ConVarT

ClinVar Data

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Variation ID	Allele ID	RS Number	Variant Type	Record	Alteration	Clinicial Sig.	Last Update	Phenotypes	Cytogenetic	Review Status	RCV Acc.N.

gnomAD

Frameshift Variant

Inframe Deletion

Missense Variant

Splice Region Variant

Stop Gained

Synonymous Variant

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Variant ID	Transcript ID	Alteration	Annotation	Allele C.	Allele N.	Allele F.	rsNumber
12-112856921-A-G	ENST00000392597	p.Thr2Thr	Synonymous Variant	0	0	0	rs768238710
12-112856927-G-A	ENST00000392597	p.Arg4Arg	Splice Region Variant	0	0	0	rs1214031315
12-112884090-C-G	ENST00000392597	p.Pro9Ala	Missense Variant	0	0	0	rs566068139
12-112884090-C-T	ENST00000392597	p.Pro9Ser	Missense Variant	1	31386	0.000032	rs566068139
12-112884091-C-A	ENST00000392597	p.Pro9Gln	Missense Variant	0	0	0	rs536503257
12-112884091-C-G	ENST00000392597	p.Pro9Arg	Missense Variant	0	0	0	rs536503257
12-112884093-A-G	ENST00000392597	p.Asn10Asp	Missense Variant	0	0	0	rs368633510
12-112884094-A-G	ENST00000392597	p.Asn10Ser	Missense Variant	0	0	0	rs200613531
12-112884096-A-G	ENST00000392597	p.Ile11Val	Missense Variant	0	0	0	rs1472357430
12-112884097-T-C	ENST00000392597	p.Ile11Thr	Missense Variant	0	0	0	rs1181579972
12-112884099-A-G	ENST00000392597	p.Thr12Ala	Missense Variant	0	0	0	rs1386827892
12-112884101-T-C	ENST00000392597	p.Thr12Thr	Synonymous Variant	0	0	0	rs760086740
12-112884113-A-G	ENST00000392597	p.Ala16Ala	Synonymous Variant	5	31408	0.000159	rs372736227
12-112884117-A-G	ENST00000392597	p.Asn18Asp	Missense Variant	0	0	0	rs776089364
12-112884118-A-G	ENST00000392597	p.Asn18Ser	Missense Variant	0	0	0	rs587778635
12-112884122-A-G	ENST00000392597	p.Leu19Leu	Synonymous Variant	0	0	0	rs764238610
12-112884123-C-G	ENST00000392597	p.Leu20Val	Missense Variant	0	0	0	rs753951666
12-112884129-A-G	ENST00000392597	p.Thr22Ala	Missense Variant	0	0	0	rs757537175
12-112884131-A-G	ENST00000392597	p.Thr22Thr	Synonymous Variant	0	0	0	rs397516808
12-112884141-G-A	ENST00000392597	p.Asp26Asn	Missense Variant	0	0	0	rs750261927

Showing 1 to 20 of 257 entries

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Post-translational Modifications (PTMs)

Acetylation

Phosphorylation

Ubiquitination

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Gene Name	ACC ID	PTM Type	Position	Mod-rsd	Site +/-7 Aa	Mw_kd	Site grpID
PTPN11	Q06124	Ubiquitination	120	K120-ub	FHGHLSGkEAEkLLT	68.44	964544628
PTPN11	Q06124	Ubiquitination	124	K124-ub	LSGkEAEkLLTEKGk	68.44	603486086
PTPN11	Q06124	Ubiquitination	131	K131-ub	kLLTEKGkHGSFLVR	68.44	964544630
PTPN11	Q06124	Phosphorylation	142	S142-p	FLVRESQsHPGDFVL	68.44	27458512
PTPN11	Q06124	Phosphorylation	153	T153-p	DFVLSVRtGDDKGES	68.44	23144280
PTPN11	Q06124	Phosphorylation	165	S165-p	GESNDGKsKVTHVMI	68.44	23144277
PTPN11	Q06124	Acetylation	178	K178-ac	MIRCQELkyDVGGGE	68.44	15296186
PTPN11	Q06124	Phosphorylation	179	Y179-p	IRCQELkyDVGGGER	68.44	23144286
PTPN11	Q06124	Phosphorylation	189	S189-p	GGGERFDsLTDLVEH	68.44	27458516
PTPN11	Q06124	Ubiquitination	198	K198-ub	TDLVEHYkKNPMVET	68.44	964544632
PTPN11	Q06124	Acetylation	198	K198-ac	TDLVEHYkKNPMVET	68.44	11318323
PTPN11	Q06124	Ubiquitination	235	K235-ub	SRVRELSkLAETTDk	68.44	964544634
PTPN11	Q06124	Ubiquitination	242	K242-ub	kLAETTDkVkQGFWE	68.44	964544636
PTPN11	Q06124	Ubiquitination	244	K244-ub	AETTDkVkQGFWEEF	68.44	964544638
PTPN11	Q06124	Ubiquitination	260	K260-ub	TLQQQECkLLysRKE	68.44	964544640
PTPN11	Q06124	Phosphorylation	263	Y263-p	QQECkLLysRKEGQR	68.44	458568
PTPN11	Q06124	Phosphorylation	264	S264-p	QECkLLysRKEGQRQ	68.44	22778106
PTPN11	Q06124	Acetylation	274	K274-ac	EGQRQENkNkNRykN	68.44	9263041
PTPN11	Q06124	Acetylation	276	K276-ac	QRQENkNkNRykNIL	68.44	9263046
PTPN11	Q06124	Phosphorylation	279	Y279-p	ENkNkNRykNILPFD	68.44	474206

Showing 1 to 20 of 53 entries

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Catalogue of Somatic Mutations in Cancer (COSMIC)

Deletion - Frameshift

Nonstop Extension

Substitution - Coding Silent

Substitution - Missense

Substitution - Nonsense

Unknown

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Gene Name	Transcript ID	Sample name	Primary Site	Primary Histology	Mutation ID	Mutation CDS	Mutation Aa	Mutation Desc.	FATHMM Prediction	FATHMM Score	Mutation Somatic Status	PUBMED PMID	Tumor Origin	Position
PTPN11_ENST00000392597	ENST00000392597	P-0002490-T01-IM3	NS	malignant_melanoma	42986080	c.1276C>T	p.H426Y	Substitution - Missense	PATHOGENIC	.98649	Confirmed somatic variant	PMID: 28481359	metastasis	426
PTPN11_ENST00000392597	ENST00000392597	JMML_27	haematopoietic_and_lymphoid_tissue	haematopoietic_neoplasm	42978829	c.227A>C	p.E76A	Substitution - Missense	PATHOGENIC	.99171	Confirmed somatic variant	PMID: 26457648	NS	76
PTPN11_ENST00000392597	ENST00000392597	1524397	haematopoietic_and_lymphoid_tissue	lymphoid_neoplasm	42979459	c.182A>T	p.D61V	Substitution - Missense	PATHOGENIC	.99061	Confirmed somatic variant	PMID: 21390130	recurrent	61
PTPN11_ENST00000392597	ENST00000392597	TCGA-51-4079-01	lung	carcinoma	42978524	c.226G>A	p.E76K	Substitution - Missense	PATHOGENIC	.99278	Confirmed somatic variant	PMID: N/A	primary	76
PTPN11_ENST00000392597	ENST00000392597	971352	haematopoietic_and_lymphoid_tissue	haematopoietic_neoplasm	42983403	c.178G>C	p.G60R	Substitution - Missense	PATHOGENIC	.99551	Reported in another cancer sample as somatic	PMID: 15928039	NS	60
PTPN11_ENST00000392597	ENST00000392597	1091911	haematopoietic_and_lymphoid_tissue	haematopoietic_neoplasm	42978524	c.226G>A	p.E76K	Substitution - Missense	PATHOGENIC	.99278	Reported in another cancer sample as somatic	PMID: 17972951	NS	76
PTPN11_ENST00000392597	ENST00000392597	1005741	haematopoietic_and_lymphoid_tissue	haematopoietic_neoplasm	42979361	c.213T>A	p.F71L	Substitution - Missense	PATHOGENIC	.93733	Reported in another cancer sample as somatic	PMID: 15842656	NS	71
PTPN11_ENST00000392597	ENST00000392597	970579	haematopoietic_and_lymphoid_tissue	lymphoid_neoplasm	42979590	c.214G>A	p.A72T	Substitution - Missense	PATHOGENIC	.98978	Confirmed somatic variant	PMID: 16358218	NS	72
PTPN11_ENST00000392597	ENST00000392597	AML_87	haematopoietic_and_lymphoid_tissue	haematopoietic_neoplasm	42979590	c.214G>A	p.A72T	Substitution - Missense	PATHOGENIC	.98978	Reported in another cancer sample as somatic	PMID: 27288520	primary	72
PTPN11_ENST00000392597	ENST00000392597	P-0008341-T01-IM5	central_nervous_system	glioma	42978954	c.181G>T	p.D61Y	Substitution - Missense	PATHOGENIC	.99353	Confirmed somatic variant	PMID: 28481359	primary	61
PTPN11_ENST00000392597	ENST00000392597	1207006	haematopoietic_and_lymphoid_tissue	haematopoietic_neoplasm	42979551	c.215C>T	p.A72V	Substitution - Missense	PATHOGENIC	.98019	Reported in another cancer sample as somatic	PMID: 19047918	NS	72
PTPN11_ENST00000392597	ENST00000392597	5-VS054-T1	skin	carcinoma	42987695	c.642G>T	p.Q214H	Substitution - Missense	PATHOGENIC	.99203	Confirmed somatic variant	PMID: 26950094	NS	214
PTPN11_ENST00000392597	ENST00000392597	A1-2A	large_intestine	carcinoma	42985888	c.14+9658del	p.?	Unknown			Confirmed somatic variant	PMID: N/A	primary	0
PTPN11_ENST00000392597	ENST00000392597	CHG-12-13407T	liver	other	42979669	c.917A>G	p.N306S	Substitution - Missense	PATHOGENIC	.99783	Confirmed somatic variant	PMID: N/A	primary	306
PTPN11_ENST00000392597	ENST00000392597	T3484	large_intestine	carcinoma	42982457	c.1027C>T	p.R343W	Substitution - Missense	PATHOGENIC	.89731	Confirmed somatic variant	PMID: 27149842	NS	343
PTPN11_ENST00000392597	ENST00000392597	PD11022a	haematopoietic_and_lymphoid_tissue	haematopoietic_neoplasm	42980089	c.211T>C	p.F71L	Substitution - Missense	PATHOGENIC	.98514	Reported in another cancer sample as somatic	PMID: 27276561	NS	71
PTPN11_ENST00000392597	ENST00000392597	J32_T	lung	carcinoma	42985215	c.642+574G>T	p.?	Unknown	NEUTRAL	.02099	Confirmed somatic variant	PMID: N/A	NS	0
PTPN11_ENST00000392597	ENST00000392597	PD8446a	haematopoietic_and_lymphoid_tissue	haematopoietic_neoplasm	42978829	c.227A>C	p.E76A	Substitution - Missense	PATHOGENIC	.99171	Reported in another cancer sample as somatic	PMID: 27276561	NS	76
PTPN11_ENST00000392597	ENST00000392597	DA1506C	endometrium	carcinoma	42980690	c.757-2584A>G	p.?	Unknown	NEUTRAL	.00687	Confirmed somatic variant	PMID: N/A	primary	0
PTPN11_ENST00000392597	ENST00000392597	1037435	haematopoietic_and_lymphoid_tissue	haematopoietic_neoplasm	42979551	c.215C>T	p.A72V	Substitution - Missense	PATHOGENIC	.98019	Reported in another cancer sample as somatic	PMID: 16518851	NS	72

Showing 1 to 20 of 664 entries

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dbSNP

Gene ID	Transcript ID	Consequence	Position	HGVSp	Impact

Protein Domains (PFAM)

Pfam Domain	Domain Name	Description	Positions	Clan	Clan Name	Organism
NO RESULT FOUND
PF00017	SH2	SH2 domain	112-197	CL0541	SH2-like	Homo sapiens
PF00017	SH2	SH2 domain	6-81	CL0541	SH2-like	Homo sapiens
PF00102	Y_phosphatase	Protein-tyrosine phosphatase	273-520	CL0031	Phosphatase	Homo sapiens

List of the diseases from DisGeNET

Disease Name	Disease Category	DSI*	DPI**
Adenocarcinoma	Neoplasms ;	0.429	0.828
Astrocytoma	Neoplasms ;	0.429	0.828
Squamous cell carcinoma	Neoplasms ;	0.429	0.828
Hypertrophic Cardiomyopathy	Cardiovascular Diseases ;	0.429	0.828
Charcot-Marie-Tooth Disease	Nervous System Diseases ; Congenital, Hereditary, and Neonatal Diseases and Abnormalities ;	0.429	0.828
Cytopenia	N/A	0.429	0.828
Enchondromatosis	Musculoskeletal Diseases ;	0.429	0.828
Hereditary Multiple Exostoses	Neoplasms ; Musculoskeletal Diseases ; Congenital, Hereditary, and Neonatal Diseases and Abnormalities ;	0.429	0.828
Hydrops Fetalis	Female Urogenital Diseases and Pregnancy Complications ; Hemic and Lymphatic Diseases ; Congenital, Hereditary, and Neonatal Diseases and Abnormalities ; Immune System Diseases ; Pathological Conditions, Signs and Symptoms ;	0.429	0.828
leukemia	Neoplasms ;	0.429	0.828
Leukemia, Myelocytic, Acute	Neoplasms ;	0.429	0.828
Leukemia, Myelomonocytic, Chronic	Neoplasms ; Hemic and Lymphatic Diseases ;	0.429	0.828
Maffucci Syndrome	Musculoskeletal Diseases ;	0.429	0.828
Acute Myeloid Leukemia, M1	Neoplasms ;	0.429	0.828
Myelomonocytic leukemia	N/A	0.429	0.828
Neuroblastoma	Neoplasms ;	0.429	0.828
Neurofibromatosis 1	Neoplasms ; Nervous System Diseases ; Congenital, Hereditary, and Neonatal Diseases and Abnormalities ;	0.429	0.828
Noonan Syndrome	Musculoskeletal Diseases ; Cardiovascular Diseases ; Congenital, Hereditary, and Neonatal Diseases and Abnormalities ; Skin and Connective Tissue Diseases ;	0.429	0.828
Cartilaginous exostosis	Neoplasms ; Musculoskeletal Diseases ;	0.429	0.828
Osteogenesis Imperfecta	Musculoskeletal Diseases ; Congenital, Hereditary, and Neonatal Diseases and Abnormalities ; Skin and Connective Tissue Diseases ;	0.429	0.828
Turner Syndrome, Male	Musculoskeletal Diseases ; Cardiovascular Diseases ; Congenital, Hereditary, and Neonatal Diseases and Abnormalities ; Skin and Connective Tissue Diseases ;	0.429	0.828
Congenital anemia	N/A	0.429	0.828
LEOPARD Syndrome	Musculoskeletal Diseases ; Cardiovascular Diseases ; Congenital, Hereditary, and Neonatal Diseases and Abnormalities ; Skin and Connective Tissue Diseases ;	0.429	0.828
Adenocarcinoma, Basal Cell	Neoplasms ;	0.429	0.828
Adenocarcinoma, Oxyphilic	Neoplasms ;	0.429	0.828
Carcinoma, Cribriform	Neoplasms ;	0.429	0.828
Carcinoma, Granular Cell	Neoplasms ;	0.429	0.828
Adenocarcinoma, Tubular	Neoplasms ;	0.429	0.828
Subependymal Giant Cell Astrocytoma	Neoplasms ;	0.429	0.828
Multiple pterygium syndrome	Congenital, Hereditary, and Neonatal Diseases and Abnormalities ; Skin and Connective Tissue Diseases ; Pathological Conditions, Signs and Symptoms ;	0.429	0.828
Juvenile Pilocytic Astrocytoma	Neoplasms ;	0.429	0.828
Diffuse Astrocytoma	Neoplasms ;	0.429	0.828
Anaplastic astrocytoma	Neoplasms ;	0.429	0.828
Protoplasmic astrocytoma	Neoplasms ;	0.429	0.828
Gemistocytic astrocytoma	Neoplasms ;	0.429	0.828
Fibrillary Astrocytoma	Neoplasms ;	0.429	0.828
Pilocytic Astrocytoma	Neoplasms ;	0.429	0.828
Childhood Cerebral Astrocytoma	Neoplasms ;	0.429	0.828
Juvenile Myelomonocytic Leukemia	Neoplasms ; Hemic and Lymphatic Diseases ;	0.429	0.828
Hematologic Neoplasms	Neoplasms ; Hemic and Lymphatic Diseases ;	0.429	0.828
Metachondromatosis	Neoplasms ; Musculoskeletal Diseases ; Congenital, Hereditary, and Neonatal Diseases and Abnormalities ;	0.429	0.828
Mixed oligoastrocytoma	Neoplasms ;	0.429	0.828
Costello syndrome (disorder)	Musculoskeletal Diseases ; Congenital, Hereditary, and Neonatal Diseases and Abnormalities ;	0.429	0.828
Cerebral Astrocytoma	Neoplasms ;	0.429	0.828
Intracranial Astrocytoma	Neoplasms ;	0.429	0.828
Cardio-facio-cutaneous syndrome	Cardiovascular Diseases ; Congenital, Hereditary, and Neonatal Diseases and Abnormalities ; Skin and Connective Tissue Diseases ; Pathological Conditions, Signs and Symptoms ;	0.429	0.828
Female Pseudo-Turner Syndrome	Musculoskeletal Diseases ; Cardiovascular Diseases ; Congenital, Hereditary, and Neonatal Diseases and Abnormalities ; Skin and Connective Tissue Diseases ;	0.429	0.828
Neurodevelopmental Disorders	Mental Disorders ;	0.429	0.828
Grade I Astrocytoma	Neoplasms ;	0.429	0.828
Acute Myeloid Leukemia (AML-M2)	Neoplasms ;	0.429	0.828
MYELODYSPLASTIC SYNDROME	Hemic and Lymphatic Diseases ;	0.429	0.828
Intellectual Disability	Nervous System Diseases ; Pathological Conditions, Signs and Symptoms ; Behavior and Behavior Mechanisms ; Mental Disorders ;	0.429	0.828
NO RESULT FOUND

Description:	protein tyrosine phosphatase, non-receptor type 11 [Source:HGNC Symbol;Acc:HGNC:9644]
Synonyms:	SH-PTP2, METCDS, BPTP3, SHP2, PTP-1D, JMML, SH-PTP3, NS1, CFC, TP2C
Other ID(s):	HGNC:9644, ENSG00000179295
Protein Accession Numbers:	ENST00000530818, NP_001361554, ENST00000392597, NP_542168, NP_001317366, ENST00000351677, NP_002825
Statistics:	ClinVar(252) gnomAD(257) COSMIC(664) PTM(53)

Classification of Clinicial Significance of ClinVar Data