IP6K1

inositol hexakisphosphate kinase 1

Basic information

Region (hg38): 3:49724294-49786542

Previous symbols: [ "IHPK1" ]

Links

ENSG00000176095 ∙ NCBI:9807 ∙ OMIM:606991 ∙ HGNC:18360 ∙ Uniprot:Q92551 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IP6K1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IP6K1 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						0
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in IP6K1

This is a list of pathogenic ClinVar variants found in the IP6K1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-49727291-C-T		not specified	Uncertain significance (May 05, 2023)
3-49727294-G-A		not specified	Uncertain significance (Sep 16, 2021)
3-49727336-G-C		not specified	Uncertain significance (Nov 24, 2024)
3-49727342-G-A		not specified	Uncertain significance (May 12, 2024)
3-49727364-C-T		not specified	Uncertain significance (Jul 09, 2024)
3-49727385-C-G		not specified	Uncertain significance (Aug 26, 2022)
3-49727391-G-A		not specified	Uncertain significance (Jul 27, 2021)
3-49727514-G-C		not specified	Uncertain significance (Oct 12, 2022)
3-49727535-G-A		not specified	Uncertain significance (Oct 07, 2024)
3-49727571-G-A		not specified	Uncertain significance (Apr 26, 2023)
3-49728158-C-T		not specified	Uncertain significance (Jul 05, 2023)
3-49728168-G-A			Uncertain significance (Jan 16, 2024)
3-49732856-C-A		not specified	Uncertain significance (Oct 07, 2024)
3-49738236-C-G		not specified	Uncertain significance (Jul 19, 2022)
3-49738236-C-T		not specified	Uncertain significance (Dec 03, 2024)
3-49738303-G-A		not specified	Uncertain significance (Nov 08, 2022)
3-49738318-G-A		not specified	Uncertain significance (Jan 04, 2022)
3-49738393-T-C		not specified	Uncertain significance (Dec 21, 2023)
3-49738417-C-T		not specified	Uncertain significance (Mar 15, 2024)
3-49747848-C-T		not specified	Uncertain significance (Dec 05, 2024)
3-49747988-C-T		not specified	Uncertain significance (Aug 19, 2024)
3-49748004-C-G		not specified	Uncertain significance (Sep 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IP6K1	protein_coding	protein_coding	ENST00000321599	5	62249

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.927	0.0732	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.44	172	289	0.596	0.0000199	2909
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

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.
• Pathway: Phosphatidylinositol signaling system - Homo sapiens (human);Inositol Phosphate Metabolism;inositol pyrophosphates biosynthesis;Metabolism;superpathway of inositol phosphate compounds;Synthesis of IPs in the nucleus;Synthesis of pyrophosphates in the cytosol;Inositol phosphate metabolism (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.336
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.82

Haploinsufficiency Scores

• pHI: 0.676
• hipred: Y
• hipred_score: 0.673
• ghis: 0.608

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.947

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ip6k1
• Phenotype: reproductive system phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: inositol phosphate biosynthetic process;inositol phosphate metabolic process;phosphatidylinositol phosphorylation;negative regulation of cold-induced thermogenesis
• Cellular component: fibrillar center;nucleus;nucleoplasm;cytosol
• 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;ATP binding;inositol hexakisphosphate 1-kinase activity;inositol hexakisphosphate 3-kinase activity;inositol 5-diphosphate pentakisphosphate 5-kinase activity;inositol diphosphate tetrakisphosphate kinase activity