NEK5

NIMA related kinase 5

Basic information

Region (hg38): 13:52033611-52129092

Links

ENSG00000197168 ∙ NCBI:341676 ∙ OMIM:616731 ∙ HGNC:7748 ∙ Uniprot:Q6P3R8 ∙ 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 NEK5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEK5 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			38	3		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	4	0

Variants in NEK5

This is a list of pathogenic ClinVar variants found in the NEK5 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-52065452-T-A		not specified	Uncertain significance (Sep 25, 2024)
13-52065459-C-T		not specified	Uncertain significance (Dec 19, 2022)
13-52065460-G-A		not specified	Uncertain significance (Sep 17, 2021)
13-52065495-G-A		not specified	Uncertain significance (Jan 04, 2024)
13-52065510-G-T		not specified	Uncertain significance (Dec 14, 2023)
13-52065517-C-T		not specified	Uncertain significance (Nov 10, 2022)
13-52065522-A-G		not specified	Likely benign (Aug 05, 2023)
13-52065569-C-G		not specified	Uncertain significance (Jan 31, 2022)
13-52065580-C-T		not specified	Uncertain significance (Jan 21, 2022)
13-52065607-A-G		not specified	Likely benign (Dec 01, 2022)
13-52072026-C-A		not specified	Uncertain significance (Dec 14, 2022)
13-52072053-A-C		not specified	Uncertain significance (Jul 21, 2021)
13-52072067-T-C			Likely benign (Nov 01, 2022)
13-52076068-C-T		not specified	Uncertain significance (Sep 29, 2023)
13-52076137-C-T		not specified	Uncertain significance (Dec 15, 2023)
13-52083347-G-T		not specified	Uncertain significance (Oct 17, 2024)
13-52086287-C-G		not specified	Uncertain significance (Jun 13, 2024)
13-52086315-T-C		not specified	Uncertain significance (Jul 27, 2022)
13-52087433-C-G		not specified	Uncertain significance (Jul 10, 2024)
13-52087453-C-A		not specified	Uncertain significance (Sep 01, 2021)
13-52089278-T-C		not specified	Uncertain significance (Aug 10, 2021)
13-52093063-G-A		not specified	Uncertain significance (Nov 28, 2023)
13-52093080-C-T			Likely benign (May 01, 2023)
13-52093130-G-A		not specified	Uncertain significance (Jul 06, 2021)
13-52093132-T-C		not specified	Uncertain significance (Apr 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEK5	protein_coding	protein_coding	ENST00000355568	20	92122

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.01e-23	0.00367	125524	2	222	125748	0.000891

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.423	346	369	0.938	0.0000184	4713
Missense in Polyphen		104	116.78	0.8906		1536
Synonymous	0.452	120	126	0.949	0.00000687	1236
Loss of Function	0.642	38	42.5	0.894	0.00000223	520

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00735	0.00723
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000485	0.000484
Middle Eastern	0.000381	0.000381
South Asian	0.000803	0.000752
Other	0.000655	0.000652

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.980
• rvis_EVS: 1.07
• rvis_percentile_EVS: 91.67

Haploinsufficiency Scores

• pHI: 0.0901
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.396

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nek5
• Phenotype: hearing/vestibular/ear phenotype

Gene ontology

• Biological process: protein phosphorylation;positive regulation of striated muscle cell differentiation;positive regulation of cysteine-type endopeptidase activity
• Molecular function: protein serine/threonine kinase activity;ATP binding;metal ion binding