PXYLP1

2-phosphoxylose phosphatase 1, the group of Acid phosphatases

Basic information

Region (hg38): 3:141228725-141367753

Previous symbols: [ "ACPL2" ]

Links

ENSG00000155893 ∙ NCBI:92370 ∙ OMIM:619732 ∙ HGNC:26303 ∙ Uniprot:Q8TE99 ∙ 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 PXYLP1 gene.

• Inborn genetic diseases (20 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PXYLP1 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in PXYLP1

This is a list of pathogenic ClinVar variants found in the PXYLP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-141260219-C-T		not specified	Uncertain significance (Dec 07, 2021)
3-141278420-C-T		not specified	Uncertain significance (Aug 02, 2023)
3-141279425-C-T		not specified	Uncertain significance (Feb 02, 2024)
3-141279450-A-G		not specified	Uncertain significance (Aug 15, 2023)
3-141279459-C-T		not specified	Uncertain significance (Jul 21, 2021)
3-141279462-A-G		not specified	Uncertain significance (Feb 06, 2023)
3-141287381-G-A		not specified	Uncertain significance (Jan 04, 2022)
3-141292303-A-T		not specified	Uncertain significance (Dec 20, 2023)
3-141292351-G-A		not specified	Likely benign (Apr 08, 2022)
3-141292462-C-T		not specified	Uncertain significance (Dec 05, 2022)
3-141292475-C-T		not specified	Uncertain significance (Apr 12, 2023)
3-141292478-T-C		not specified	Uncertain significance (Mar 07, 2024)
3-141292489-G-A		not specified	Uncertain significance (Dec 03, 2021)
3-141292541-G-A		not specified	Uncertain significance (Feb 16, 2023)
3-141292556-G-A		not specified	Uncertain significance (Jan 17, 2023)
3-141292615-C-T		not specified	Uncertain significance (Jan 05, 2022)
3-141292654-A-G		not specified	Uncertain significance (Jun 06, 2023)
3-141292912-C-A		not specified	Uncertain significance (Sep 13, 2023)
3-141293056-A-G		not specified	Uncertain significance (Dec 22, 2023)
3-141293077-C-T		not specified	Uncertain significance (Nov 03, 2023)
3-141293078-A-T		not specified	Uncertain significance (Nov 03, 2023)
3-141293084-G-T		not specified	Uncertain significance (Mar 22, 2022)
3-141293105-C-T		not specified	Uncertain significance (Aug 30, 2021)
3-141293122-C-T		not specified	Uncertain significance (May 18, 2022)
3-141293123-G-A		not specified	Uncertain significance (Nov 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PXYLP1	protein_coding	protein_coding	ENST00000286353	5	66181

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00309	0.987	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.720	253	287	0.880	0.0000168	3175
Missense in Polyphen		81	100.05	0.80963		1108
Synonymous	-0.260	117	113	1.03	0.00000666	938
Loss of Function	2.25	7	17.0	0.412	8.26e-7	213

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000907	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000968	0.0000967
Middle Eastern	0.0000544	0.0000544
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Responsible for the 2-O-dephosphorylation of xylose in the glycosaminoglycan-protein linkage region of proteoglycans thereby regulating the amount of mature glycosaminoglycan (GAG) chains. Sulfated glycosaminoglycans (GAGs), including heparan sulfate and chondroitin sulfate, are synthesized on the so-called common GAG-protein linkage region (GlcUAbeta1-3Galbeta1-3Galbeta1- 4Xylbeta1-O-Ser) of core proteins, which is formed by the stepwise addition of monosaccharide residues by the respective specific glycosyltransferases. Xylose 2-O-dephosphorylation during completion of linkage region formation is a prerequisite for the initiation and efficient elongation of the repeating disaccharide region of GAG chains. {ECO:0000269|PubMed:24425863}.

Intolerance Scores

• rvis_EVS: -0.38
• rvis_percentile_EVS: 28.01

Haploinsufficiency Scores

• pHI: 0.182
• hipred: Y
• hipred_score: 0.595
• ghis: 0.466

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Pxylp1
• Phenotype: hematopoietic system phenotype; skeleton phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: glycosaminoglycan biosynthetic process;positive regulation of heparan sulfate proteoglycan biosynthetic process;dephosphorylation;chondroitin sulfate proteoglycan biosynthetic process
• Cellular component: Golgi membrane;Golgi apparatus;integral component of membrane
• Molecular function: protein binding;phosphatase activity