Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	5782
Gene name	Protein tyrosine phosphatase non-receptor type 12
Gene symbol	PTPN12
Synonyms (NCBI Gene)	PTP-PESTPTPG1
Chromosome	7
Chromosome location	7q11.23
Summary	The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation.

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SNP ID	Visualize variation	Clinical significance	Consequence
rs121434623	A>G	Pathogenic	Non coding transcript variant, missense variant, 5 prime UTR variant, coding sequence variant

127

Show/Hide all (127)

miRTarBase ID	miRNA	Experiments	Reference
MIRT000198	hsa-miR-200b-3p	Northern blotqRT-PCRWestern blot	16762633
MIRT002567	hsa-miR-124-3p	Microarray	15685193
MIRT005893	hsa-miR-194-5p	Luciferase reporter assayqRT-PCRWestern blot	20979124
MIRT019770	hsa-miR-375	Microarray	20215506
MIRT002567	hsa-miR-124-3p	Microarray	18668037
MIRT002567	hsa-miR-124-3p	Microarray	15685193
MIRT687147	hsa-miR-494-3p	HITS-CLIP	23313552
MIRT687146	hsa-miR-4301	HITS-CLIP	23313552
MIRT687145	hsa-miR-6740-3p	HITS-CLIP	23313552
MIRT687144	hsa-miR-4666a-5p	HITS-CLIP	23313552
MIRT687143	hsa-miR-3156-3p	HITS-CLIP	23313552
MIRT687142	hsa-miR-607	HITS-CLIP	23313552
MIRT687141	hsa-miR-576-5p	HITS-CLIP	23313552
MIRT687140	hsa-miR-599	HITS-CLIP	23313552
MIRT005893	hsa-miR-194-5p	Luciferase reporter assayqRT-PCRWestern blot	27486333
MIRT687147	hsa-miR-494-3p	HITS-CLIP	23313552
MIRT687146	hsa-miR-4301	HITS-CLIP	23313552
MIRT687145	hsa-miR-6740-3p	HITS-CLIP	23313552
MIRT687144	hsa-miR-4666a-5p	HITS-CLIP	23313552
MIRT687143	hsa-miR-3156-3p	HITS-CLIP	23313552
MIRT687142	hsa-miR-607	HITS-CLIP	23313552
MIRT687141	hsa-miR-576-5p	HITS-CLIP	23313552
MIRT687140	hsa-miR-599	HITS-CLIP	23313552
MIRT1274582	hsa-miR-106a	CLIP-seq
MIRT1274583	hsa-miR-106b	CLIP-seq
MIRT1274584	hsa-miR-124	CLIP-seq
MIRT1274585	hsa-miR-125a-5p	CLIP-seq
MIRT1274586	hsa-miR-125b	CLIP-seq
MIRT1274587	hsa-miR-1283	CLIP-seq
MIRT1274588	hsa-miR-145	CLIP-seq
MIRT1274589	hsa-miR-17	CLIP-seq
MIRT1274590	hsa-miR-194	CLIP-seq
MIRT1274591	hsa-miR-200b	CLIP-seq
MIRT1274592	hsa-miR-200c	CLIP-seq
MIRT1274593	hsa-miR-2054	CLIP-seq
MIRT1274594	hsa-miR-20a	CLIP-seq
MIRT1274595	hsa-miR-20b	CLIP-seq
MIRT1274596	hsa-miR-3074-3p	CLIP-seq
MIRT1274597	hsa-miR-3143	CLIP-seq
MIRT1274598	hsa-miR-3180-5p	CLIP-seq
MIRT1274599	hsa-miR-3609	CLIP-seq
MIRT1274600	hsa-miR-3616-5p	CLIP-seq
MIRT1274601	hsa-miR-3618	CLIP-seq
MIRT1274602	hsa-miR-3647-5p	CLIP-seq
MIRT1274603	hsa-miR-3685	CLIP-seq
MIRT1274604	hsa-miR-369-3p	CLIP-seq
MIRT1274605	hsa-miR-3714	CLIP-seq
MIRT1274606	hsa-miR-380	CLIP-seq
MIRT1274607	hsa-miR-384	CLIP-seq
MIRT1274608	hsa-miR-3910	CLIP-seq
MIRT1274609	hsa-miR-429	CLIP-seq
MIRT1274610	hsa-miR-4319	CLIP-seq
MIRT1274611	hsa-miR-4495	CLIP-seq
MIRT1274612	hsa-miR-4635	CLIP-seq
MIRT1274613	hsa-miR-4670-3p	CLIP-seq
MIRT1274614	hsa-miR-4678	CLIP-seq
MIRT1274615	hsa-miR-4698	CLIP-seq
MIRT1274616	hsa-miR-4711-3p	CLIP-seq
MIRT1274617	hsa-miR-4712-5p	CLIP-seq
MIRT1274618	hsa-miR-4732-3p	CLIP-seq
MIRT1274619	hsa-miR-4796-3p	CLIP-seq
MIRT1274620	hsa-miR-487a	CLIP-seq
MIRT1274621	hsa-miR-503	CLIP-seq
MIRT1274622	hsa-miR-506	CLIP-seq
MIRT1274623	hsa-miR-519d	CLIP-seq
MIRT1274624	hsa-miR-548ah	CLIP-seq
MIRT1274625	hsa-miR-548m	CLIP-seq
MIRT1274626	hsa-miR-573	CLIP-seq
MIRT1274627	hsa-miR-595	CLIP-seq
MIRT1274628	hsa-miR-656	CLIP-seq
MIRT1274629	hsa-miR-670	CLIP-seq
MIRT1274630	hsa-miR-770-5p	CLIP-seq
MIRT1274631	hsa-miR-93	CLIP-seq
MIRT1274632	hsa-miR-934	CLIP-seq
MIRT1274584	hsa-miR-124	CLIP-seq
MIRT1274587	hsa-miR-1283	CLIP-seq
MIRT1274633	hsa-miR-186	CLIP-seq
MIRT1274634	hsa-miR-188-3p	CLIP-seq
MIRT1274590	hsa-miR-194	CLIP-seq
MIRT1274591	hsa-miR-200b	CLIP-seq
MIRT1274592	hsa-miR-200c	CLIP-seq
MIRT1274635	hsa-miR-2114	CLIP-seq
MIRT1274596	hsa-miR-3074-3p	CLIP-seq
MIRT1274636	hsa-miR-3123	CLIP-seq
MIRT1274637	hsa-miR-3133	CLIP-seq
MIRT1274597	hsa-miR-3143	CLIP-seq
MIRT1274600	hsa-miR-3616-5p	CLIP-seq
MIRT1274601	hsa-miR-3618	CLIP-seq
MIRT1274602	hsa-miR-3647-5p	CLIP-seq
MIRT1274638	hsa-miR-3671	CLIP-seq
MIRT1274604	hsa-miR-369-3p	CLIP-seq
MIRT1274605	hsa-miR-3714	CLIP-seq
MIRT1274608	hsa-miR-3910	CLIP-seq
MIRT1274609	hsa-miR-429	CLIP-seq
MIRT1274639	hsa-miR-4540	CLIP-seq
MIRT1274612	hsa-miR-4635	CLIP-seq
MIRT1274613	hsa-miR-4670-3p	CLIP-seq
MIRT1274614	hsa-miR-4678	CLIP-seq
MIRT1274615	hsa-miR-4698	CLIP-seq
MIRT1274640	hsa-miR-4731-3p	CLIP-seq
MIRT1274641	hsa-miR-4801	CLIP-seq
MIRT1274620	hsa-miR-487a	CLIP-seq
MIRT1274621	hsa-miR-503	CLIP-seq
MIRT1274622	hsa-miR-506	CLIP-seq
MIRT1274642	hsa-miR-548ag	CLIP-seq
MIRT1274643	hsa-miR-548ai	CLIP-seq
MIRT1274625	hsa-miR-548m	CLIP-seq
MIRT1274626	hsa-miR-573	CLIP-seq
MIRT1274628	hsa-miR-656	CLIP-seq
MIRT1274632	hsa-miR-934	CLIP-seq
MIRT1274638	hsa-miR-3671	CLIP-seq
MIRT1274596	hsa-miR-3074-3p	CLIP-seq
MIRT1274638	hsa-miR-3671	CLIP-seq
MIRT1274587	hsa-miR-1283	CLIP-seq
MIRT1274634	hsa-miR-188-3p	CLIP-seq
MIRT1274635	hsa-miR-2114	CLIP-seq
MIRT1274597	hsa-miR-3143	CLIP-seq
MIRT1274601	hsa-miR-3618	CLIP-seq
MIRT1274638	hsa-miR-3671	CLIP-seq
MIRT2306833	hsa-miR-4477a	CLIP-seq
MIRT1274639	hsa-miR-4540	CLIP-seq
MIRT1274614	hsa-miR-4678	CLIP-seq
MIRT1274621	hsa-miR-503	CLIP-seq
MIRT1274642	hsa-miR-548ag	CLIP-seq
MIRT1274643	hsa-miR-548ai	CLIP-seq
MIRT1274628	hsa-miR-656	CLIP-seq
MIRT1274632	hsa-miR-934	CLIP-seq

Show/Hide all (30)

GO ID	Ontology	Definition	Evidence	Reference
GO:0002102	Component	Podosome	IEA
GO:0004721	Function	Phosphoprotein phosphatase activity	IDA	27134172
GO:0004721	Function	Phosphoprotein phosphatase activity	IEA
GO:0004725	Function	Protein tyrosine phosphatase activity	EXP	21376233
GO:0004725	Function	Protein tyrosine phosphatase activity	IBA
GO:0004725	Function	Protein tyrosine phosphatase activity	IEA
GO:0004726	Function	Non-membrane spanning protein tyrosine phosphatase activity	IEA
GO:0004726	Function	Non-membrane spanning protein tyrosine phosphatase activity	TAS	8454633
GO:0005515	Function	Protein binding	IPI	9285683, 11971877, 12614164, 19167335, 19380743, 20029029, 21376233, 24189400, 24412244, 24658140, 27880917, 28065597, 31980649, 32296183, 33961781, 35152348, 35271311
GO:0005634	Component	Nucleus	IBA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	TAS	1472029
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005925	Component	Focal adhesion	IEA
GO:0006470	Process	Protein dephosphorylation	IDA	27134172
GO:0006470	Process	Protein dephosphorylation	TAS	8454633
GO:0016787	Function	Hydrolase activity	IEA
GO:0017124	Function	SH3 domain binding	IPI	9285683
GO:0035335	Process	Peptidyl-tyrosine dephosphorylation	IDA	27134172
GO:0042058	Process	Regulation of epidermal growth factor receptor signaling pathway	IBA
GO:0042058	Process	Regulation of epidermal growth factor receptor signaling pathway	IMP	27134172
GO:0042246	Process	Tissue regeneration	IEA
GO:0042995	Component	Cell projection	IEA
GO:0070161	Component	Anchoring junction	IEA
GO:0071364	Process	Cellular response to epidermal growth factor stimulus	IMP	27134172
GO:1901185	Process	Negative regulation of ERBB signaling pathway	TAS
GO:2000587	Process	Negative regulation of platelet-derived growth factor receptor-beta signaling pathway	TAS

MIM	HGNC	e!Ensembl
600079	9645	ENSG00000127947

Q05209

Protein name

Tyrosine-protein phosphatase non-receptor type 12 (EC 3.1.3.48) (PTP-PEST) (Protein-tyrosine phosphatase G1) (PTPG1)

Protein 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

PDB

5HDE , 5J8R , 5O2P

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00102	Y_phosphatase	58 → 292	Protein-tyrosine phosphatase	Domain

Sequence

MEQVEILRKFIQRVQAMKSPDHNGEDNFARDFMRLRRLSTKYRTEKIYPTATGEKEENVK
KNRYKDILPFDHSRVKLTLKTPSQDSDYINANFIKGVYGPKAYVATQGPLANTVIDFWRM
IWEYNVVIIVMACREFEMGRKKCERYWPLYGEDPITFAPFKISCEDEQARTDYFIRTLLL
EFQNESRRLYQFHYVNWPDHDVPSSFDSILDMISLMRKYQEHEDVPICIHCSAGCGRTGA
ICAIDYTWNLLKAGKIPEEFNVFNLIQEMRTQRHSAVQTKEQYELVHRAIAQLFEKQLQL
YEIHGAQKIADGVNEINTENMVSSIEPEKQDSPPPKPPRTRSCLVEGDAKEEILQPPEPH
PVPPILTPSPPSAFPTVTTVWQDNDRYHPKPVLHMVSSEQHSADLNRNYSKSTELPGKNE
STIEQIDKKLERNLSFEIKKVPLQEGPKSFDGNTLLNRGHAIKIKSASPCIADKISKPQE
LSSDLNVGDTSQNSCVDCSVTQSNKVSVTPPEESQNSDTPPRPDRLPLDEKGHVTWSFHG
PENAIPIPDLSEGNSSDINYQTRKTVSLTPSPTTQVETPDLVDHDNTSPLFRTPLSFTNP
LHSDDSDSDERNSDGAVTQNKTNISTASATVSAATSTESISTRKVLPMSIARHNIAGTTH
SGAEKDVDVSEDSPPPLPERTPESFVLASEHNTPVRSEWSELQSQERSEQKKSEGLITSE
NEKCDHPAGGIHYEMCIECPPTFSDKREQISENPTEATDIGFGNRCGKPKGPRDPPSEWT

Sequence length

780

Interactions

View interactions

	Reactome
			SHC1 events in ERBB2 signaling EGFR downregulation Signaling by PDGF Downregulation of ERBB2 signaling Interleukin-37 signaling Constitutive Signaling by Overexpressed ERBB2

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Carcinoma of colon	Pathogenic	rs121434623	RCV000010055	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (5)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
COLORECTAL CANCER	—	ClinVar, HPO ClinVar, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL NEOPLASMS	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPOTHYROIDISM	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PTPN12-related disorder	Benign; Likely benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (36)

Disease Name	Relationship Type	References	Evidence Score
Associations from Text MiningDisease associations identified through Pubtator
Breast Neoplasms	Associate	23044628, 23534739, 27608899	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Associate	29278368, 7509295	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Associate	24475046, 27075395, 29742497	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Inhibit	32812952	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Non Small Cell Lung	Associate	25868976	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Associate	26537073, 30297534	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Inhibit	33292053	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Squamous Cell	Associate	25868976	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colonic Neoplasms	Associate	24284071	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Associate	26901136, 7509295	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Dementia	Associate	28600779	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Associate	35290144	★★★★★ ★☆☆☆☆ Found in Text Mining only
Disease	Associate	30297534	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma	Associate	21510904	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hepatitis B	Associate	27075395	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hereditary Breast and Ovarian Cancer Syndrome	Associate	23044628	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hereditary leiomyomatosis and renal cell cancer	Associate	30297534	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypoxia	Associate	35290144	★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Associate	28600779	★★★★★ ★☆☆☆☆ Found in Text Mining only
Kidney Neoplasms	Associate	33292053	★★★★★ ★☆☆☆☆ Found in Text Mining only
Lead Poisoning Nervous System	Associate	35290144	★★★★★ ★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Inhibit	23044628	★★★★★ ★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Associate	23534739	★★★★★ ★☆☆☆☆ Found in Text Mining only
Lymphoma Large Cell Anaplastic	Stimulate	17077326	★★★★★ ★☆☆☆☆ Found in Text Mining only
Nasopharyngeal Carcinoma	Associate	25663493	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasm Metastasis	Associate	23044628, 23534739, 25663493, 26537073	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Associate	21376233, 25663493, 25868976	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Inhibit	23044628, 24475046, 30297534, 31606028, 32812952, 7509295	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Stimulate	26537073	★★★★★ ★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Associate	21483099	★★★★★ ★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Associate	17329398, 31606028	★★★★★ ★☆☆☆☆ Found in Text Mining only
Rhabdomyosarcoma	Associate	8454633	★★★★★ ★☆☆☆☆ Found in Text Mining only
Spondylitis Ankylosing	Associate	25506924	★★★★★ ★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Associate	21376233, 23044628, 23534739	★★★★★ ★☆☆☆☆ Found in Text Mining only
Urinary Bladder Neoplasms	Associate	23345605	★★★★★ ★☆☆☆☆ Found in Text Mining only
Uveal melanoma	Associate	37563735	★★★★★ ★☆☆☆☆ Found in Text Mining only

PTPN12 (protein tyrosine phosphatase non-receptor type 12)