PTPRN2

protein tyrosine phosphatase receptor type N2, the group of MicroRNA protein coding host genes|Protein tyrosine phosphatases receptor type

Basic information

Region (hg38): 7:157539056-158587823

Links

ENSG00000155093 ∙ NCBI:5799 ∙ OMIM:601698 ∙ HGNC:9677 ∙ Uniprot:Q92932 ∙ 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 PTPRN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPRN2 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				12	16	28
missense			55	8	10	73
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	2	4
non coding						0
Total	0	0	55	20	27

Variants in PTPRN2

This is a list of pathogenic ClinVar variants found in the PTPRN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-157540717-C-A			Benign (Oct 01, 2023)
7-157540784-T-C		not specified	Uncertain significance (Aug 10, 2021)
7-157548964-G-A			Benign (Dec 31, 2019)
7-157548964-G-C			Likely benign (Oct 19, 2018)
7-157568929-C-G		not specified	Uncertain significance (Apr 06, 2024)
7-157571467-C-T		not specified	Uncertain significance (May 31, 2023)
7-157571487-T-C			Likely benign (Jun 05, 2018)
7-157576606-G-A			Benign (Dec 31, 2019)
7-157576675-G-C		not specified	Uncertain significance (Apr 16, 2024)
7-157576706-G-A		not specified	Uncertain significance (Apr 12, 2022)
7-157578025-T-C		not specified	Uncertain significance (Jan 31, 2024)
7-157578031-T-C		not specified	Uncertain significance (Mar 18, 2024)
7-157578083-C-T		not specified	Uncertain significance (Jun 11, 2024)
7-157595247-G-T		not specified	Uncertain significance (Jul 11, 2023)
7-157595289-C-T			Likely benign (Jun 05, 2018)
7-157595301-C-T			Benign (Jun 01, 2018)
7-157595307-G-A			Likely benign (Oct 10, 2018)
7-157621363-G-A			Likely benign (Dec 31, 2019)
7-157621367-A-G		Malignant tumor of prostate	Uncertain significance (-)
7-157621372-G-GGCCAGTTTCCACCGCCCGTAACCCAGGCTTCCTGCCCCCGGGGCTGGTACGTACAGGTCAGCACA			Benign (Dec 31, 2019)
7-157621435-C-T			Benign (Jun 01, 2018)
7-157621454-G-A		not specified	Uncertain significance (Aug 02, 2021)
7-157621456-T-C			Benign (Nov 06, 2018)
7-157621475-C-T		not specified	Uncertain significance (Jun 24, 2022)
7-157656369-G-T			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPRN2	protein_coding	protein_coding	ENST00000389418	23	1048731

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.39e-7	1.00	125706	1	41	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0573	630	634	0.994	0.0000423	6455
Missense in Polyphen		182	233.28	0.78018		2470
Synonymous	0.242	292	297	0.982	0.0000229	2106
Loss of Function	4.04	20	51.1	0.391	0.00000258	569

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000416	0.000414
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000172	0.000167
Middle Eastern	0.000165	0.000163
South Asian	0.000267	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in vesicle-mediated secretory processes. Required for normal accumulation of secretory vesicles in hippocampus, pituitary and pancreatic islets. Required for the accumulation of normal levels of insulin-containing vesicles and preventing their degradation. Plays a role in insulin secretion in response to glucose stimuli. Required for normal accumulation of the neurotransmitters norepinephrine, dopamine and serotonin in the brain. In females, but not in males, required for normal accumulation and secretion of pituitary hormones, such as luteinizing hormone (LH) and follicle-stimulating hormone (FSH) (By similarity). Required to maintain normal levels of renin expression and renin release (By similarity). May regulate catalytic active protein-tyrosine phosphatases such as PTPRA through dimerization (By similarity). Has phosphatidylinositol phosphatase activity; the PIPase activity is involved in its ability to regulate insulin secretion. Can dephosphorylate phosphatidylinositol 4,5-biphosphate (PI(4,5)P2), phosphatidylinositol 5-phosphate and phosphatidylinositol 3- phosphate (By similarity). Regulates PI(4,5)P2 level in the plasma membrane and localization of cofilin at the plasma membrane and thus is indirectly involved in regulation of actin dynamics related to cell migration and metastasis; upon hydrolyzation of PI(4,5)P2 cofilin is released from the plasma membrane and acts in the cytoplasm in severing F-actin filaments (PubMed:26620550). {ECO:0000250|UniProtKB:P80560, ECO:0000250|UniProtKB:Q63475, ECO:0000269|PubMed:26620550}.
• Disease: DISEASE: Note=Autoantigen in insulin-dependent diabetes mellitus (IDDM). {ECO:0000269|PubMed:8637868, ECO:0000269|PubMed:8798755, ECO:0000269|PubMed:8878534}.
• Pathway: Type I diabetes mellitus - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.0998

Intolerance Scores

• loftool: 0.730
• rvis_EVS: 0.89
• rvis_percentile_EVS: 89.2

Haploinsufficiency Scores

• pHI: 0.188
• hipred: N
• hipred_score: 0.361
• ghis: 0.466

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.780

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptprn2
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein dephosphorylation;lipid metabolic process;neurotransmitter secretion;negative regulation of GTPase activity;peptidyl-tyrosine dephosphorylation;insulin secretion involved in cellular response to glucose stimulus;neutrophil degranulation
• Cellular component: endoplasmic reticulum lumen;plasma membrane;integral component of plasma membrane;cell junction;integral component of synaptic vesicle membrane;secretory granule membrane;synaptic vesicle membrane;terminal bouton;receptor complex;ficolin-1-rich granule membrane
• Molecular function: transmembrane receptor protein tyrosine phosphatase activity