alpha4 beta1 integrin signaling events (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.101
• rvis_EVS: -1.09
• rvis_percentile_EVS: 7.15

Haploinsufficiency Scores

• pHI: 0.344
• hipred: Y
• hipred_score: 0.825
• ghis: 0.660

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.701

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptpra
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); growth/size/body region phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: ptpra
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: dead

Gene ontology

• Biological process: MAPK cascade;axon guidance;insulin receptor signaling pathway;peptidyl-tyrosine dephosphorylation;modulation of chemical synaptic transmission
• Cellular component: plasma membrane;integral component of plasma membrane;receptor complex;extracellular exosome;Schaffer collateral - CA1 synapse;integral component of synaptic membrane
• Molecular function: protein tyrosine phosphatase activity;transmembrane receptor protein tyrosine phosphatase activity;Ras guanyl-nucleotide exchange factor activity;protein binding