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.

• not_specified (117 variants)

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. These statistics are base on transcript: NM_000198268.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1			1
missense			116	5		121
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3			3
Total	0	0	120	5	0

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
		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

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

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