HIPK3

homeodomain interacting protein kinase 3

Basic information

Region (hg38): 11:33256672-33357023

Links

ENSG00000110422 ∙ NCBI:10114 ∙ OMIM:604424 ∙ HGNC:4915 ∙ Uniprot:Q9H422 ∙ 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 HIPK3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HIPK3 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			69	1	1	71
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	69	1	1

Variants in HIPK3

This is a list of pathogenic ClinVar variants found in the HIPK3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-33286542-C-T		not specified	Uncertain significance (Jul 13, 2021)
11-33286586-A-G		not specified	Uncertain significance (Jul 07, 2022)
11-33286625-C-T		not specified	Uncertain significance (Mar 03, 2022)
11-33286629-G-A		not specified	Uncertain significance (Sep 16, 2021)
11-33286656-G-A		not specified	Uncertain significance (Dec 23, 2024)
11-33286697-A-G		not specified	Uncertain significance (Sep 13, 2023)
11-33286746-C-T		not specified	Uncertain significance (Jul 09, 2021)
11-33286752-G-A		not specified	Uncertain significance (Feb 06, 2023)
11-33286785-G-A		not specified	Uncertain significance (May 31, 2023)
11-33287181-A-G		not specified	Uncertain significance (Oct 27, 2022)
11-33287321-C-T		not specified	Uncertain significance (Dec 06, 2024)
11-33287358-G-C		not specified	Uncertain significance (Jan 17, 2024)
11-33287402-T-G		not specified	Uncertain significance (Mar 28, 2024)
11-33287417-C-T		not specified	Uncertain significance (Dec 20, 2021)
11-33287498-T-C		not specified	Uncertain significance (Sep 14, 2023)
11-33328602-C-T		not specified	Uncertain significance (Jan 08, 2025)
11-33337138-T-A		not specified	Uncertain significance (Aug 05, 2024)
11-33338770-A-G		not specified	Uncertain significance (Jul 31, 2024)
11-33338834-T-G		not specified	Uncertain significance (Feb 17, 2024)
11-33338835-G-A			Benign (Aug 03, 2017)
11-33338838-G-A		not specified	Uncertain significance (Jul 02, 2024)
11-33338839-C-T		not specified	Likely benign (Jul 02, 2024)
11-33339362-A-G		not specified	Uncertain significance (May 30, 2024)
11-33339387-T-C		not specified	Uncertain significance (Jun 07, 2023)
11-33339477-C-T		not specified	Uncertain significance (Aug 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HIPK3	protein_coding	protein_coding	ENST00000303296	16	100352

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.277	0.723	125721	0	26	125747	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.73	519	642	0.808	0.0000319	7944
Missense in Polyphen		179	254.58	0.70311		3234
Synonymous	-0.167	238	235	1.01	0.0000119	2388
Loss of Function	5.35	13	56.3	0.231	0.00000305	672

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000458	0.000456
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000930	0.0000924
European (Non-Finnish)	0.0000974	0.0000967
Middle Eastern	0.0000544	0.0000544
South Asian	0.000100	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine/threonine-protein kinase involved in transcription regulation, apoptosis and steroidogenic gene expression. Phosphorylates JUN and RUNX2. Seems to negatively regulate apoptosis by promoting FADD phosphorylation. Enhances androgen receptor-mediated transcription. May act as a transcriptional corepressor for NK homeodomain transcription factors. The phosphorylation of NR5A1 activates SF1 leading to increased steroidogenic gene expression upon cAMP signaling pathway stimulation. In osteoblasts, supports transcription activation: phosphorylates RUNX2 that synergizes with SPEN/MINT to enhance FGFR2-mediated activation of the osteocalcin FGF- responsive element (OCFRE). {ECO:0000269|PubMed:14766760, ECO:0000269|PubMed:17210646}.
• Pathway: Cellular senescence - Homo sapiens (human);miR-targeted genes in adipocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.683
• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.24

Haploinsufficiency Scores

• pHI: 0.999
• hipred: Y
• hipred_score: 0.704
• ghis: 0.604

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.845

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hipk3
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: protein phosphorylation;apoptotic process;mRNA transcription;peptidyl-serine phosphorylation;peptidyl-threonine phosphorylation;negative regulation of apoptotic process;negative regulation of JUN kinase activity
• Cellular component: cytosol;nuclear body;PML body
• Molecular function: protein kinase activity;protein serine/threonine kinase activity;ATP binding