PTPN3

protein tyrosine phosphatase non-receptor type 3, the group of Protein tyrosine phosphatases non-receptor type|FERM domain containing|PDZ domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 9:109375466-109498313

Links

ENSG00000070159 ∙ ∙ OMIM:176877 ∙ HGNC:9655 ∙ Uniprot:P26045 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PTPN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPN3 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				2	1	3
missense			53	2		55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	4	1

Variants in PTPN3

This is a list of pathogenic ClinVar variants found in the PTPN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-109379566-T-C		not specified	Uncertain significance (Apr 06, 2024)
9-109379617-A-G		not specified	Uncertain significance (Mar 23, 2023)
9-109381726-T-C		not specified	Uncertain significance (Dec 17, 2023)
9-109381768-C-T		not specified	Uncertain significance (Dec 08, 2023)
9-109381773-C-T		not specified	Uncertain significance (Oct 17, 2023)
9-109381780-T-C		not specified	Uncertain significance (Nov 09, 2023)
9-109382319-G-A			Likely benign (Apr 01, 2023)
9-109382353-T-C		not specified	Uncertain significance (Apr 07, 2023)
9-109382354-T-A		not specified	Uncertain significance (Dec 22, 2023)
9-109382384-C-T		not specified	Uncertain significance (Nov 08, 2022)
9-109382394-G-C		not specified	Uncertain significance (Sep 14, 2023)
9-109382411-C-T		not specified	Uncertain significance (Jan 30, 2024)
9-109383500-C-T		not specified	Likely benign (Mar 07, 2024)
9-109389296-C-A		not specified	Uncertain significance (Apr 25, 2023)
9-109389318-T-C		not specified	Uncertain significance (Aug 17, 2022)
9-109389341-G-A			Benign (Dec 31, 2019)
9-109391539-C-T		not specified	Uncertain significance (Oct 13, 2023)
9-109404467-G-A		not specified	Uncertain significance (Mar 16, 2024)
9-109404471-C-T		not specified	Uncertain significance (May 03, 2023)
9-109404566-T-G		not specified	Uncertain significance (Jun 22, 2023)
9-109404586-G-T		not specified	Uncertain significance (Mar 21, 2024)
9-109406497-T-C		not specified	Uncertain significance (Oct 19, 2021)
9-109406519-T-C		not specified	Uncertain significance (Aug 13, 2021)
9-109406530-A-T		not specified	Uncertain significance (Feb 21, 2024)
9-109408362-T-G		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPN3	protein_coding	protein_coding	ENST00000374541	25	122845

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.71e-9	1.00	125680	0	68	125748	0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.706	495	541	0.915	0.0000322	5999
Missense in Polyphen		188	221.52	0.84867		2398
Synonymous	-0.259	214	209	1.02	0.0000135	1716
Loss of Function	4.31	25	61.5	0.407	0.00000369	649

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000751	0.000749
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.000399	0.000381
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000264	0.000264
Middle Eastern	0.000399	0.000381
South Asian	0.000265	0.000261
Other	0.000498	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act at junctions between the membrane and the cytoskeleton. Possesses tyrosine phosphatase activity.
• Pathway: Signal Transduction;TCR;EGFR downregulation;Signaling by EGFR;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.609

Intolerance Scores

• loftool: 0.286
• rvis_EVS: -1.17
• rvis_percentile_EVS: 6.07

Haploinsufficiency Scores

• pHI: 0.332
• hipred: Y
• hipred_score: 0.544
• ghis: 0.493

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.851

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptpn3
• Phenotype: normal phenotype; skeleton phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: protein dephosphorylation;peptidyl-tyrosine dephosphorylation;negative regulation of epidermal growth factor receptor signaling pathway;negative regulation of mitotic cell cycle;negative regulation of membrane protein ectodomain proteolysis;liver regeneration;regulation of membrane depolarization during action potential;regulation of sodium ion transmembrane transporter activity
• Cellular component: cytoplasm;cytoskeleton;plasma membrane;cytoplasmic side of plasma membrane
• Molecular function: phosphotyrosine residue binding;protein tyrosine phosphatase activity;protein binding;cytoskeletal protein binding;sodium channel regulator activity;ATPase binding