PTPN9

protein tyrosine phosphatase non-receptor type 9, the group of Protein tyrosine phosphatases non-receptor type

Basic information

Region (hg38): 15:75463251-75579315

Links

ENSG00000169410 ∙ NCBI:5780 ∙ OMIM:600768 ∙ HGNC:9661 ∙ Uniprot:P43378 ∙ 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 PTPN9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTPN9 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					1	1
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	20	0	1

Variants in PTPN9

This is a list of pathogenic ClinVar variants found in the PTPN9 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-75468800-C-T		not specified	Uncertain significance (Dec 23, 2023)
15-75469787-G-A			Likely benign (May 01, 2023)
15-75469858-G-A		not specified	Uncertain significance (Aug 11, 2022)
15-75469861-C-T		not specified	Uncertain significance (Jul 27, 2022)
15-75469987-G-A		not specified	Uncertain significance (Jun 07, 2023)
15-75470703-T-C		not specified	Uncertain significance (Aug 13, 2021)
15-75470714-T-A		not specified	Uncertain significance (Jun 24, 2022)
15-75470733-C-T		not specified	Uncertain significance (Jun 29, 2023)
15-75470753-A-G		not specified	Uncertain significance (Jan 09, 2024)
15-75470769-T-C		not specified	Uncertain significance (Mar 21, 2024)
15-75470774-G-A		not specified	Uncertain significance (Mar 04, 2024)
15-75505696-A-G		not specified	Uncertain significance (Feb 28, 2023)
15-75505702-T-A		not specified	Uncertain significance (Jan 04, 2022)
15-75505734-G-C		not specified	Uncertain significance (Jan 09, 2023)
15-75505874-G-A		not specified	Uncertain significance (Jun 13, 2024)
15-75505913-C-T		not specified	Uncertain significance (Dec 06, 2022)
15-75505928-C-G		not specified	Uncertain significance (Apr 22, 2022)
15-75505960-C-T		not specified	Uncertain significance (Jun 07, 2023)
15-75509009-A-C		not specified	Uncertain significance (Jun 13, 2024)
15-75509012-G-A		not specified	Uncertain significance (Mar 27, 2023)
15-75523156-C-T			Benign (Jul 23, 2018)
15-75524233-G-C		not specified	Uncertain significance (May 30, 2024)
15-75524243-C-T		not specified	Uncertain significance (Apr 07, 2023)
15-75524295-T-C		not specified	Uncertain significance (Mar 28, 2024)
15-75527224-G-A		not specified	Uncertain significance (Dec 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTPN9	protein_coding	protein_coding	ENST00000306726	13	112169

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.110	0.890	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.10	223	331	0.675	0.0000180	3900
Missense in Polyphen		62	123.76	0.50096		1486
Synonymous	1.07	107	122	0.877	0.00000637	1147
Loss of Function	3.85	8	31.2	0.256	0.00000165	362

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000968	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.000326	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein-tyrosine phosphatase that could participate in the transfer of hydrophobic ligands or in functions of the Golgi apparatus. {ECO:0000269|PubMed:19167335}.
• Pathway: VEGFA-VEGFR2 Signaling Pathway (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.193
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.54

Haploinsufficiency Scores

• pHI: 0.360
• hipred: Y
• hipred_score: 0.628
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptpn9
• Phenotype: immune system phenotype; skeleton 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); 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); hematopoietic system 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); embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; craniofacial phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: ptpn9a
• Affected structure: blood cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: protein dephosphorylation;negative regulation of neuron projection development;peptidyl-tyrosine dephosphorylation;cellular response to cytokine stimulus;positive regulation of protein localization to plasma membrane
• Cellular component: nucleoplasm;cytoplasm;neuron projection terminus
• Molecular function: protein tyrosine phosphatase activity;non-membrane spanning protein tyrosine phosphatase activity;protein binding