IP6K2
inositol hexakisphosphate kinase 2
Basic information
Region (hg38): 3:48688003-48740353
Previous symbols: [ "IHPK2" ]
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 IP6K2 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 | 19 | 21 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 19 | 2 | 0 |
Variants in IP6K2
This is a list of pathogenic ClinVar variants found in the IP6K2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-48688296-T-G | not specified | Uncertain significance (Oct 04, 2022) | ||
| 3-48688412-A-G | not specified | Uncertain significance (Dec 16, 2024) | ||
| 3-48688434-C-T | not specified | Likely benign (Feb 24, 2022) | ||
| 3-48688460-C-T | not specified | Uncertain significance (Dec 01, 2022) | ||
| 3-48688580-C-T | not specified | Uncertain significance (Mar 01, 2024) | ||
| 3-48688665-G-A | not specified | Uncertain significance (Sep 06, 2022) | ||
| 3-48688737-T-G | Likely benign (Jul 01, 2024) | |||
| 3-48689602-T-G | not specified | Uncertain significance (Dec 27, 2022) | ||
| 3-48689627-C-T | not specified | Uncertain significance (Dec 01, 2022) | ||
| 3-48689683-C-T | not specified | Uncertain significance (Mar 07, 2025) | ||
| 3-48689684-G-A | not specified | Uncertain significance (Apr 28, 2023) | ||
| 3-48691318-C-T | not specified | Uncertain significance (Dec 19, 2023) | ||
| 3-48691319-G-A | not specified | Uncertain significance (Jan 03, 2024) | ||
| 3-48691456-C-A | not specified | Uncertain significance (Jan 20, 2023) | ||
| 3-48692984-C-T | not specified | Uncertain significance (Oct 11, 2024) | ||
| 3-48692985-G-A | not specified | Uncertain significance (Mar 12, 2024) | ||
| 3-48693147-C-T | not specified | Uncertain significance (Oct 26, 2021) | ||
| 3-48693164-C-T | not specified | Uncertain significance (Jun 07, 2024) | ||
| 3-48693165-G-T | not specified | Uncertain significance (Jan 24, 2024) | ||
| 3-48695185-T-C | not specified | Uncertain significance (Jun 04, 2024) | ||
| 3-48695195-G-A | not specified | Uncertain significance (Jun 21, 2023) | ||
| 3-48695257-G-T | not specified | Uncertain significance (Nov 03, 2023) | ||
| 3-48695276-T-C | not specified | Uncertain significance (Feb 13, 2024) |
GnomAD
Source:
| 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:
- 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