NEK10

NIMA related kinase 10, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 3:27106484-27369460

Links

ENSG00000163491 ∙ NCBI:152110 ∙ OMIM:618726 ∙ HGNC:18592 ∙ Uniprot:Q6ZWH5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• ciliary dyskinesia, primary, 44 (Limited), mode of inheritance: AR
• primary ciliary dyskinesia (Supportive), mode of inheritance: AD
• ciliary dyskinesia, primary, 44 (Strong), mode of inheritance: AR
• ciliary dyskinesia, primary, 44 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ciliary dyskinesia, primary, 44	AR	Allergy/Immunology/Infectious; Pulmonary	Pulmonary surveillance may be beneficial to assess respiratory function and institute early management measures; In order to facilitate mucus clearance, aggressive interventions (eg, chest percussion and oscillatory vest), as well as vaccinations and early and aggressive treatment of respiratory infections may be beneficial	Allergy/Immunology/Infectious; Pulmonary	20301301; 31959991

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NEK10 gene.

• Ciliary dyskinesia, primary, 44 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEK10 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	5	6
missense		1	32	5	4	42
nonsense						0
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding					2	2
Total	1	1	32	6	11

Variants in NEK10

This is a list of pathogenic ClinVar variants found in the NEK10 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-27115957-G-T		not specified • Ciliary dyskinesia, primary, 44	Conflicting classifications of pathogenicity (Mar 26, 2024)
3-27162561-G-A		Ciliary dyskinesia, primary, 44	Benign (Sep 05, 2021)
3-27171827-G-A			Likely benign (Oct 01, 2024)
3-27174461-G-T		Ciliary dyskinesia, primary, 44	Uncertain significance (-)
3-27192007-C-A		Ciliary dyskinesia, primary, 44	Benign (Sep 05, 2021)
3-27192103-G-A			Uncertain significance (Feb 03, 2022)
3-27192217-G-A		Ciliary dyskinesia, primary, 44	Pathogenic (Feb 24, 2020)
3-27192225-G-A			Benign (May 01, 2023)
3-27201554-G-C		Ciliary dyskinesia, primary, 44	Benign (Sep 05, 2021)
3-27201558-G-A		Ciliary dyskinesia, primary, 44	Pathogenic (Feb 24, 2020)
3-27202466-G-A		Ciliary dyskinesia, primary, 44	Likely pathogenic (Mar 25, 2024)
3-27215741-G-A			Likely benign (Nov 01, 2022)
3-27256325-G-C		Ciliary dyskinesia, primary, 44	Benign (Sep 05, 2021)
3-27284606-G-T		Ciliary dyskinesia, primary, 44	Benign (Sep 05, 2021)
3-27284640-T-C			Benign (Jul 13, 2018)
3-27284881-G-GA		Ciliary dyskinesia, primary, 44	Pathogenic (Feb 24, 2020)
3-27284940-A-G		not specified	Uncertain significance (Dec 06, 2021)
3-27284960-A-G		Ciliary dyskinesia, primary, 44	Benign (Sep 05, 2021)
3-27290658-C-T		NEK10-related disorder	Uncertain significance (Aug 26, 2022)
3-27290667-C-T		not specified	Uncertain significance (Jul 15, 2021)
3-27290673-C-T		not specified	Uncertain significance (Jun 01, 2023)
3-27290681-T-C		not specified	Uncertain significance (Apr 25, 2022)
3-27290686-T-C		Ciliary dyskinesia, primary, 44	Benign (Sep 05, 2021)
3-27290744-T-C		not specified	Likely benign (Feb 28, 2024)
3-27291329-A-G		Ciliary dyskinesia, primary, 44	Benign (Feb 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEK10	protein_coding	protein_coding	ENST00000341435	23	259376

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.66e-10	0.999	125712	0	35	125747	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.616	325	358	0.908	0.0000178	4685
Missense in Polyphen		81	111.79	0.72457		1526
Synonymous	0.733	115	125	0.917	0.00000638	1263
Loss of Function	2.91	22	42.4	0.518	0.00000215	550

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000351	0.000337
Ashkenazi Jewish	0.00	0.00
East Asian	0.000169	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000148	0.000141
Middle Eastern	0.000169	0.000163
South Asian	0.000271	0.000261
Other	0.000332	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0824

Intolerance Scores

• loftool: 0.655
• rvis_EVS: 0.89
• rvis_percentile_EVS: 89.19

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.414
• ghis: 0.410

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.675

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nek10
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: protein phosphorylation;positive regulation of protein autophosphorylation;positive regulation of MAP kinase activity;regulation of ERK1 and ERK2 cascade;regulation of cell cycle G2/M phase transition
• Cellular component: protein kinase complex
• Molecular function: protein kinase activity;protein serine/threonine kinase activity;ATP binding;metal ion binding