IP6K3

protein-coding

inositol hexakisphosphate kinase 3

Gene summary

This gene encodes a protein that belongs to the inositol phosphokinase (IPK) family. This protein is likely responsible for the conversion of inositol hexakisphosphate (InsP6) to diphosphoinositol pentakisphosphate (InsP7/PP-InsP5). It may also convert 1,3,4,5,6-pentakisphosphate (InsP5) to PP-InsP4. Alternative splicing results in multiple transcript variants encoding the same protein.[provided by RefSeq, Dec 2008]

Previous symbols:

IHPK3

MANE transcript

NM_054111.5

Inheritance

—

ClinVar variants

U:77B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.75

Max pathogenic AF

—

Genomic locus

chr6:33,721,662-33,746,905

External References & Databases

Ensembl (ENSG00000161896)

Transcript & Mutation Effects

hg38 • Region Span ~25.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to IP6K3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 77

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_054111.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			76 clinvar	4 clinvar		80
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	77	4	0	81

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 67 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_054111.5	RefSeq	NP_473452.2	5	MANE Select
ENST00000293756.5	Ensembl	ENSP00000293756.4	5	MANE Select
NM_001142883.2	RefSeq	NP_001136355.1	5	Standard
ENST00000451316.6	Ensembl	ENSP00000398861.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Phosphatidylinositol signaling system - Homo sapiens (human)
Farnesoid X Receptor Pathway
Nuclear Receptors Meta-Pathway
inositol pyrophosphates biosynthesis
Metabolism

Biological Process

protein phosphorylation
inositol phosphate biosynthetic process
inositol phosphate metabolic process
phosphatidylinositol metabolic process

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

Cellular Component

nucleus
cytoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000451316
Coding exons: 5
Length: 25319
Individuals with no LoFs: 125535
Homozygous LoFs: 0
Heterozygous LoFs: 213
Defined: 125748
p: 0.000847

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.340	236	251	0.940	0.0000151	2674
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.0012	0.0012	notable
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0.0015	0.00087	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.0011	0.0011	notable
South Asian	0.00049	0.00049	rare
Other	0.0017	0.0016	notable

dbNSFP Gene Annotations

Source: dbNSFP

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}.;

Recessive Scores

pRec: 0.0903

Intolerance Scores

LoFtool: 0.718
RVIS EVS: 0.71
RVIS percentile EVS: 85.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.171

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium