IPPK
Basic information
Region (hg38): 9:92613183-92670131
Previous symbols: [ "C9orf12" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (68 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the IPPK gene is commonly pathogenic or not. These statistics are base on transcript: NM_000022755.6. 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 | 67 | 68 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 67 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IPPK | protein_coding | protein_coding | ENST00000287996 | 13 | 57082 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.874 | 0.126 | 125737 | 0 | 11 | 125748 | 0.0000437 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.00 | 200 | 297 | 0.673 | 0.0000180 | 3206 |
| Missense in Polyphen | 49 | 103.81 | 0.472 | 1179 | ||
| Synonymous | 0.149 | 123 | 125 | 0.983 | 0.00000837 | 920 |
| Loss of Function | 4.11 | 5 | 28.8 | 0.174 | 0.00000145 | 324 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000163 | 0.000149 |
| Ashkenazi Jewish | 0.000101 | 0.0000992 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000355 | 0.0000352 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Phosphorylates Ins(1,3,4,5,6)P5 at position 2 to form Ins(1,2,3,4,5,6)P6 (InsP6 or phytate). InsP6 is involved in many processes such as mRNA export, non-homologous end-joining, endocytosis, ion channel regulation. It also protects cells from TNF-alpha-induced apoptosis. {ECO:0000269|PubMed:12084730, ECO:0000269|PubMed:15967797}.;
- Pathway
- Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Inositol Phosphate Metabolism;Inositol Metabolism;1D-<i>myo</i>-inositol hexakisphosphate biosynthesis II (mammalian);inositol pyrophosphates biosynthesis;Metabolism;superpathway of inositol phosphate compounds;Synthesis of IPs in the nucleus;Synthesis of pyrophosphates in the cytosol;Inositol phosphate metabolism;1D-<i>myo</i>-inositol hexakisphosphate biosynthesis V (from Ins(1,3,4)P3)
(Consensus)
Recessive Scores
- pRec
- 0.119
Intolerance Scores
- loftool
- 0.265
- rvis_EVS
- -0.02
- rvis_percentile_EVS
- 52.09
Haploinsufficiency Scores
- pHI
- 0.0890
- hipred
- Y
- hipred_score
- 0.717
- ghis
- 0.523
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.711
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ippk
- 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);
Zebrafish Information Network
- Gene name
- ippk
- Affected structure
- central canal
- Phenotype tag
- abnormal
- Phenotype quality
- decreased functionality
Gene ontology
- Biological process
- inositol phosphate biosynthetic process;inositol phosphate metabolic process;inositol phosphorylation;positive regulation of transcription of nucleolar large rRNA by RNA polymerase I
- Cellular component
- nucleus;nucleoplasm;nucleolus;cytosol
- Molecular function
- protein binding;ATP binding;protein-containing complex scaffold activity;inositol pentakisphosphate 2-kinase activity