NEK3

NIMA related kinase 3

Basic information

Region (hg38): 13:52132639-52159597

Links

ENSG00000136098 ∙ NCBI:4752 ∙ OMIM:604044 ∙ HGNC:7746 ∙ Uniprot:P51956 ∙ 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 NEK3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEK3 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			24		1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	1

Variants in NEK3

This is a list of pathogenic ClinVar variants found in the NEK3 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-52133792-G-A		not specified	Uncertain significance (May 03, 2023)
13-52136142-G-T		not specified	Uncertain significance (Jan 10, 2022)
13-52136175-A-G		not specified	Uncertain significance (May 23, 2023)
13-52136185-T-C		not specified	Uncertain significance (Oct 27, 2022)
13-52136221-T-C		not specified	Uncertain significance (Jul 13, 2022)
13-52136803-T-C		not specified	Uncertain significance (Mar 31, 2024)
13-52136897-C-G		not specified	Uncertain significance (Jun 04, 2024)
13-52143951-T-A		not specified	Uncertain significance (Feb 13, 2024)
13-52144693-C-T		not specified	Uncertain significance (Oct 10, 2023)
13-52144720-G-A		not specified	Uncertain significance (Dec 07, 2021)
13-52144720-G-C			Benign (Jun 13, 2018)
13-52144722-G-A		not specified	Uncertain significance (Jun 02, 2023)
13-52144755-G-A		not specified	Uncertain significance (May 27, 2022)
13-52144827-G-A		not specified	Uncertain significance (May 18, 2022)
13-52144845-C-G		not specified	Uncertain significance (Mar 19, 2024)
13-52148417-G-T		not specified	Uncertain significance (Mar 22, 2023)
13-52151161-G-A		not specified	Uncertain significance (Oct 12, 2021)
13-52151194-T-C		not specified	Uncertain significance (Jan 04, 2024)
13-52151227-A-G		not specified	Uncertain significance (May 06, 2022)
13-52151332-G-T		not specified	Uncertain significance (Dec 18, 2023)
13-52151337-C-T		not specified	Uncertain significance (Feb 28, 2024)
13-52152619-A-G		not specified	Uncertain significance (Mar 19, 2024)
13-52152620-T-C		not specified	Uncertain significance (Dec 19, 2023)
13-52152638-G-A		not specified	Uncertain significance (Jul 09, 2021)
13-52152671-T-C		not specified	Uncertain significance (Apr 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEK3	protein_coding	protein_coding	ENST00000400357	14	27222

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.32e-18	0.00636	124466	0	188	124654	0.000754

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.197	242	251	0.965	0.0000126	3207
Missense in Polyphen		105	109.94	0.9551		1359
Synonymous	0.909	79	90.0	0.878	0.00000484	856
Loss of Function	0.136	27	27.8	0.972	0.00000152	348

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00100	0.000975
Ashkenazi Jewish	0.00	0.00
East Asian	0.00452	0.00452
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.000641	0.000637
Middle Eastern	0.00452	0.00452
South Asian	0.000286	0.000261
Other	0.000668	0.000661

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein kinase which influences neuronal morphogenesis and polarity through effects on microtubules. Regulates microtubule acetylation in neurons. Contributes to prolactin- mediated phosphorylation of PXN and VAV2. Implicated in prolactin- mediated cytoskeletal reorganization and motility of breast cancer cells through mechanisms involving RAC1 activation and phosphorylation of PXN and VAV2. {ECO:0000269|PubMed:15618286, ECO:0000269|PubMed:17297458}.
• Pathway: Prolactin Signaling Pathway;JAK-STAT;Prolactin (Consensus)

Recessive Scores

• pRec: 0.0888

Intolerance Scores

• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.3

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.219
• ghis: 0.490

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.832

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nek3

Gene ontology

• Biological process: mitotic cell cycle;protein phosphorylation;establishment of cell polarity;neuron projection morphogenesis;cell division;regulation of tubulin deacetylation
• Cellular component: nucleus;cytoplasm;axon
• Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding;metal ion binding