HIPK4

homeodomain interacting protein kinase 4

Basic information

Region (hg38): 19:40379270-40390181

Links

ENSG00000160396 ∙ NCBI:147746 ∙ OMIM:611712 ∙ HGNC:19007 ∙ Uniprot:Q8NE63 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility with azoospermia or oligozoospermia due to single gene mutation (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HIPK4 gene.

• Inborn genetic diseases (24 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HIPK4 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					1	1
missense			21	3	3	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	3	4

Variants in HIPK4

This is a list of pathogenic ClinVar variants found in the HIPK4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-40379691-C-T		not specified	Likely benign (Jul 06, 2021)
19-40380334-T-C		not specified	Uncertain significance (Aug 08, 2023)
19-40380384-A-C		not specified	Uncertain significance (Jul 05, 2023)
19-40380403-C-T		not specified	Uncertain significance (Jul 06, 2021)
19-40380457-G-T		not specified	Uncertain significance (May 11, 2022)
19-40380549-C-T		not specified	Uncertain significance (Nov 09, 2021)
19-40380648-T-C		not specified	Uncertain significance (Jul 30, 2023)
19-40380703-C-G		not specified	Uncertain significance (Oct 20, 2021)
19-40380712-C-T		Malignant tumor of prostate	Uncertain significance (-)
19-40380730-C-T			Benign (Dec 31, 2019)
19-40380747-C-T		not specified	Uncertain significance (Oct 25, 2023)
19-40380766-C-T		not specified	Likely benign (Aug 02, 2021)
19-40380773-A-C			Benign (Apr 12, 2018)
19-40380796-T-C		not specified	Likely benign (Nov 17, 2022)
19-40380891-C-T		not specified	Uncertain significance (Aug 30, 2022)
19-40380922-C-T		not specified	Uncertain significance (Mar 29, 2023)
19-40380944-C-T		not specified	Uncertain significance (Dec 27, 2023)
19-40380949-A-T		not specified	Uncertain significance (Jun 18, 2021)
19-40380959-G-A			Benign (Jul 23, 2018)
19-40381069-G-A		not specified	Uncertain significance (Oct 26, 2021)
19-40381080-G-A			Benign (Feb 26, 2018)
19-40381092-G-T		not specified	Uncertain significance (Jun 23, 2021)
19-40381121-C-A		not specified	Uncertain significance (Feb 13, 2024)
19-40381164-C-T		not specified	Uncertain significance (Dec 15, 2023)
19-40383787-G-A		not specified	Uncertain significance (Jul 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HIPK4	protein_coding	protein_coding	ENST00000291823	4	10917

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000214	0.979	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	336	404	0.831	0.0000277	4022
Missense in Polyphen		109	171.15	0.63686		1817
Synonymous	-0.203	178	175	1.02	0.0000127	1255
Loss of Function	2.08	11	21.4	0.515	0.00000117	219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000264	0.000264
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000534	0.0000462
European (Non-Finnish)	0.000108	0.000105
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.000336	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein kinase that phosphorylates human TP53 at Ser-9, and thus induces TP53 repression of BIRC5 promoter (By similarity). May act as a corepressor of transcription factors (Potential). {ECO:0000250, ECO:0000305}.
• Pathway: Cellular senescence - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.560
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.15

Haploinsufficiency Scores

• pHI: 0.148
• hipred: N
• hipred_score: 0.242
• ghis: 0.491

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.744

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hipk4

Gene ontology

• Biological process: histone phosphorylation;peptidyl-serine phosphorylation;protein autophosphorylation;regulation of signal transduction by p53 class mediator
• Cellular component: nucleus;cytoplasm
• Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding