PTPRN

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

Basic information

Region (hg38): 2:219289623-219309648

Links

ENSG00000054356 ∙ NCBI:5798 ∙ OMIM:601773 ∙ HGNC:9676 ∙ Uniprot:Q16849 ∙ 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 PTPRN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPRN 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				3	2	5
missense			55	4		59
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	55	7	2

Variants in PTPRN

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

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

Position	Type	Phenotype	Significance	ClinVar
2-219290266-G-A		not specified	Uncertain significance (Nov 07, 2022)
2-219290270-C-T		not specified	Uncertain significance (Mar 07, 2024)
2-219290545-C-T		not specified	Uncertain significance (Feb 16, 2023)
2-219290854-G-C		not specified	Uncertain significance (Sep 29, 2023)
2-219290879-C-T		not specified	Uncertain significance (Apr 06, 2024)
2-219291483-T-C		not specified	Uncertain significance (Oct 14, 2023)
2-219291498-G-A		not specified	Uncertain significance (Jun 07, 2024)
2-219295006-C-T		not specified	Uncertain significance (Mar 31, 2024)
2-219295035-A-T		not specified	Uncertain significance (Sep 21, 2023)
2-219295068-G-T		not specified	Uncertain significance (Dec 18, 2023)
2-219295074-A-C		not specified	Uncertain significance (Feb 09, 2023)
2-219296231-A-G		not specified	Uncertain significance (Jan 31, 2022)
2-219296244-G-A			Likely benign (Apr 16, 2018)
2-219296320-A-T		not specified	Uncertain significance (Nov 06, 2023)
2-219296330-C-T		not specified	Uncertain significance (May 12, 2024)
2-219296344-A-G		not specified	Uncertain significance (Mar 11, 2022)
2-219296458-G-A		not specified	Uncertain significance (Nov 08, 2021)
2-219296808-T-C		not specified	Uncertain significance (Oct 22, 2021)
2-219297035-G-A		not specified	Uncertain significance (Aug 20, 2023)
2-219297063-G-C		not specified	Uncertain significance (Feb 22, 2023)
2-219297098-C-T		not specified	Uncertain significance (Apr 28, 2023)
2-219297105-G-A		not specified	Uncertain significance (Jun 29, 2023)
2-219297121-C-A		not specified	Uncertain significance (Apr 20, 2024)
2-219297131-G-A		not specified	Uncertain significance (Aug 28, 2023)
2-219297249-G-A		not specified	Uncertain significance (May 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPRN	protein_coding	protein_coding	ENST00000295718	23	20026

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.96e-7	1.00	125690	0	58	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	485	595	0.815	0.0000353	6239
Missense in Polyphen		182	247.18	0.73631		2622
Synonymous	0.747	228	243	0.939	0.0000138	2125
Loss of Function	3.86	19	47.8	0.398	0.00000213	538

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000639	0.000636
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000602	0.000601
European (Non-Finnish)	0.000186	0.000185
Middle Eastern	0.000218	0.000217
South Asian	0.000131	0.000131
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in vesicle-mediated secretory processes (PubMed:24843546). Required for normal accumulation of secretory vesicles in hippocampus, pituitary and pancreatic islets (By similarity). Required for the accumulation of normal levels of insulin-containing vesicles and preventing their degradation (PubMed:24843546). Plays a role in insulin secretion in response to glucose stimuli (PubMed:24843546). Required for normal accumulation of the neurotransmitters norepinephrine, dopamine and serotonin in the brain (By similarity). 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). Seems to lack intrinsic enzyme activity (By similarity). May regulate catalytic active protein-tyrosine phosphatases such as PTPRA through dimerization (By similarity). {ECO:0000250|UniProtKB:Q60673, ECO:0000269|PubMed:24843546}.; FUNCTION: ICA512-cleaved cytosolic fragment: ICA512-CCF translocated to the nucleus promotes expression of insulin and other granule-related genes; the function implicates binding to and regulating activity of STAT5B probably by preventing its dephosphorylation and potentially by inducing its sumoylation by recruiting PIAS4 (PubMed:15596545, PubMed:16622421, PubMed:18178618). Enhances pancreatic beta-cell proliferation by converging with signaling by STAT5B and STAT3 (PubMed:15596545, PubMed:16622421, PubMed:18178618). ICA512-CCF located in the cytoplasm regulates dynamics and exocytosis of insulin secretory granules (SGs) by dimerizing with ICA512-TMF and displacing SNTB2 thus enhancing SGs mobility and exocytosis (PubMed:18824546, PubMed:20886068). {ECO:0000269|PubMed:15596545, ECO:0000269|PubMed:16622421, ECO:0000269|PubMed:18178618, ECO:0000269|PubMed:18824546, ECO:0000269|PubMed:20886068}.
• Disease: DISEASE: Note=Autoantigen in insulin-dependent diabetes mellitus (IDDM). {ECO:0000269|PubMed:8144912, ECO:0000269|PubMed:8641276}.
• Pathway: Type I diabetes mellitus - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.323

Intolerance Scores

• loftool: 0.469
• rvis_EVS: -1.39
• rvis_percentile_EVS: 4.27

Haploinsufficiency Scores

• pHI: 0.504
• hipred: Y
• hipred_score: 0.660
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.855

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptprn
• Phenotype: immune system phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: response to reactive oxygen species;luteinization;cytokine-mediated signaling pathway;insulin secretion;response to insulin;peptidyl-tyrosine dephosphorylation;insulin secretion involved in cellular response to glucose stimulus;response to estrogen;positive regulation of transcription by RNA polymerase II;response to cAMP;positive regulation of type B pancreatic cell proliferation;dense core granule maturation
• Cellular component: nucleus;endosome;Golgi apparatus;plasma membrane;synaptic vesicle;integral component of membrane;cell junction;secretory granule;transport vesicle membrane;neuronal cell body;perikaryon;axon terminus;synapse
• Molecular function: protein tyrosine phosphatase activity;protein binding;transcription factor binding;spectrin binding;ubiquitin-like protein ligase binding;GTPase binding