IP6K3

inositol hexakisphosphate kinase 3

Basic information

Region (hg38): 6:33721662-33746905

Previous symbols: [ "IHPK3" ]

Links

ENSG00000161896

∙ NCBI:117283 ∙ OMIM:606993 ∙ HGNC:17269 ∙ Uniprot:Q96PC2 ∙ 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 IP6K3 gene.

not_specified (71 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IP6K3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000054111.5. 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			68 clinvar	3 clinvar		71
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	68	3	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IP6K3	protein_coding	protein_coding	ENST00000451316	5	25319

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.09e-7	0.544	125535	0	213	125748	0.000847

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.340	236	251	0.940	0.0000151	2674
Missense in Polyphen		85	92.221	0.9217		977
Synonymous	0.224	109	112	0.973	0.00000761	802
Loss of Function	0.928	12	16.0	0.750	6.79e-7	193

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00135	0.00135
Ashkenazi Jewish	0.000114	0.0000992
East Asian	0.00147	0.000870
Finnish	0.00	0.00
European (Non-Finnish)	0.00113	0.00112
Middle Eastern	0.00147	0.000870
South Asian	0.000493	0.000490
Other	0.00166	0.00163

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:11502751}.;
Pathway: Phosphatidylinositol signaling system - Homo sapiens (human);Farnesoid X Receptor Pathway;Nuclear Receptors Meta-Pathway;inositol pyrophosphates biosynthesis;Metabolism;superpathway of inositol phosphate compounds;Synthesis of pyrophosphates in the cytosol;Inositol phosphate metabolism (Consensus)

Recessive Scores

pRec: 0.0903

Intolerance Scores

loftool: 0.718
rvis_EVS: 0.71
rvis_percentile_EVS: 85.76

Haploinsufficiency Scores

pHI: 0.410
hipred: N
hipred_score: 0.272
ghis: 0.475

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.171

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ip6k3
Phenotype: reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Gene ontology

Biological process: protein phosphorylation;inositol phosphate biosynthetic process;inositol phosphate metabolic process;phosphatidylinositol metabolic process
Cellular component: nucleus;cytoplasm;cytosol
Molecular function: inositol-1,3,4,5,6-pentakisphosphate kinase activity;inositol hexakisphosphate kinase activity;inositol heptakisphosphate kinase activity;inositol hexakisphosphate 6-kinase activity;inositol hexakisphosphate 5-kinase activity;ATP binding;inositol hexakisphosphate 1-kinase activity;inositol hexakisphosphate 3-kinase activity;inositol 5-diphosphate pentakisphosphate 5-kinase activity;inositol diphosphate tetrakisphosphate kinase activity