IPPK

inositol-pentakisphosphate 2-kinase

Basic information

Region (hg38): 9:92613183-92670131

Previous symbols: [ "C9orf12" ]

Links

ENSG00000127080 ∙ NCBI:64768 ∙ OMIM:619043 ∙ HGNC:14645 ∙ Uniprot:Q9H8X2 ∙ 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 IPPK gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IPPK 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			37	1		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	1	0

Variants in IPPK

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

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

Position	Type	Phenotype	Significance	ClinVar
9-92615842-T-C		not specified	Uncertain significance (Apr 12, 2022)
9-92615849-C-T		not specified	Uncertain significance (Feb 28, 2023)
9-92615864-C-T		not specified	Uncertain significance (May 24, 2023)
9-92615878-C-T		not specified	Uncertain significance (Sep 01, 2024)
9-92615884-G-A		not specified	Uncertain significance (Dec 23, 2024)
9-92615909-G-A		not specified	Likely benign (Jun 06, 2023)
9-92615933-C-T		not specified	Uncertain significance (Jun 02, 2023)
9-92615951-T-G		not specified	Uncertain significance (Aug 04, 2024)
9-92615972-C-T		not specified	Uncertain significance (Jun 23, 2021)
9-92615990-G-C		not specified	Uncertain significance (Aug 20, 2024)
9-92616038-C-T		not specified	Uncertain significance (Feb 13, 2024)
9-92619543-A-C		not specified	Uncertain significance (Jan 18, 2025)
9-92634390-G-A		not specified	Uncertain significance (Jun 11, 2024)
9-92635164-T-C		not specified	Uncertain significance (Oct 06, 2022)
9-92635165-C-T		not specified	Uncertain significance (Aug 10, 2023)
9-92635185-C-T		not specified	Uncertain significance (Aug 04, 2024)
9-92635194-C-T		not specified	Uncertain significance (Nov 12, 2021)
9-92635287-G-A		not specified	Uncertain significance (Aug 04, 2021)
9-92638009-C-T		not specified	Uncertain significance (Aug 02, 2021)
9-92638010-G-A		not specified	Uncertain significance (Dec 22, 2023)
9-92638073-T-C		not specified	Uncertain significance (Dec 28, 2024)
9-92638099-G-A		not specified	Uncertain significance (Feb 11, 2022)
9-92638117-C-T		not specified	Uncertain significance (May 24, 2023)
9-92638213-T-A		not specified	Uncertain significance (Jan 29, 2024)
9-92638222-T-C		not specified	Uncertain significance (Jan 02, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IPPK	protein_coding	protein_coding	ENST00000287996	13	57082

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.874	0.126	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.00	200	297	0.673	0.0000180	3206
Missense in Polyphen		49	103.81	0.472		1179
Synonymous	0.149	123	125	0.983	0.00000837	920
Loss of Function	4.11	5	28.8	0.174	0.00000145	324

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000163	0.000149
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000355	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phosphorylates Ins(1,3,4,5,6)P5 at position 2 to form Ins(1,2,3,4,5,6)P6 (InsP6 or phytate). InsP6 is involved in many processes such as mRNA export, non-homologous end-joining, endocytosis, ion channel regulation. It also protects cells from TNF-alpha-induced apoptosis. {ECO:0000269|PubMed:12084730, ECO:0000269|PubMed:15967797}.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Inositol Phosphate Metabolism;Inositol Metabolism;1D-<i>myo</i>-inositol hexakisphosphate biosynthesis II (mammalian);inositol pyrophosphates biosynthesis;Metabolism;superpathway of inositol phosphate compounds;Synthesis of IPs in the nucleus;Synthesis of pyrophosphates in the cytosol;Inositol phosphate metabolism;1D-<i>myo</i>-inositol hexakisphosphate biosynthesis V (from Ins(1,3,4)P3) (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.265
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.09

Haploinsufficiency Scores

• pHI: 0.0890
• hipred: Y
• hipred_score: 0.717
• ghis: 0.523

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.711

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ippk
• 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)

Zebrafish Information Network

• Gene name: ippk
• Affected structure: central canal
• Phenotype tag: abnormal
• Phenotype quality: decreased functionality

Gene ontology

• Biological process: inositol phosphate biosynthetic process;inositol phosphate metabolic process;inositol phosphorylation;positive regulation of transcription of nucleolar large rRNA by RNA polymerase I
• Cellular component: nucleus;nucleoplasm;nucleolus;cytosol
• Molecular function: protein binding;ATP binding;protein-containing complex scaffold activity;inositol pentakisphosphate 2-kinase activity