IP6K3
inositol hexakisphosphate kinase 3
Basic information
Region (hg38): 6:33721662-33746905
Previous symbols: [ "IHPK3" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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.
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 | 0 | |||||
| missense | 30 | 30 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 30 | 0 | 0 |
Variants in IP6K3
This is a list of pathogenic ClinVar variants found in the IP6K3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-33722856-C-T | not specified | Uncertain significance (Feb 15, 2023) | ||
| 6-33722857-G-A | not specified | Uncertain significance (Jun 06, 2022) | ||
| 6-33722877-C-G | not specified | Uncertain significance (Apr 27, 2024) | ||
| 6-33722893-C-T | not specified | Uncertain significance (May 29, 2024) | ||
| 6-33722964-T-C | not specified | Uncertain significance (Oct 16, 2023) | ||
| 6-33722967-A-G | not specified | Uncertain significance (Nov 09, 2023) | ||
| 6-33722974-G-C | not specified | Uncertain significance (Mar 14, 2023) | ||
| 6-33722992-A-G | not specified | Uncertain significance (Mar 26, 2024) | ||
| 6-33723034-G-C | not specified | Uncertain significance (Apr 06, 2023) | ||
| 6-33723040-G-C | not specified | Uncertain significance (Sep 13, 2023) | ||
| 6-33723051-G-T | not specified | Uncertain significance (May 17, 2023) | ||
| 6-33723064-C-T | not specified | Uncertain significance (Nov 18, 2022) | ||
| 6-33723069-C-T | not specified | Uncertain significance (Aug 09, 2021) | ||
| 6-33723082-C-T | not specified | Uncertain significance (May 08, 2024) | ||
| 6-33725449-C-G | not specified | Uncertain significance (Dec 19, 2022) | ||
| 6-33725469-C-T | not specified | Uncertain significance (Jun 06, 2023) | ||
| 6-33725509-C-G | not specified | Uncertain significance (Mar 18, 2024) | ||
| 6-33725530-C-A | not specified | Uncertain significance (Nov 01, 2022) | ||
| 6-33725580-G-A | not specified | Uncertain significance (Nov 27, 2023) | ||
| 6-33726736-C-T | not specified | Uncertain significance (Jan 23, 2024) | ||
| 6-33726737-G-A | not specified | Uncertain significance (Mar 19, 2024) | ||
| 6-33726755-C-T | not specified | Uncertain significance (Aug 15, 2023) | ||
| 6-33726766-C-T | not specified | Uncertain significance (Jan 26, 2022) | ||
| 6-33726803-G-T | not specified | Uncertain significance (Aug 11, 2022) | ||
| 6-33726805-T-C | not specified | Uncertain significance (Sep 27, 2021) |
GnomAD
Source:
| 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:
- 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