PTP4A1

protein tyrosine phosphatase 4A1, the group of Protein tyrosine phosphatase 4A family

Basic information

Region (hg38): 6:63521746-63583588

Links

ENSG00000112245 ∙ NCBI:7803 ∙ OMIM:601585 ∙ HGNC:9634 ∙ Uniprot:Q93096 ∙ 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 PTP4A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTP4A1 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					2	2
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	2

Variants in PTP4A1

This is a list of pathogenic ClinVar variants found in the PTP4A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-63576972-A-G		not specified	Uncertain significance (Feb 06, 2024)
6-63578936-G-C		not specified	Uncertain significance (Dec 15, 2022)
6-63578977-G-A		not specified	Uncertain significance (Sep 22, 2023)
6-63580063-G-T			Benign (Jun 27, 2018)
6-63580065-G-A		not specified	Uncertain significance (Aug 13, 2021)
6-63580091-C-T			Benign (Jun 27, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTP4A1	protein_coding	protein_coding	ENST00000370651	5	61827

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.282	0.698	125638	0	3	125641	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.05	44	102	0.430	0.00000596	1136
Missense in Polyphen		0	12.498	0		191
Synonymous	0.0383	31	31.3	0.991	0.00000168	323
Loss of Function	1.96	2	7.95	0.252	3.33e-7	109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000554	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000179	0.0000176
Middle Eastern	0.0000554	0.0000544
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. May play a role in the development and maintenance of differentiating epithelial tissues. Enhances cell proliferation, cell motility and invasive activity, and promotes cancer metastasis. {ECO:0000269|PubMed:12235145, ECO:0000269|PubMed:12782572, ECO:0000269|PubMed:14643450}.
• Pathway: Signaling events mediated by PRL (Consensus)

Intolerance Scores

• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.211
• hipred: Y
• hipred_score: 0.754
• ghis: 0.620

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptp4a1
• Phenotype: reproductive 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); growth/size/body region phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: cell cycle;multicellular organism development;positive regulation of cell migration;peptidyl-tyrosine dephosphorylation
• Cellular component: nucleus;cytoplasm;early endosome;endoplasmic reticulum;spindle;cytoplasmic side of plasma membrane
• Molecular function: protein tyrosine phosphatase activity;protein binding;protein tyrosine/serine/threonine phosphatase activity