IP6K2

inositol hexakisphosphate kinase 2

Basic information

Region (hg38): 3:48688003-48740353

Previous symbols: [ "IHPK2" ]

Links

ENSG00000068745

∙ NCBI:51447 ∙ OMIM:606992 ∙ HGNC:17313 ∙ Uniprot:Q9UHH9 ∙ 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 IP6K2 gene.

not_specified (33 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IP6K2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016291.4. 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			32 clinvar	2 clinvar		34
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	34	2	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IP6K2	protein_coding	protein_coding	ENST00000328631	5	52351

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.973	0.0270	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.63	134	251	0.533	0.0000147	2810
Missense in Polyphen		30	87.828	0.34158		999
Synonymous	1.20	81	96.0	0.844	0.00000526	805
Loss of Function	3.72	2	20.0	0.100	0.00000112	230

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000998	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000664	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Converts inositol hexakisphosphate (InsP6) to diphosphoinositol pentakisphosphate (InsP7/PP-InsP5). Converts 1,3,4,5,6-pentakisphosphate (InsP5) to PP-InsP4. {ECO:0000269|PubMed:10574768}.;
Pathway: Phosphatidylinositol signaling system - Homo sapiens (human);Cytokine Signaling in Immune system;inositol pyrophosphates biosynthesis;Immune System;Metabolism;superpathway of inositol phosphate compounds;Synthesis of IPs in the nucleus;Inositol phosphate metabolism;Interferon alpha/beta signaling;Interferon Signaling (Consensus)

Recessive Scores

pRec: 0.0886

Intolerance Scores

loftool: 0.794
rvis_EVS: 0.24
rvis_percentile_EVS: 69.37

Haploinsufficiency Scores

pHI: 0.275
hipred: Y
hipred_score: 0.775
ghis: 0.506

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.694

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ip6k2
Phenotype: cellular phenotype; immune system phenotype; homeostasis/metabolism phenotype; neoplasm; 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); hematopoietic system phenotype; digestive/alimentary phenotype;

Zebrafish Information Network

Gene name: ip6k2a
Affected structure: neural crest cell
Phenotype tag: abnormal
Phenotype quality: decreased amount

Gene ontology

Biological process: phosphate ion transport;negative regulation of cell growth;inositol phosphate biosynthetic process;positive regulation of apoptotic process;inositol phosphate metabolic process;phosphatidylinositol phosphorylation;type I interferon signaling pathway
Cellular component: fibrillar center;nucleus;nucleoplasm;cell junction
Molecular function: inositol-1,3,4,5,6-pentakisphosphate kinase activity;inositol hexakisphosphate kinase activity;inositol heptakisphosphate kinase activity;inositol hexakisphosphate 5-kinase activity;protein binding;ATP binding;inositol hexakisphosphate 1-kinase activity;inositol hexakisphosphate 3-kinase activity;inositol 5-diphosphate pentakisphosphate 5-kinase activity;inositol diphosphate tetrakisphosphate kinase activity