PTPRA

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

Basic information

Region (hg38): 20:2873420-3039076

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.

• not_specified (71 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. These statistics are base on transcript: NM_001385305.1. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			70	1		71
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	70	1	1

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