IPMK

inositol polyphosphate multikinase

Basic information

Region (hg38): 10:58191517-58267894

Links

ENSG00000151151NCBI:253430OMIM:609851HGNC:20739Uniprot:Q8NFU5AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • hereditary neuroendocrine tumor of small intestine (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Small intestinal carcinoid, hereditaryADOncologicIndividuals have been described as at high risk of small intestinal carcinoid tumors, and awareness may allow surveillance and prompt managementOncologic25865046

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IPMK gene.

  • not_specified (52 variants)
  • not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IPMK gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152230.5. 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
2
missense
49
clinvar
3
clinvar
52
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 49 3 2
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
IPMKprotein_codingprotein_codingENST00000373935 676417
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9630.0374125712081257200.0000318
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7731832150.8520.00001002723
Missense in Polyphen3458.3560.58263740
Synonymous-0.7319182.61.100.00000397772
Loss of Function3.62219.10.1059.90e-7245

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001230.000123
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.00004620.0000462
European (Non-Finnish)0.00003560.0000352
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Inositol phosphate kinase with a broad substrate specificity. Has a preference for inositol 1,4,5-trisphosphate (Ins(1,4,5)P3) and inositol 1,3,4,6-tetrakisphosphate (Ins(1,3,4,6)P4) (PubMed:12027805, PubMed:12223481). Plays an important role in MLKL-mediated necroptosis. Produces highly phosphorylated inositol phosphates such as inositolhexakisphosphate (InsP6) which bind to MLKL mediating the release of an N-terminal auto-inhibitory region leading to its activation. Essential for activated phospho-MLKL to oligomerize and localize to the cell membrane during necroptosis (PubMed:29883610). {ECO:0000269|PubMed:12027805, ECO:0000269|PubMed:12223481, ECO:0000269|PubMed:29883610}.;
Pathway
Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Inositol Phosphate Metabolism;Inositol Metabolism;D-<i>myo</i>-inositol (1,3,4)-trisphosphate biosynthesis;superpathway of D-<i>myo</i>-inositol (1,4,5)-trisphosphate metabolism;D-<i>myo</i>-inositol (3,4,5,6)-tetrakisphosphate biosynthesis;1D-<i>myo</i>-inositol hexakisphosphate biosynthesis II (mammalian);Inositol phosphate metabolism;inositol pyrophosphates biosynthesis;Metabolism;superpathway of inositol phosphate compounds;Phosphatidylinositol phosphate metabolism;Synthesis of IPs in the nucleus;D-<i>myo</i>-inositol (1,4,5,6)-tetrakisphosphate biosynthesis;Inositol phosphate metabolism;1D-<i>myo</i>-inositol hexakisphosphate biosynthesis V (from Ins(1,3,4)P3) (Consensus)

Recessive Scores

pRec
0.0941

Intolerance Scores

loftool
0.228
rvis_EVS
0.06
rvis_percentile_EVS
58.74

Haploinsufficiency Scores

pHI
0.510
hipred
Y
hipred_score
0.701
ghis
0.475

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
K
gene_indispensability_pred
E
gene_indispensability_score
0.841

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ipmk
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); embryo phenotype; 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); growth/size/body region phenotype;

Zebrafish Information Network

Gene name
ipmkb
Affected structure
cranium
Phenotype tag
abnormal
Phenotype quality
hypoplastic

Gene ontology

Biological process
phosphorylation;inositol phosphate biosynthetic process;inositol phosphate metabolic process;necroptotic process
Cellular component
nucleus;nucleoplasm;nucleolus
Molecular function
inositol-1,4,5-trisphosphate 6-kinase activity;inositol tetrakisphosphate 3-kinase activity;inositol tetrakisphosphate 6-kinase activity;ATP binding;inositol-1,4,5-trisphosphate 3-kinase activity;inositol tetrakisphosphate 5-kinase activity