GeneBe

IPMK

inositol polyphosphate multikinase

Basic information

Region (hg38): 10:58191517-58267894

Links

ENSG00000151151 ∙ NCBI:253430 ∙ OMIM:609851 ∙ HGNC:20739 ∙ Uniprot:Q8NFU5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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.

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.

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
1
clinvar
 1
missense
27
clinvar
 27
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
 1
non coding
0
Total 0 0 27 0 1

Variants in IPMK

This is a list of pathogenic ClinVar variants found in the IPMK region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
10-58196090-T-C not specified Uncertain significance (Jun 22, 2023)2605328
10-58196248-G-T not specified Uncertain significance (Jul 05, 2024)3529563
10-58196288-T-G not specified Uncertain significance (Nov 10, 2024)3529566
10-58196296-T-C not specified Uncertain significance (Jun 02, 2024)3286298
10-58196353-T-C not specified Uncertain significance (Feb 10, 2022)2217196
10-58196371-G-A not specified Uncertain significance (Jul 13, 2021)2344391
10-58196425-G-A not specified Uncertain significance (Jan 26, 2022)2273753
10-58196428-G-A not specified Uncertain significance (Mar 24, 2023)2517714
10-58196481-T-A not specified Uncertain significance (May 05, 2023)2543965
10-58196487-T-G not specified Uncertain significance (Aug 08, 2023)2617093
10-58196509-A-G not specified Uncertain significance (May 26, 2022)2405215
10-58196579-C-T not specified Uncertain significance (Apr 01, 2024)3286297
10-58196597-T-C not specified Uncertain significance (Dec 28, 2023)3110293
10-58196644-G-A not specified Uncertain significance (Dec 27, 2023)3110292
10-58199249-T-C not specified Uncertain significance (Jan 23, 2023)2462875
10-58199273-C-T not specified Uncertain significance (Dec 02, 2022)2331796
10-58199303-C-T not specified Uncertain significance (Sep 22, 2022)2312850
10-58199318-A-G not specified Uncertain significance (Nov 02, 2023)3110291
10-58216171-T-C not specified Uncertain significance (Aug 14, 2023)2617996
10-58216171-T-G not specified Uncertain significance (Dec 06, 2021)2265023
10-58216267-T-A not specified Uncertain significance (Jul 26, 2024)3529565
10-58216278-T-A not specified Uncertain significance (Dec 21, 2023)2377001
10-58227044-G-A Benign (May 15, 2018)770963
10-58227061-G-A not specified Uncertain significance (Jan 26, 2022)2273063
10-58227073-C-T not specified Uncertain significance (Jul 13, 2022)2301687

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