IP6K1

protein-coding

inositol hexakisphosphate kinase 1

Gene summary

This gene encodes a member of the inositol phosphokinase family. The encoded protein may be 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. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jun 2011]

Previous symbols:

IHPK1

MANE transcript

NM_153273.4

Inheritance

—

ClinVar variants

U:44

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr3:49,724,294-49,786,542

External References & Databases

Ensembl (ENSG00000176095)

Transcript & Mutation Effects

hg38 • Region Span ~62.2 kb

Loading mutation effect viewer...

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 IP6K1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 39

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153273.4. 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			2 clinvar			2
missense			41 clinvar			41
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	44	0	0	44

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153273.4	RefSeq	NP_695005.1	5	MANE Select
ENST00000321599.9	Ensembl	ENSP00000323780.4	5	MANE Select
NM_001006115.3	RefSeq	NP_001006115.1	3	Standard
NM_001242829.2	RefSeq	NP_001229758.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Phosphatidylinositol signaling system - Homo sapiens (human)
Inositol Phosphate Metabolism
inositol pyrophosphates biosynthesis
Metabolism
superpathway of inositol phosphate compounds

Biological Process

inositol phosphate biosynthetic process
inositol phosphate metabolic process
phosphatidylinositol phosphorylation
negative regulation of cold-induced thermogenesis

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

Cellular Component

fibrillar center
nucleus
nucleoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000321599
Coding exons: 5
Length: 62249
Individuals with no LoFs: 125741
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125748
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.44	172	289	0.596	0.0000199	2909
Missense (PolyPhen)		47	132.49	0.35473		1316
Synonymous	0.154	111	113	0.982	0.00000698	871
Loss of Function	3.39	2	17.2	0.117	8.99e-7	198

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

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.;

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.336
RVIS EVS: -0.2
RVIS percentile EVS: 38.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.947

Gene Damage Prediction

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