PDXP

pyridoxal phosphatase, the group of HAD Asp-based protein phosphatases

Basic information

Region (hg38): 22:37658722-37666932

Links

ENSG00000241360 ∙ NCBI:57026 ∙ OMIM:609246 ∙ HGNC:30259 ∙ Uniprot:Q96GD0 ∙ 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 PDXP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDXP 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in PDXP

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

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

Position	Type	Phenotype	Significance	ClinVar
22-37658800-G-C		not specified	Uncertain significance (Dec 19, 2022)
22-37658828-C-G		not specified	Uncertain significance (Jul 13, 2022)
22-37658846-G-A		not specified	Uncertain significance (Aug 08, 2022)
22-37658876-A-G		not specified	Uncertain significance (Sep 19, 2022)
22-37658882-G-C		not specified	Uncertain significance (Jan 20, 2023)
22-37658886-G-A		not specified	Uncertain significance (Dec 06, 2022)
22-37658918-C-T		not specified	Uncertain significance (Jan 10, 2022)
22-37659030-A-C		not specified	Uncertain significance (Jul 14, 2023)
22-37659071-C-T		not specified	Uncertain significance (Jul 14, 2023)
22-37659080-C-G		not specified	Uncertain significance (Mar 13, 2023)
22-37659125-G-A		not specified	Uncertain significance (Apr 08, 2022)
22-37659347-C-G		not specified	Uncertain significance (May 24, 2024)
22-37659348-G-T		not specified	Uncertain significance (May 24, 2024)
22-37665591-C-T		not specified	Uncertain significance (Sep 15, 2021)
22-37665648-C-T		not specified	Uncertain significance (Sep 12, 2023)
22-37665675-G-A		not specified	Uncertain significance (Jan 29, 2024)
22-37665675-G-T		not specified	Uncertain significance (Jun 03, 2022)
22-37665683-A-T		not specified	Uncertain significance (Apr 12, 2022)
22-37665713-C-T		not specified	Uncertain significance (Dec 19, 2022)
22-37665767-C-T		not specified	Uncertain significance (Jan 24, 2023)
22-37665795-C-T		not specified	Uncertain significance (Nov 16, 2021)
22-37665815-G-A		not specified	Uncertain significance (Feb 16, 2023)
22-37665842-G-A		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDXP	protein_coding	protein_coding	ENST00000215904	2	8208

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.256	0.649	125429	0	7	125436	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.904	78	104	0.750	0.00000680	1820
Missense in Polyphen		19	31.503	0.60311		551
Synonymous	0.110	48	49.0	0.980	0.00000358	688
Loss of Function	1.23	1	3.47	0.288	1.49e-7	58

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000616
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000598	0.0000464
European (Non-Finnish)	0.0000371	0.0000353
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein serine phosphatase that dephosphorylates 'Ser-3' in cofilin and probably also dephosphorylates phospho-serine residues in DSTN. Regulates cofilin-dependent actin cytoskeleton reorganization. Required for normal progress through mitosis and normal cytokinesis. Does not dephosphorylate phospho-threonines in LIMK1. Does not dephosphorylate peptides containing phospho- tyrosine (PubMed:15580268). Pyridoxal phosphate (PLP) phosphatase, which also catalyzes the dephosphorylation of pyridoxine 5'- phosphate (PNP) and pyridoxamine 5'-phosphate (PMP), with order of substrate preference PLP > PNP > PMP (PubMed:14522954). {ECO:0000269|PubMed:14522954, ECO:0000269|PubMed:15580268}.
• Pathway: Vitamin B6 metabolism - Homo sapiens (human);Hypophosphatasia;Vitamin B6 Metabolism;pyridoxal 5,-phosphate salvage (Consensus)

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.354
• ghis: 0.439

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.940

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdxp

Gene ontology

• Biological process: protein dephosphorylation;regulation of mitotic nuclear division;dephosphorylation;positive regulation of actin filament depolymerization;actin rod assembly;pyridoxal phosphate catabolic process;regulation of cytokinesis;cellular response to ATP
• Cellular component: cytoplasm;cytosol;plasma membrane;cell-cell junction;actin cytoskeleton;lamellipodium;midbody;lamellipodium membrane;cleavage furrow;ruffle membrane;contractile ring
• Molecular function: magnesium ion binding;phosphoserine phosphatase activity;phosphoprotein phosphatase activity;protein binding;phosphatase activity;heat shock protein binding;pyridoxal phosphatase activity;protein homodimerization activity