PTPN9

protein-coding

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

Gene summary

The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP contains an N-terminal domain that shares a significant similarity with yeast SEC14, which is a protein that has phosphatidylinositol transfer activity and is required for protein secretion through the Golgi complex in yeast. This PTP was found to be activated by polyphosphoinositide, and is thought to be involved in signaling events regulating phagocytosis. [provided by RefSeq, Jul 2008]

MANE transcript

NM_002833.4

Inheritance

—

ClinVar variants

U:74B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.26

Max pathogenic AF

—

Genomic locus

chr15:75,463,251-75,579,315

External References & Databases

Ensembl (ENSG00000169410)

Transcript & Mutation Effects

hg38 • Region Span ~116.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PTPN9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 67

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002833.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	2 clinvar	1 clinvar	6
missense			68 clinvar			68
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	74	2	1	77

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002833.4	RefSeq	NP_002824.1	13	MANE Select
ENST00000618819.5	Ensembl	ENSP00000482732.1	13	MANE Select
ENST00000561731.1	Ensembl	ENSP00000455934.1	4	Standard
ENST00000893934.1	Ensembl	ENSP00000563993.1	12	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
ptpn9a	Danio rerio	Structure: blood cell Quality: decreased amount abnormal

Gene / Model

Organism

Observed Phenotype

ptpn9a

Danio rerio

Structure: blood cell

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

VEGFA-VEGFR2 Signaling Pathway

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

Molecular Function

protein tyrosine phosphatase activity
non-membrane spanning protein tyrosine phosphatase activity
protein binding

Cellular Component

nucleoplasm
cytoplasm
neuron projection terminus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000306726
Coding exons: 13
Length: 112169
Individuals with no LoFs: 125728
Homozygous LoFs: 0
Heterozygous LoFs: 20
Defined: 125748
p: 0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.10	223	331	0.675	0.0000180	3900
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000097	0.000097	rare
South Asian	0.000098	0.000098	rare
Other	0.00033	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.112

Intolerance Scores

LoFtool: 0.193
RVIS EVS: -0.56
RVIS percentile EVS: 19.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.801

Gene Damage Prediction

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