BPNT1

3'(2'), 5'-bisphosphate nucleotidase 1, the group of Phosphoinositide phosphatases

Basic information

Region (hg38): 1:220057482-220090462

Links

ENSG00000162813

∙ NCBI:10380 ∙ OMIM:604053 ∙ HGNC:1096 ∙ Uniprot:O95861 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BPNT1 gene.

not_specified (24 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BPNT1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006085.6. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			24 clinvar	1 clinvar		25
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	24	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BPNT1	protein_coding	protein_coding	ENST00000469520	8	32981

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000223	0.915	124772	0	22	124794	0.0000881

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.36	119	169	0.706	0.00000850	1982
Missense in Polyphen		49	71.106	0.68911		822
Synonymous	0.389	56	59.8	0.936	0.00000292	617
Loss of Function	1.62	10	17.2	0.580	9.65e-7	198

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000190	0.000190
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000887	0.0000883
Middle Eastern	0.0000556	0.0000556
South Asian	0.000204	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Converts adenosine 3'-phosphate 5'-phosphosulfate (PAPS) to adenosine 5'-phosphosulfate (APS) and 3'(2')-phosphoadenosine 5'- phosphate (PAP) to AMP. Has 1000-fold lower activity towards inositol 1,4-bisphosphate (Ins(1,4)P2) and inositol 1,3,4- trisphosphate (Ins(1,3,4)P3), but does not hydrolyze Ins(1)P, Ins(3,4)P2, Ins(1,3,4,5)P4 or InsP6. {ECO:0000269|PubMed:10224133}.;
Pathway: Sulfur metabolism - Homo sapiens (human);Sulfate/Sulfite Metabolism;Sulfite oxidase deficiency;Phase II - Conjugation of compounds;Biological oxidations;Metabolism;Cytosolic sulfonation of small molecules (Consensus)

Recessive Scores

pRec: 0.0964

Intolerance Scores

loftool: 0.657
rvis_EVS: 0.46
rvis_percentile_EVS: 78.28

Haploinsufficiency Scores

pHI: 0.187
hipred: N
hipred_score: 0.290
ghis: 0.407

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap
gene_indispensability_pred: E
gene_indispensability_score: 0.818

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Bpnt1
Phenotype: homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); liver/biliary system phenotype;

Gene ontology

Biological process: nucleobase-containing compound metabolic process;nervous system development;dephosphorylation;phosphatidylinositol phosphorylation;3'-phosphoadenosine 5'-phosphosulfate metabolic process
Cellular component: cytosol
Molecular function: 3'(2'),5'-bisphosphate nucleotidase activity;metal ion binding