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.

not_specified (137 variants)
not_provided (5 variants)

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. These statistics are base on transcript: NM_000002846.4. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar	2 clinvar	6
missense			128 clinvar	8 clinvar		136
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	128	12	2

Loading clinvar variants...

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