HIPK1

homeodomain interacting protein kinase 1

Basic information

Region (hg38): 1:113929324-113977869

Links

ENSG00000163349 ∙ NCBI:204851 ∙ OMIM:608003 ∙ HGNC:19006 ∙ Uniprot:Q86Z02 ∙ 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 HIPK1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HIPK1 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			65	4		69
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	66	4	0

Variants in HIPK1

This is a list of pathogenic ClinVar variants found in the HIPK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-113940409-C-T		not specified	Uncertain significance (Apr 07, 2023)
1-113940421-T-C		not specified	Uncertain significance (Feb 05, 2024)
1-113940424-C-T		not specified	Uncertain significance (Dec 10, 2024)
1-113940445-C-T		not specified	Uncertain significance (Mar 24, 2023)
1-113940496-G-T		not specified	Uncertain significance (May 27, 2022)
1-113940502-A-G		not specified	Uncertain significance (Sep 13, 2023)
1-113940688-G-A		not specified	Uncertain significance (Sep 07, 2022)
1-113940725-G-C		not specified	Uncertain significance (Jan 26, 2023)
1-113940738-C-A		not specified	Uncertain significance (Nov 23, 2024)
1-113940883-G-A		not specified	Uncertain significance (Feb 06, 2024)
1-113940923-T-G		not specified	Uncertain significance (Jul 12, 2023)
1-113941231-A-G		not specified	Uncertain significance (Feb 07, 2023)
1-113941428-T-C		not specified	Uncertain significance (Jun 30, 2023)
1-113941434-A-G		not specified	Uncertain significance (Aug 23, 2021)
1-113952814-G-A		not specified	Uncertain significance (Apr 07, 2022)
1-113955612-G-A		not specified	Uncertain significance (Mar 30, 2024)
1-113956757-T-C		not specified	Uncertain significance (Sep 08, 2024)
1-113956760-A-G		not specified	Uncertain significance (Jan 19, 2024)
1-113956802-A-G		not specified	Uncertain significance (Jan 05, 2022)
1-113958105-A-C		not specified	Uncertain significance (Nov 28, 2023)
1-113958112-C-G		not specified	Uncertain significance (Nov 03, 2023)
1-113958204-G-C		not specified	Uncertain significance (Feb 15, 2023)
1-113958238-C-G		not specified	Uncertain significance (Mar 06, 2023)
1-113958283-C-T		not specified	Uncertain significance (Nov 13, 2023)
1-113962334-A-G		not specified	Likely benign (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HIPK1	protein_coding	protein_coding	ENST00000369558	15	48613

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.82e-7	125739	0	5	125744	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.48	477	656	0.727	0.0000343	7836
Missense in Polyphen		84	182.98	0.45906		2288
Synonymous	-0.224	264	259	1.02	0.0000146	2518
Loss of Function	6.42	2	51.9	0.0386	0.00000274	577

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00000882	0.00000879
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine/threonine-protein kinase involved in transcription regulation and TNF-mediated cellular apoptosis. Plays a role as a corepressor for homeodomain transcription factors. Phosphorylates DAXX and MYB. Phosphorylates DAXX in response to stress, and mediates its translocation from the nucleus to the cytoplasm. Inactivates MYB transcription factor activity by phosphorylation. Prevents MAP3K5-JNK activation in the absence of TNF. TNF triggers its translocation to the cytoplasm in response to stress stimuli, thus activating nuclear MAP3K5-JNK by derepression and promoting apoptosis. May be involved in anti- oxidative stress responses. Involved in the regulation of eye size, lens formation and retinal lamination during late embryogenesis. Promotes angiogenesis and to be involved in erythroid differentiation. May be involved in malignant squamous cell tumor formation. {ECO:0000269|PubMed:12702766, ECO:0000269|PubMed:12968034, ECO:0000269|PubMed:15701637, ECO:0000269|PubMed:16390825, ECO:0000269|PubMed:19646965}.
• Pathway: Cellular senescence - Homo sapiens (human);miR-222 in Exercise-Induced Cardiac Growth;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Regulation of TP53 Activity through Phosphorylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53 (Consensus)

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.0177
• rvis_EVS: -1.64
• rvis_percentile_EVS: 2.8

Haploinsufficiency Scores

• pHI: 0.994
• hipred: Y
• hipred_score: 0.739
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.982

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hipk1
• Phenotype: growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; embryo phenotype; neoplasm; 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); vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: eye development;protein phosphorylation;smoothened signaling pathway;positive regulation of cell population proliferation;anterior/posterior pattern specification;regulation of tumor necrosis factor-mediated signaling pathway;retina layer formation;neuron differentiation;adherens junction assembly;intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator;positive regulation of angiogenesis;embryonic camera-type eye morphogenesis;embryonic retina morphogenesis in camera-type eye;definitive hemopoiesis;lens induction in camera-type eye;iris morphogenesis;endothelial cell apoptotic process;extrinsic apoptotic signaling pathway;regulation of signal transduction by p53 class mediator
• Cellular component: nucleus;nucleoplasm;cytoplasm;centrosome;cytosol;PML body;nuclear speck
• Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding