PXYLP1

Chr 3

2-phosphoxylose phosphatase 1

Also known as: ACPL2, HEL124, XYLP

NCBI Gene: 92370 ENSG00000155893 UniProt: Q8TE99 OMIM: 619732

Enables phosphatase activity. Involved in chondroitin sulfate proteoglycan biosynthetic process and positive regulation of heparan sulfate proteoglycan biosynthetic process. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

LOEUF 0.77

Clinical Summary— PXYLP1

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

66 VUS of 77 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.77LOEUF

pLI 0.003

Z-score 2.25

OE 0.41 (0.23–0.77)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.72Z-score

OE missense 0.88 (0.79–0.98)

253 obs / 287.4 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.41 (0.23–0.77)

0≤0.351.4

Missense OE?0.88 (0.79–0.98)

0≤0.61.4

Synonymous OE?1.03

0≤1.21.6

LoF obs/exp: 7 / 17.0Missense obs/exp: 253 / 287.4Syn Z: -0.26

ClinVar Variant Classifications

77 submitted variants in ClinVar

ClinVar

Classification Summary

VUS66

Likely Benign3

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	66	66
Likely Benign	3	3
Benign	0	0
Total	69	69

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

22 pathogenic / likely-pathogenic (of 23) ClinVar copy-number / structural variants overlap PXYLP1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →