BPNT2

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

Basic information

Region (hg38): 8:56957931-56993867

Previous symbols: [ "IMPAD1" ]

Links

ENSG00000104331 ∙ NCBI:54928 ∙ OMIM:614010 ∙ HGNC:26019 ∙ Uniprot:Q9NX62 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• chondrodysplasia with joint dislocations, gPAPP type (Definitive), mode of inheritance: AR
• chondrodysplasia with joint dislocations, gPAPP type (Supportive), mode of inheritance: AR
• chondrodysplasia with joint dislocations, gPAPP type (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Chondrodysplasia with joint dislocations, GPAPP type	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal	21549340; 22903787

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BPNT2 gene.

• not provided (3 variants)
• Chondrodysplasia with joint dislocations, gPAPP type (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BPNT2 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			5	29	1	35
missense		1	57	1	1	60
nonsense	2					2
start loss						0
frameshift	2	2				4
inframe indel			2			2
splice donor/acceptor (+/-2bp)			2			2
splice region				3	1	4
non coding			113	27	28	168
Total	4	3	179	57	30

Variants in BPNT2

This is a list of pathogenic ClinVar variants found in the BPNT2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
8-56957972-G-A		Chondrodysplasia with joint dislocations, gPAPP type	Uncertain significance (Jan 12, 2018)
8-56957989-C-T		Chondrodysplasia with joint dislocations, gPAPP type	Uncertain significance (Jan 13, 2018)
8-56957990-G-A		Chondrodysplasia with joint dislocations, gPAPP type	Uncertain significance (Jan 13, 2018)
8-56957996-G-A		Chondrodysplasia with joint dislocations, gPAPP type	Likely benign (Jan 12, 2018)
8-56958007-A-G		Chondrodysplasia with joint dislocations, gPAPP type	Uncertain significance (Jan 13, 2018)
8-56958041-C-T		Chondrodysplasia with joint dislocations, gPAPP type	Uncertain significance (Jan 13, 2018)
8-56958063-T-C		Chondrodysplasia with joint dislocations, gPAPP type	Benign (Jan 13, 2018)
8-56958101-T-C		Chondrodysplasia with joint dislocations, gPAPP type	Uncertain significance (Jan 12, 2018)
8-56958103-T-TG		Chondrodysplasia	Likely benign (Jun 14, 2016)
8-56958159-T-C		Chondrodysplasia with joint dislocations, gPAPP type	Likely benign (Jan 13, 2018)
8-56958186-G-T		Chondrodysplasia with joint dislocations, gPAPP type	Uncertain significance (Jan 12, 2018)
8-56958281-A-G		Chondrodysplasia with joint dislocations, gPAPP type	Benign (Jan 13, 2018)
8-56958288-T-C		Chondrodysplasia with joint dislocations, gPAPP type	Benign (Jan 13, 2018)
8-56958301-C-T		Chondrodysplasia with joint dislocations, gPAPP type	Likely benign (Jan 13, 2018)
8-56958330-C-G		Chondrodysplasia with joint dislocations, gPAPP type	Uncertain significance (Jan 12, 2018)
8-56958398-T-C		Chondrodysplasia with joint dislocations, gPAPP type	Uncertain significance (Jan 13, 2018)
8-56958439-T-C		Chondrodysplasia with joint dislocations, gPAPP type	Uncertain significance (Jan 13, 2018)
8-56958454-A-G		Chondrodysplasia with joint dislocations, gPAPP type	Uncertain significance (Jan 13, 2018)
8-56958466-G-C		Chondrodysplasia with joint dislocations, gPAPP type	Uncertain significance (Jan 13, 2018)
8-56958491-G-A		Chondrodysplasia with joint dislocations, gPAPP type	Likely benign (Jan 12, 2018)
8-56958493-C-A		Chondrodysplasia with joint dislocations, gPAPP type	Uncertain significance (Jan 12, 2018)
8-56958504-G-A		Chondrodysplasia with joint dislocations, gPAPP type	Uncertain significance (Jan 13, 2018)
8-56958590-T-A		Chondrodysplasia with joint dislocations, gPAPP type	Uncertain significance (Jan 13, 2018)
8-56958600-T-C		Chondrodysplasia with joint dislocations, gPAPP type	Uncertain significance (Jan 12, 2018)
8-56958633-G-T		Chondrodysplasia with joint dislocations, gPAPP type	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BPNT2	protein_coding	protein_coding	ENST00000262644	5	35912

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0153	0.961	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.830	159	191	0.831	0.00000935	2312
Missense in Polyphen		55	73.524	0.74806		853
Synonymous	-1.79	97	77.0	1.26	0.00000399	747
Loss of Function	1.97	5	12.5	0.399	5.95e-7	156

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000567	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000979	0.0000967
Middle Eastern	0.0000567	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the formation of skeletal elements derived through endochondral ossification, possibly by clearing adenosine 3',5'-bisphosphate produced by Golgi sulfotransferases during glycosaminoglycan sulfation. {ECO:0000250}.
• Disease: DISEASE: Chondrodysplasia with joint dislocations, GPAPP type (CDP-GPAPP) [MIM:614078]: A condition consisting of congenital joint dislocations, chondrodysplasia with short stature, micrognathia and cleft palate, and a distinctive face. {ECO:0000269|PubMed:21549340}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Sulfur metabolism - Homo sapiens (human);superpathway of D-<i>myo</i>-inositol (1,4,5)-trisphosphate metabolism;Phase II - Conjugation of compounds;D-<i>myo</i>-inositol (1,4,5)-trisphosphate degradation;Biological oxidations;Metabolism;Cytosolic sulfonation of small molecules;<i>myo</i>-inositol <i>de novo</i> biosynthesis (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.242
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.69

Haploinsufficiency Scores

• pHI: 0.230
• hipred: Y
• hipred_score: 0.507
• ghis: 0.638

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Impad1
• Phenotype: growth/size/body region phenotype; craniofacial phenotype; respiratory system 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); limbs/digits/tail phenotype; digestive/alimentary phenotype; skeleton phenotype

Gene ontology

• Biological process: skeletal system development;endochondral ossification;chondrocyte development;inositol biosynthetic process;post-embryonic development;dephosphorylation;chondroitin sulfate metabolic process;embryonic digit morphogenesis;phosphatidylinositol phosphorylation;3'-phosphoadenosine 5'-phosphosulfate metabolic process
• Cellular component: nucleus;Golgi apparatus;Golgi lumen;cytosol;membrane;integral component of membrane;nuclear body
• Molecular function: 3'-nucleotidase activity;3'(2'),5'-bisphosphate nucleotidase activity;inositol monophosphate 1-phosphatase activity;metal ion binding;inositol monophosphate 3-phosphatase activity;inositol monophosphate 4-phosphatase activity