Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	54928
Gene name	3'(2'), 5'-bisphosphate nucleotidase 2
Gene symbol	BPNT2
Synonyms (NCBI Gene)	GPAPPIMP 3IMP-3IMPA3IMPAD1
Chromosome	8
Chromosome location	8q12.1
Summary	This gene encodes a member of the inositol monophosphatase family. The encoded protein is localized to the Golgi apparatus and catalyzes the hydrolysis of phosphoadenosine phosphate (PAP) to adenosine monophosphate (AMP). Mutations in this gene are a caus

Show/Hide all (5)

SNP ID	Visualize variation	Clinical significance	Consequence
rs387907101	C>T	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs387907102	T>G	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs387907103	G>A	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs724160003	G>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1554537963	AA>-	Likely-pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant

Show/Hide all (26)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001501	Process	Skeletal system development	IBA
GO:0001501	Process	Skeletal system development	IEA
GO:0001958	Process	Endochondral ossification	IEA
GO:0002063	Process	Chondrocyte development	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005794	Component	Golgi apparatus	IDA	18695242
GO:0005794	Component	Golgi apparatus	IEA
GO:0005796	Component	Golgi lumen	TAS
GO:0005829	Component	Cytosol	IDA
GO:0008254	Function	3'-nucleotidase activity	IBA
GO:0008254	Function	3'-nucleotidase activity	IEA
GO:0008441	Function	3'(2'),5'-bisphosphate nucleotidase activity	IEA
GO:0009791	Process	Post-embryonic development	IEA
GO:0012505	Component	Endomembrane system	IBA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016020	Component	Membrane	IEA
GO:0016604	Component	Nuclear body	IDA
GO:0016787	Function	Hydrolase activity	IEA
GO:0032588	Component	Trans-Golgi network membrane	IEA
GO:0032588	Component	Trans-Golgi network membrane	ISS
GO:0042733	Process	Embryonic digit morphogenesis	IEA
GO:0046854	Process	Phosphatidylinositol phosphate biosynthetic process	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0050654	Process	Chondroitin sulfate proteoglycan metabolic process	IEA
GO:0097657	Function	3',5'-nucleotide bisphosphate phosphatase activity	IEA
GO:0097657	Function	3',5'-nucleotide bisphosphate phosphatase activity	ISS

MIM	HGNC	e!Ensembl
614010	26019	ENSG00000104331

Q9NX62

Protein name

Golgi-resident adenosine 3',5'-bisphosphate 3'-phosphatase (Golgi-resident PAP phosphatase) (gPAPP) (EC 3.1.3.7) (3'(2'), 5'-bisphosphate nucleotidase 2) (Inositol monophosphatase domain-containing protein 1) (Myo-inositol monophosphatase A3) (Phosphoaden

Protein function

Exhibits 3'-nucleotidase activity toward adenosine 3',5'-bisphosphate (PAP), namely hydrolyzes adenosine 3',5'-bisphosphate into adenosine 5'-monophosphate (AMP) and a phosphate. May play a role in the formation of skeletal elements derived thro

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00459	Inositol_P	62 → 355	Inositol monophosphatase family	Family

Sequence

MAPMGIRLSPLGVAVFCLLGLGVLYHLYSGFLAGRFSLFGLGGEPGGGAAGPAAAADGGT
VDLREMLAVSVLAAVRGGDEVRRVRESNVLHEKSKGKTREGAEDKMTSGDVLSNRKMFYL
LKTAFPSVQINTEEHVDAADQEVILWDHKIPEDILKEVTTPKEVPAESVTVWIDPLDATQ
EYTEDLRKYVTTMVCVAVNGKPMLGVIHKPFSEYTAWAMVDGGSNVKARSSYNEKTPRIV
VSRSHSGMVKQVALQTFGNQTTIIPAGGAGYKVLALLDVPDKSQEKADLYIHVTYIKKWD
ICAGNAILKALGGHMTTLSGEEISYTGSDGIEGGLLASIRMNHQALVRKLPDLEKTGHK

Sequence length

359

Interactions

View interactions

	KEGG		Reactome
	Sulfur metabolism Metabolic pathways Phosphatidylinositol signaling system		Cytosolic sulfonation of small molecules

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Chondrodysplasia with joint dislocations, gPAPP type	Pathogenic; Likely pathogenic	rs2129205425, rs724160003, rs2487082948, rs1805889752, rs387907101, rs387907102, rs387907103	RCV001507085 RCV000149814 RCV003989028 RCV003991963 RCV000024085 RCV000024086 RCV000024087 View all (2 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (7)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
BPNT2-related disorder	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chondrodysplasia	Uncertain significance; Likely benign	ClinVar Disgenet	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
CHONDRODYSPLASIA WITH JOINT DISLOCATIONS GPAPP TYPE	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DIVERTICULITIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MOOD DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (29)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Brachydactyly	Brachydactyly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Catel Manzke syndrome	Catel Manzke Syndrome	BEFREE	22887726		★★★★★ ★☆☆☆☆ Found in Text Mining only
CHONDRODYSPLASIA WITH JOINT DISLOCATIONS, GPAPP TYPE	Chondrodysplasia With Joint Dislocations	ORPHANET_DG	21549340		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
CHONDRODYSPLASIA WITH JOINT DISLOCATIONS, GPAPP TYPE	Chondrodysplasia With Joint Dislocations	GENOMICS_ENGLAND_DG	21549340, 22887726		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
CHONDRODYSPLASIA WITH JOINT DISLOCATIONS, GPAPP TYPE	Chondrodysplasia With Joint Dislocations	UNIPROT_DG	21549340		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Chondrodysplasia with joint dislocations, gPAPP type	Chondrodysplasia With Joint Dislocations	Orphanet			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
CHONDRODYSPLASIA WITH JOINT DISLOCATIONS, GPAPP TYPE	Chondrodysplasia With Joint Dislocations	BEFREE	22887726		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
CHONDRODYSPLASIA WITH JOINT DISLOCATIONS, GPAPP TYPE	Chondrodysplasia With Joint Dislocations	CLINVAR_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
CHONDRODYSPLASIA WITH JOINT DISLOCATIONS, GPAPP TYPE	Chondrodysplasia With Joint Dislocations	CTD_human_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Coronal craniosynostosis	Coronal craniosynostosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Desbuquois syndrome	Desbuquois Syndrome	BEFREE	22887726		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Developmental Disabilities	Developmental disability	Pubtator	21549340	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Exophthalmos	Proptosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Facial Dysmorphism with Multiple Malformations	Facial dysmorphism syndrome	Pubtator	21549340	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	30283018	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	32753652, 36170810	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	22012575		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	23812426		★★★★★ ★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	20483645		★★★★★ ★☆☆☆☆ Found in Text Mining only
Merkel cell carcinoma	Merkel cell carcinoma	BEFREE	31218705		★★★★★ ★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Microstomia	Microstomia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	15753088, 22012575		★★★★★ ★☆☆☆☆ Found in Text Mining only
NEUROTICISM	Neuroticism	BEFREE	25994864		★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteochondrodysplasias	Osteochondrodysplasias	Pubtator	21549340	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of esophagus	Esophagus Neoplasm	BEFREE	31656650		★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	22012575		★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach Neoplasms	BEFREE	22012575		★★★★★ ★☆☆☆☆ Found in Text Mining only

BPNT2 (3'(2'), 5'-bisphosphate nucleotidase 2)