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; glycosaminoglycan biosynthetic process; and positive regulation of heparan sulfate proteoglycan biosynthetic process. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Jun 2026]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.77

LOEUF

—

Mechanism

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

Background carrier burden — how many people carry a rare variant somewhere in PXYLP1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 99

586 rare PASS variants

Rare truncating (LoF)

1 in 420

64 rare PASS variants

Rare synonymous (reference)

1 in 200

245 rare PASS variants

Rare missense and truncating variants are carried at similar rates in PXYLP1; this gene does not show strong loss-of-function constraint by this measure. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 160	1 in 2,200
South Asian	~43k	1 in 77	1 in 1,400
Remaining (unassigned)	~30k	1 in 61	1 in 620
European (Finnish)	~27k	1 in 360	≈ 1 in 10,000
Admixed American	~22k	1 in 85	1 in 1,000
African / African American	~21k	1 in 110	1 in 1,000
East Asian	~20k	1 in 73	≈ 1 in 5,000
Ashkenazi Jewish	~13k	1 in 280	≈ 1 in 5,400
Middle Eastern	~2,884	1 in 72	≈ 1 in 2,900

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 5 coding exons well covered in gnomAD exomes and genomes.? see exons ↓