HomeAboutRankingsData Sources
Β© 2026 GeneE
🧬
GeneE
2 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
BPNT2
3'(2'), 5'-bisphosphate nucleotidase 2
Chromosome 8 Β· 8q12.1
NCBI Gene: 54928Ensembl: ENSG00000104331.10HGNC: HGNC:26019UniProt: Q9NX62
34PubMed Papers
21Diseases
0Drugs
11Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
Golgi apparatusmembraneskeletal system developmentendomembrane systemchondrodysplasia with joint dislocations, gPAPP typechronic kidney diseasebone remodeling diseasebreast disease
✦AI Summary

BPNT2 is a 3'-nucleotidase that hydrolyzes adenosine 3',5'-bisphosphate (PAP) to AMP and phosphate. Located in the Golgi apparatus and trans-Golgi network, it exhibits 3',5'-nucleotide bisphosphate phosphatase activity. Based on limited published evidence, BPNT2 likely plays roles in: (1) clearing PAP produced during glycosaminoglycan sulfation by Golgi sulfotransferases, supporting endochondral ossification and skeletal development; and (2) regulating intracellular pAp levels for mammalian rapid tRNA decay (mRTD) pathway function under stress conditions 1. Mutations cause chondrodysplasia with joint dislocations, GPAPP type.

Sources cited
1
BPNT2 controls intracellular pAp levels as part of the mammalian rapid tRNA decay (mRTD) pathway for tRNA quality control under heat stress
PMID: 40595590
⚠Limited data available β€” This gene has 1 indexed publication. Summary and analysis may be incomplete.
Disease Associationsβ“˜21
chondrodysplasia with joint dislocations, gPAPP typeOpen Targets
0.74Strong
chronic kidney diseaseOpen Targets
0.32Weak
bone remodeling diseaseOpen Targets
0.23Weak
breast diseaseOpen Targets
0.20Weak
liver diseaseOpen Targets
0.20Weak
chondrodysplasiaOpen Targets
0.19Weak
Abruptio PlacentaeOpen Targets
0.19Weak
rheumatoid arthritisOpen Targets
0.19Weak
Benign Thyroid Gland NeoplasmOpen Targets
0.19Weak
adolescent idiopathic scoliosisOpen Targets
0.18Weak
alcohol drinkingOpen Targets
0.17Weak
ovarian neoplasmOpen Targets
0.17Weak
temporomandibular joint disorderOpen Targets
0.17Weak
placental retentionOpen Targets
0.13Weak
diabetes mellitusOpen Targets
0.13Weak
type 2 diabetes mellitusOpen Targets
0.13Weak
connective tissue diseaseOpen Targets
0.13Weak
allergic diseaseOpen Targets
0.12Weak
asthmaOpen Targets
0.12Weak
breast cancerOpen Targets
0.08Suggestive
Chondrodysplasia with joint dislocations, GPAPP typeUniProt
Pathogenic Variants11
NM_017813.5(BPNT2):c.559C>T (p.Arg187Ter)Pathogenic
Chondrodysplasia with joint dislocations, gPAPP type|not provided
β˜…β˜…β˜†β˜†2022β†’ Residue 187
NM_017813.5(BPNT2):c.421C>T (p.Gln141Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 141
NM_017813.5(BPNT2):c.532dup (p.Ala178fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 178
NM_017813.5(BPNT2):c.118_130dup (p.Glu44fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 44
NM_017813.5(BPNT2):c.1007T>C (p.Leu336Pro)Likely pathogenic
Chondrodysplasia with joint dislocations, gPAPP type
β˜…β˜†β˜†β˜†2024β†’ Residue 336
NM_017813.5(BPNT2):c.713_714insCTTCCTATGG (p.Arg238fs)Likely pathogenic
Chondrodysplasia with joint dislocations, gPAPP type
β˜…β˜†β˜†β˜†2024β†’ Residue 238
NM_017813.5(BPNT2):c.473_474dup (p.Thr159Ter)Pathogenic
Chondrodysplasia with joint dislocations, gPAPP type
β˜…β˜†β˜†β˜†2021β†’ Residue 159
NM_017813.5(BPNT2):c.972_973del (p.Ser324fs)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2017β†’ Residue 324
NM_017813.5(BPNT2):c.324del (p.Ser108fs)Pathogenic
Chondrodysplasia with joint dislocations, gPAPP type
β˜†β˜†β˜†β˜†2012β†’ Residue 108
NM_017813.5(BPNT2):c.547A>C (p.Thr183Pro)Pathogenic
Chondrodysplasia with joint dislocations, gPAPP type
β˜†β˜†β˜†β˜†2011β†’ Residue 183
NM_017813.5(BPNT2):c.529G>A (p.Asp177Asn)Pathogenic
Chondrodysplasia with joint dislocations, gPAPP type
β˜†β˜†β˜†β˜†2011β†’ Residue 177
View on ClinVar β†—
Related Genes
PAPSS2Protein interaction98%MTM1Protein interaction94%INPP1Protein interaction93%BPNT1Protein interaction93%IMPA2Protein interaction91%ISYNA1Protein interaction91%
Tissue Expression6 tissues
Heart
100%
Brain
99%
Liver
53%
Lung
44%
Bone Marrow
29%
Ovary
27%
Gene Interaction Network
Click a node to explore
BPNT2PAPSS2MTM1INPP1BPNT1IMPA2ISYNA1
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q9NX62
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.62LoF Tolerant
pLIβ“˜
0.79Intermediate
Observed/Expected LoF0.33 [0.19–0.62]
RankingsWhere BPNT2 stands among ~20K protein-coding genes
  • #11,120of 20,598
    Most Researched34
  • #2,797of 5,498
    Most Pathogenic Variants11
  • #4,336of 17,882
    Most Constrained (LOEUF)0.62 Β· top quartile
Genes detectedBPNT2
Sources retrieved2 papers
Response timeβ€”
πŸ“„ Sources
2
1
Mammalian tRNA acetylation determines translation efficiency and tRNA quality control.
PMID: 40595590
Nat Commun Β· 2025
1.00
2
PMID: 34634304
0.50