NEK4

NIMA related kinase 4

Basic information

Region (hg38): 3:52708443-52770946

Previous symbols: [ "STK2" ]

Links

ENSG00000114904 ∙ NCBI:6787 ∙ OMIM:601959 ∙ HGNC:11399 ∙ Uniprot:P51957 ∙ 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 NEK4 gene.

• Inborn genetic diseases (29 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEK4 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			26	3		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	4	0

Variants in NEK4

This is a list of pathogenic ClinVar variants found in the NEK4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-52711865-C-T		not specified	Likely benign (Sep 30, 2021)
3-52737634-T-C			Likely benign (Dec 28, 2017)
3-52737656-C-T		not specified	Likely benign (Sep 01, 2021)
3-52739479-C-T		not specified	Uncertain significance (Jan 25, 2023)
3-52739575-A-G		not specified	Uncertain significance (Jan 24, 2024)
3-52739578-T-C		not specified	Uncertain significance (Aug 13, 2021)
3-52739603-C-T		not specified	Uncertain significance (Nov 08, 2021)
3-52741450-G-A		not specified	Uncertain significance (Jun 05, 2023)
3-52741459-C-G		not specified	Uncertain significance (Sep 28, 2022)
3-52741480-C-T		not specified	Uncertain significance (Nov 27, 2023)
3-52741486-A-AT		Ciliopathy	Likely pathogenic (-)
3-52743381-G-A		not specified	Likely benign (Sep 16, 2021)
3-52743397-C-A		not specified	Uncertain significance (Sep 12, 2023)
3-52743426-C-G		not specified	Uncertain significance (Aug 02, 2023)
3-52744295-A-G		not specified	Uncertain significance (Dec 18, 2023)
3-52744305-C-G		not specified	Uncertain significance (Apr 18, 2023)
3-52746119-C-T		not specified	Uncertain significance (Nov 15, 2021)
3-52746140-T-C		not specified	Uncertain significance (Aug 04, 2023)
3-52746774-T-C		not specified	Uncertain significance (Dec 04, 2023)
3-52746780-G-C		not specified	Uncertain significance (Jan 16, 2024)
3-52746802-G-A		not specified	Uncertain significance (Feb 23, 2023)
3-52746837-T-C		not specified	Likely benign (Dec 18, 2023)
3-52746852-T-C		not specified	Likely benign (Oct 06, 2021)
3-52746879-A-G		not specified	Uncertain significance (Nov 09, 2023)
3-52751966-T-C		not specified	Uncertain significance (Feb 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEK4	protein_coding	protein_coding	ENST00000233027	16	60166

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.69e-27	0.00152	125520	1	227	125748	0.000907

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.883	381	433	0.881	0.0000226	5448
Missense in Polyphen		115	142.52	0.80692		1796
Synonymous	1.06	141	158	0.893	0.00000766	1630
Loss of Function	0.675	43	48.0	0.895	0.00000303	541

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00121	0.00121
Ashkenazi Jewish	0.00	0.00
East Asian	0.00191	0.00185
Finnish	0.000231	0.000231
European (Non-Finnish)	0.00104	0.00104
Middle Eastern	0.00191	0.00185
South Asian	0.000786	0.000784
Other	0.00198	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein kinase that seems to act exclusively upon threonine residues (By similarity). Required for normal entry into proliferative arrest after a limited number of cell divisions, also called replicative senescence. Required for normal cell cycle arrest in response to double-stranded DNA damage. {ECO:0000250|UniProtKB:Q9Z1J2, ECO:0000269|PubMed:22851694}.

Recessive Scores

• pRec: 0.0739

Intolerance Scores

• loftool: 0.993
• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.43

Haploinsufficiency Scores

• pHI: 0.501
• hipred: N
• hipred_score: 0.169
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.257

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nek4

Gene ontology

• Biological process: mitotic cell cycle;protein phosphorylation;cellular response to DNA damage stimulus;signal transduction by protein phosphorylation;stress-activated protein kinase signaling cascade;activation of protein kinase activity;positive regulation of transcription, DNA-templated;cell division;regulation of replicative cell aging;regulation of cellular senescence;regulation of response to DNA damage stimulus
• Cellular component: cytoplasm;cytosol;ciliary rootlet;ciliary transition zone;ciliary basal body;ciliary plasm
• Molecular function: protein serine/threonine kinase activity;ATP binding;manganese ion binding