PTP4A2

protein tyrosine phosphatase 4A2, the group of Protein tyrosine phosphatase 4A family

Basic information

Region (hg38): 1:31906420-31944856

Previous symbols: [ "PTP4A" ]

Links

ENSG00000184007 ∙ NCBI:8073 ∙ OMIM:601584 ∙ HGNC:9635 ∙ Uniprot:Q12974 ∙ 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 PTP4A2 gene.

• Inborn genetic diseases (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTP4A2 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						0
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in PTP4A2

This is a list of pathogenic ClinVar variants found in the PTP4A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-31908874-T-C		not specified	Uncertain significance (Jul 12, 2023)
1-31910077-C-T		not specified	Uncertain significance (Jul 25, 2023)
1-31915941-G-A		not specified	Uncertain significance (Feb 23, 2023)
1-31918995-T-C		not specified	Uncertain significance (Mar 23, 2022)
1-31919061-T-C		not specified	Uncertain significance (Sep 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTP4A2	protein_coding	protein_coding	ENST00000344035	5	38436

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.966	0.0337	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.07	37	93.2	0.397	0.00000518	1084
Missense in Polyphen		9	32.236	0.27919		403
Synonymous	-0.472	35	31.6	1.11	0.00000171	319
Loss of Function	3.01	0	10.5	0.00	6.76e-7	117

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein tyrosine phosphatase which stimulates progression from G1 into S phase during mitosis. Promotes tumors. Inhibits geranylgeranyl transferase type II activity by blocking the association between RABGGTA and RABGGTB. {ECO:0000269|PubMed:14643450}.
• Pathway: Post-translational protein modification;Metabolism of proteins;RAB geranylgeranylation;Signaling events mediated by PRL (Consensus)

Recessive Scores

• pRec: 0.0861

Intolerance Scores

• loftool: 0.151
• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.0899
• hipred: Y
• hipred_score: 0.662
• ghis: 0.547

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.948

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptp4a2
• Phenotype: embryo phenotype; hematopoietic system 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); reproductive system phenotype; immune system phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: peptidyl-tyrosine dephosphorylation;post-translational protein modification
• Cellular component: nucleus;cytoplasm;early endosome;cytosol;plasma membrane
• Molecular function: protein tyrosine phosphatase activity;prenylated protein tyrosine phosphatase activity