PTPRE

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

Basic information

Region (hg38): 10:127907103-128085855

Links

ENSG00000132334 ∙ NCBI:5791 ∙ OMIM:600926 ∙ HGNC:9669 ∙ Uniprot:P23469 ∙ 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 PTPRE gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPRE 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			30	3		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	4	0

Variants in PTPRE

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

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

Position	Type	Phenotype	Significance	ClinVar
10-128040930-G-A		not specified	Likely benign (Jun 06, 2023)
10-128040939-C-G		not specified	Uncertain significance (Jun 02, 2023)
10-128040972-G-A		not specified	Uncertain significance (Jun 19, 2024)
10-128040982-C-T		not specified	Uncertain significance (Mar 20, 2024)
10-128047393-C-T		not specified	Uncertain significance (Sep 16, 2021)
10-128047396-C-T		not specified	Uncertain significance (Jun 29, 2023)
10-128047417-C-T		not specified	Uncertain significance (Oct 26, 2021)
10-128047476-G-A		not specified	Uncertain significance (Aug 26, 2022)
10-128049562-C-A		not specified	Uncertain significance (Jun 30, 2022)
10-128049620-G-A		not specified	Uncertain significance (Nov 07, 2023)
10-128049624-C-G		not specified	Uncertain significance (Feb 02, 2022)
10-128056141-A-C		not specified	Uncertain significance (Apr 04, 2024)
10-128063140-C-T		not specified	Uncertain significance (Feb 23, 2023)
10-128063148-G-A		not specified	Uncertain significance (Nov 17, 2023)
10-128066099-G-A		not specified	Uncertain significance (Apr 22, 2024)
10-128066130-G-A		not specified	Uncertain significance (May 18, 2022)
10-128066138-G-A		not specified	Uncertain significance (Jan 27, 2022)
10-128066150-G-A		not specified	Uncertain significance (Aug 15, 2023)
10-128068131-C-T			Likely benign (Oct 01, 2022)
10-128068132-G-A		not specified	Uncertain significance (Feb 26, 2024)
10-128068244-C-T		not specified	Likely benign (Aug 12, 2021)
10-128068270-A-G		not specified	Uncertain significance (Apr 04, 2023)
10-128068273-G-A		not specified	Uncertain significance (Apr 25, 2022)
10-128069798-A-G		not specified	Uncertain significance (Sep 06, 2022)
10-128070403-G-A		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPRE	protein_coding	protein_coding	ENST00000254667	19	178795

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000816	0.999	125707	0	41	125748	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.08	310	431	0.718	0.0000258	4635
Missense in Polyphen		112	179.41	0.62426		1880
Synonymous	0.703	167	179	0.933	0.0000128	1297
Loss of Function	4.47	15	48.7	0.308	0.00000296	479

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000163	0.000163
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.000163	0.000163
South Asian	0.000397	0.000392
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1 plays a critical role in signaling transduction pathways and phosphoprotein network topology in red blood cells. May play a role in osteoclast formation and function (By similarity). {ECO:0000250}.; FUNCTION: Isoform 1 and isoform 2 act as a negative regulator of FceRI-mediated signal transduction leading to cytokine production and degranulation, most likely by acting at the level of SYK to affect downstream events such as phosphorylation of SLP76 and LAT and mobilization of Ca(2+). {ECO:0000250}.
• Pathway: EGFR1;IL6-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.304
• rvis_EVS: -1.28
• rvis_percentile_EVS: 5.11

Haploinsufficiency Scores

• pHI: 0.142
• hipred: Y
• hipred_score: 0.744
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.864

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptpre
• Phenotype: cellular phenotype; skeleton phenotype; hematopoietic system phenotype; 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); limbs/digits/tail phenotype; immune system phenotype

Gene ontology

• Biological process: protein dephosphorylation;peptidyl-tyrosine dephosphorylation;negative regulation of insulin receptor signaling pathway
• Cellular component: nucleus;cytoplasm;plasma membrane;integral component of membrane
• Molecular function: transmembrane receptor protein tyrosine phosphatase activity;protein binding