HomeAboutRankingsData Sources
© 2026 GeneE
🧬
GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
ⓘGeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
PUDP
pseudouridine 5'-phosphatase
Chromosome X · Xp22.31
NCBI Gene: 8226Ensembl: ENSG00000130021.16HGNC: HGNC:16818UniProt: Q08623
19PubMed Papers
20Diseases
0Drugs
1Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
protein bindingpseudouridine 5'-phosphatase activityphosphatase activitycytosolneoplasmhepatocellular carcinomaearly-onset non-syndromic cataractTotal congenital cataract
✦AI Summary

PUDP (pseudouridine 5'-phosphatase), encoded by the HDHD1 gene located on chromosome X, functions as a highly specific phosphatase that dephosphorylates pseudouridine 5'-phosphate, a potential intermediate in RNA degradation 1. The enzyme exhibits exceptional substrate specificity with a Km of 0.3 μM for pseudouridine 5'-phosphate and catalytic efficiency at least 1000-fold higher than for other phosphate esters, including 5'-UMP 1. PUDP belongs to the haloacid dehalogenase family of phosphatases, requires Mg2+ for activity, and is inhibited by Ca2+ and vanadate 1. The enzyme facilitates the excretion of pseudouridine intact in urine, as pseudouridine is not metabolized in mammals 1. PUDP demonstrates sex-linked expression patterns, with 1.5-fold higher activity in female erythrocytes compared to males, consistent with partial X-inactivation escape 1. The gene is frequently deleted in X-linked ichthyosis patients alongside the STS gene, resulting in negligible enzyme activity (<10% of controls) 1. PUDP is among 14 X-chrX genes showing consistent expression patterns across tissues in sex chromosome X, suggesting potential roles in epigenetic regulation 2.

Sources cited
1
PUDP is encoded by HDHD1 gene, functions as pseudouridine-5'-phosphatase with high specificity, belongs to haloacid dehalogenase family, shows sex-linked expression, and is deleted in X-linked ichthyosis
PMID: 20722631
2
PUDP is among 14 X-chromosomal genes showing consistent expression patterns across tissues in sex chromosome aneuploidies
PMID: 36978128
⚠Limited data available — This gene has 2 indexed publications. Summary and analysis may be incomplete.
Disease Associationsⓘ20
neoplasmOpen Targets
0.08Suggestive
hepatocellular carcinomaOpen Targets
0.07Suggestive
early-onset non-syndromic cataractOpen Targets
0.06Suggestive
Total congenital cataractOpen Targets
0.05Suggestive
Cataract-microcornea syndromeOpen Targets
0.05Suggestive
Cataract with Y-shaped suture opacitiesOpen Targets
0.05Suggestive
MODYOpen Targets
0.05Suggestive
Posterior polar cataractOpen Targets
0.05Suggestive
Partial congenital cataractOpen Targets
0.05Suggestive
Familial ocular anterior segment mesenchymal dysgenesisOpen Targets
0.05Suggestive
early-onset zonular cataractOpen Targets
0.04Suggestive
Juvenile cataract - microcornea - renal glucosuriaOpen Targets
0.04Suggestive
juvenile cataract-microcornea-renal glucosuria syndromeOpen Targets
0.04Suggestive
Anterior polar cataractOpen Targets
0.04Suggestive
maturity-onset diabetes of the young type 3Open Targets
0.04Suggestive
Persistent pupillary membraneOpen Targets
0.04Suggestive
granular corneal dystrophy type IOpen Targets
0.04Suggestive
cataract 35Open Targets
0.04Suggestive
hereditary hyperferritinemia with congenital cataractsOpen Targets
0.04Suggestive
cataract 38Open Targets
0.04Suggestive
Pathogenic Variants1
GRCh38/hg38 Xp22.31(chrX:6832908-6906043)x1Pathogenic
See cases
★☆☆☆2011
View on ClinVar ↗
Related Genes
PGGHGProtein interaction91%AGXTProtein interaction90%YIPF6Protein interaction89%STSProtein interaction87%PNPLA4Protein interaction87%YRDCProtein interaction85%
Tissue Expression6 tissues
Heart
100%
Lung
36%
Ovary
31%
Brain
30%
Liver
30%
Bone Marrow
9%
Gene Interaction Network
Click a node to explore
PUDPPGGHGAGXTYIPF6STSPNPLA4YRDC
PROTEIN STRUCTURE
Preparing viewer…
PDB9M7M · 1.26 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
1.53LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.85 [0.50–1.53]
RankingsWhere PUDP stands among ~20K protein-coding genes
  • #14,511of 20,598
    Most Researched19
  • #5,391of 5,498
    Most Pathogenic Variants1
  • #15,329of 17,882
    Most Constrained (LOEUF)1.53
Genes detectedPUDP
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
PMID: 37895274
Genes (Basel) · 2023
1.00
2
Genome-wide association analysis of treatment resistant schizophrenia for variant discovery and polygenic assessment.
PMID: 39334510
Hum Genomics · 2024
0.90
3
X chromosome dosage and the genetic impact across human tissues.
PMID: 36978128
Genome Med · 2023
0.80
4
Explaining the Differences in Opioid Overdose Deaths between Scotland and England/Wales: Implications for European Opioid Policies.
PMID: 33965949
Eur Addict Res · 2021
0.70
5
DNA polymorphisms predict time to progression from uncomplicated to complicated Crohn's disease.
PMID: 29293112
Eur J Gastroenterol Hepatol · 2018
0.60