NEK7

NIMA related kinase 7

Basic information

Region (hg38): 1:198156994-198322420

Links

ENSG00000151414 ∙ NCBI:140609 ∙ OMIM:606848 ∙ HGNC:13386 ∙ Uniprot:Q8TDX7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 68.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_133494.3	NP_598001.1	9	yes	-
ENST00000367385.9	ENSP00000356355.4	9	yes	-
ENST00000538004.5	ENSP00000444621.1	9	-	-
ENST00000367383.5	ENSP00000356353.1	3	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NEK7 gene.

• not_specified (22 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEK7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_133494.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			24			24
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2			2
Total	0	0	26	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEK7	protein_coding	protein_coding	ENST00000367385	9	165458

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125680	0	12	125692	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.29	83	166	0.499	0.00000838	1986
Missense in Polyphen		15	53.426	0.28076		635
Synonymous	-0.247	59	56.6	1.04	0.00000297	553
Loss of Function	3.54	3	20.1	0.149	0.00000116	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.0000546	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000534	0.0000528
Middle Eastern	0.0000546	0.0000544
South Asian	0.0000674	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein kinase which plays an important role in mitotic cell cycle progression. Required for microtubule nucleation activity of the centrosome, robust mitotic spindle formation and cytokinesis. Phosphorylates RPS6KB1. {ECO:0000269|PubMed:17101132, ECO:0000269|PubMed:17586473, ECO:0000269|PubMed:19414596}.
• Pathway: NOD-like receptor signaling pathway - Homo sapiens (human);Nuclear Pore Complex (NPC) Disassembly;Activation of NIMA Kinases NEK9, NEK6, NEK7;Nuclear Envelope Breakdown;Mitotic Prophase;M Phase;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.532
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.989

Gene Damage Prediction

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

Gene ontology

• Biological process: protein phosphorylation;regulation of mitotic cell cycle;positive regulation of telomere maintenance via telomerase;spindle assembly;positive regulation of telomerase activity;positive regulation of telomere capping
• Cellular component: spindle pole;nucleoplasm;cytoplasm;microtubule organizing center;microtubule
• Molecular function: protein serine/threonine kinase activity;ATP binding;metal ion binding