NEK11

NIMA related kinase 11

Basic information

Region (hg38): 3:131026850-131350465

Links

ENSG00000114670 ∙ NCBI:79858 ∙ OMIM:609779 ∙ HGNC:18593 ∙ Uniprot:Q8NG66 ∙ 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 NEK11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEK11 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				4		4
missense			38	1	2	41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	5	2

Variants in NEK11

This is a list of pathogenic ClinVar variants found in the NEK11 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-131029721-C-A		not specified	Uncertain significance (Jun 24, 2022)
3-131029746-G-T		not specified	Uncertain significance (Aug 16, 2022)
3-131029775-A-G		not specified	Uncertain significance (Jan 26, 2022)
3-131029804-A-G			Likely benign (Jun 01, 2023)
3-131029871-G-C		not specified	Uncertain significance (Aug 05, 2023)
3-131080442-T-A		not specified	Uncertain significance (May 27, 2022)
3-131080512-A-G		not specified	Uncertain significance (Jul 21, 2021)
3-131080550-G-C		not specified	Uncertain significance (Apr 15, 2024)
3-131080574-A-G		not specified	Uncertain significance (Dec 15, 2023)
3-131109807-G-A		not specified	Uncertain significance (Jul 20, 2021)
3-131109825-T-C		not specified	Uncertain significance (Feb 22, 2024)
3-131109857-C-T		not specified	Uncertain significance (Oct 17, 2023)
3-131109897-T-C		not specified	Uncertain significance (Jun 29, 2023)
3-131132770-T-C		not specified	Uncertain significance (Dec 06, 2022)
3-131132777-A-G			Uncertain significance (Nov 01, 2022)
3-131133858-G-A		not specified	Uncertain significance (Nov 08, 2022)
3-131133866-G-T		not specified	Uncertain significance (Oct 04, 2022)
3-131133881-C-T		not specified	Uncertain significance (Jun 29, 2022)
3-131133886-A-G		not specified	Uncertain significance (Apr 19, 2023)
3-131133929-A-G		not specified	Uncertain significance (Jul 05, 2023)
3-131133948-G-A			Likely benign (Nov 01, 2022)
3-131152485-A-G		not specified	Uncertain significance (Nov 08, 2022)
3-131152509-C-T		not specified	Uncertain significance (Aug 14, 2024)
3-131152512-A-G		not specified	Uncertain significance (Dec 13, 2022)
3-131152518-C-G		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEK11	protein_coding	protein_coding	ENST00000383366	16	323616

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.04e-21	0.00408	125562	0	186	125748	0.000740

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.280	353	339	1.04	0.0000168	4259
Missense in Polyphen		110	99.309	1.1077		1305
Synonymous	0.526	113	120	0.939	0.00000648	1152
Loss of Function	0.455	34	37.0	0.919	0.00000191	465

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00169	0.00162
Ashkenazi Jewish	0.00	0.00
East Asian	0.000274	0.000272
Finnish	0.000970	0.000971
European (Non-Finnish)	0.00100	0.000985
Middle Eastern	0.000274	0.000272
South Asian	0.000433	0.000425
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein kinase which plays an important role in the G2/M checkpoint response to DNA damage. Controls degradation of CDC25A by directly phosphorylating it on residues whose phosphorylation is required for BTRC-mediated polyubiquitination and degradation. {ECO:0000269|PubMed:12154088, ECO:0000269|PubMed:19734889, ECO:0000269|PubMed:20090422}.

Recessive Scores

• pRec: 0.0904

Intolerance Scores

• loftool: 0.983
• rvis_EVS: 0.47
• rvis_percentile_EVS: 78.83

Haploinsufficiency Scores

• pHI: 0.0888
• hipred: N
• hipred_score: 0.187
• ghis: 0.470

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.458

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nek11
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein phosphorylation;histone phosphorylation;intra-S DNA damage checkpoint;intracellular signal transduction;mitotic cell cycle phase transition;regulation of mitotic cell cycle phase transition
• Cellular component: nucleoplasm;nucleolus
• Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding;metal ion binding