PTPN12

protein tyrosine phosphatase non-receptor type 12, the group of Protein tyrosine phosphatases non-receptor type

Basic information

Region (hg38): 7:77537295-77640069

Links

ENSG00000127947 ∙ ∙ OMIM:600079 ∙ HGNC:9645 ∙ Uniprot:Q05209 ∙ 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 PTPN12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPN12 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	1	4
missense			25	1	3	29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3	1	4
non coding				1		1
Total	0	0	25	5	4

Variants in PTPN12

This is a list of pathogenic ClinVar variants found in the PTPN12 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-77537627-C-G		not specified	Uncertain significance (Oct 27, 2022)
7-77571075-A-T		PTPN12-related disorder	Benign (Oct 18, 2019)
7-77571119-A-G		not specified	Uncertain significance (Jul 26, 2022)
7-77571160-A-G		Carcinoma of colon	Pathogenic (Feb 21, 1994)
7-77581471-G-C		not specified	Uncertain significance (Jan 26, 2022)
7-77583557-C-T		PTPN12-related disorder	Likely benign (Nov 16, 2019)
7-77583558-G-A		not specified	Uncertain significance (Jun 06, 2023)
7-77583599-A-G		PTPN12-related disorder	Likely benign (Jan 20, 2020)
7-77585562-G-A		not specified	Uncertain significance (Aug 02, 2021)
7-77585588-A-G		PTPN12-related disorder	Likely benign (Mar 22, 2023)
7-77600660-G-A		PTPN12-related disorder	Likely benign (Jan 01, 2024)
7-77600671-G-A		not specified	Uncertain significance (Mar 01, 2023)
7-77600765-A-G			Likely benign (Dec 01, 2022)
7-77611018-A-G		PTPN12-related disorder • not specified	Uncertain significance (Jan 16, 2024)
7-77611033-T-C		not specified	Uncertain significance (Jul 14, 2021)
7-77611042-G-A		not specified	Uncertain significance (Jul 20, 2022)
7-77618504-G-A		PTPN12-related disorder	Benign (Oct 16, 2019)
7-77626750-G-A		PTPN12-related disorder	Likely benign (Aug 20, 2019)
7-77626763-G-A		not specified	Uncertain significance (Mar 14, 2023)
7-77626812-C-G		not specified	Uncertain significance (Apr 04, 2024)
7-77626959-A-T		not specified	Uncertain significance (Nov 30, 2022)
7-77627048-A-C		not specified	Uncertain significance (Aug 26, 2022)
7-77627133-T-C		not specified	Uncertain significance (May 23, 2023)
7-77627220-C-T		not specified	Uncertain significance (Oct 06, 2022)
7-77627252-C-T		not specified	Likely benign (Jul 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPN12	protein_coding	protein_coding	ENST00000248594	18	102797

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000419	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	330	395	0.836	0.0000184	5123
Missense in Polyphen		60	93.927	0.6388		1229
Synonymous	-0.927	146	132	1.10	0.00000643	1438
Loss of Function	5.56	3	41.7	0.0719	0.00000210	537

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000700	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000143	0.000141
Middle Eastern	0.000700	0.000544
South Asian	0.000165	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dephosphorylates a range of proteins, and thereby regulates cellular signaling cascades (PubMed:18559503). Dephosphorylates cellular tyrosine kinases, such as ERBB2 and PTK2B/PYK2, and thereby regulates signaling via ERBB2 and PTK2B/PYK2 (PubMed:17329398, PubMed:27134172). Selectively dephosphorylates ERBB2 phosphorylated at 'Tyr-1112', 'Tyr-1196', and/or 'Tyr-1248' (PubMed:27134172). {ECO:0000269|PubMed:17329398, ECO:0000269|PubMed:18559503, ECO:0000269|PubMed:27134172}.
• Pathway: EGF-EGFR Signaling Pathway;SHC1 events in ERBB2 signaling;Signal Transduction;Signaling by PDGF;TCR;EGFR downregulation;Signaling by EGFR;Downregulation of ERBB2 signaling;EGFR1;Signaling by ERBB2;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.168

Intolerance Scores

• loftool: 0.350
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.65

Haploinsufficiency Scores

• pHI: 0.376
• hipred: Y
• hipred_score: 0.825
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.234

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptpn12
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); immune system phenotype; liver/biliary system phenotype; embryo phenotype

Zebrafish Information Network

• Gene name: ptpn12
• Affected structure: pharyngeal arch 3-7
• Phenotype tag: abnormal
• Phenotype quality: hypoplastic

Gene ontology

• Biological process: protein dephosphorylation;peptidyl-tyrosine dephosphorylation;ERBB2 signaling pathway;regulation of epidermal growth factor receptor signaling pathway;tissue regeneration;cellular response to cytokine stimulus;cellular response to epidermal growth factor stimulus;negative regulation of ERBB signaling pathway;negative regulation of platelet-derived growth factor receptor-beta signaling pathway
• Cellular component: podosome;nucleoplasm;cytoplasm;cytosol;focal adhesion;cell projection
• Molecular function: phosphoprotein phosphatase activity;protein tyrosine phosphatase activity;non-membrane spanning protein tyrosine phosphatase activity;protein binding;SH3 domain binding