NEK3 NIMA related kinase 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NEK3provided by HGNC
Official Full Name: NIMA related kinase 3provided by HGNC
Primary source: HGNC:HGNC:7746
See related: Ensembl:ENSG00000136098 MIM:604044; AllianceGenome:HGNC:7746
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: HSPK36
Summary: This gene encodes a member of the NimA (never in mitosis A) family of serine/threonine protein kinases. The encoded protein differs from other NimA family members in that it is not cell cycle regulated and is found primarily in the cytoplasm. The kinase is activated by prolactin stimulation, leading to phosphorylation of VAV2 guanine nucleotide exchange factor, paxillin, and activation of the RAC1 GTPase. Two functional alleles for this gene have been identified in humans. The reference genome assembly (GRCh38) represents a functional allele that is associated with the inclusion of an additional coding exon in protein-coding transcripts, compared to an alternate functional allele that lacks the exon. [provided by RefSeq, Sep 2019]
Annotation information: Note: Genetic polymorphisms result in both protein coding and non-coding alleles of this gene.; Note: Available sequence data supports two haplotypes in the human population that differ by a 1 nt indel (rs3837575) at the end of exon 10. Both haplotypes appear to encode functional proteins via alternative splicing of exon 11. The GRCh38 reference assembly includes the extra nt and expresses a full-length protein that includes exon 11, whereas haplotypes that lack the extra nt express a full-length protein lacking exon 11. [30 Sep 2019]
Expression: Broad expression in testis (RPKM 10.8), placenta (RPKM 6.5) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 13q14.3

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (52132647..52159860, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (51347480..51374691, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (52706783..52733995, complement)

Chromosome 13 - NC_000013.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

the NEK protein kinases emerge as important proteins in thyroid cancer development and may help to identify malignancy and aggressiveness features during diagnosis.
Title: Expression of the NEK family in normal and cancer tissue: an immunohistochemical study.
NEK3 kinase phosphorylates SNAP29 on its serine 105. NEK3-mediated phosphorylation determines membrane localization of SNAP29. Membrane-associated SNAP29 regulates Golgi and focal adhesion structures.
Title: NEK3-mediated SNAP29 phosphorylation modulates its membrane association and SNARE fusion dependent processes.
The data demonstrate that NEK3 is overexpressed in gastric cancer, which promotes the malignancy of gastric cancer
Title: Overexpression of NEK3 is associated with poor prognosis in patients with gastric cancer.
these data support a modulatory role for phosphorylation at NEK3 Thr-165 in focal adhesion maturation and/or turnover to promote breast cancer cell migration.
Title: Identification of NEK3 Kinase Threonine 165 as a Novel Regulatory Phosphorylation Site That Modulates Focal Adhesion Remodeling Necessary for Breast Cancer Cell Migration.
EHD2 interacts with Nek3 [NIMA (never in mitosis in Aspergillus nidulans)-related kinase 3], a serine/threonine kinase.
Title: EHD2 mediates trafficking from the plasma membrane by modulating Rac1 activity.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Nek3 contributes to prolactin-mediated breast cancer motility through mechanisms involving Rac1 activation and paxillin phosphorylation.
Title: Nek3 kinase regulates prolactin-mediated cytoskeletal reorganization and motility of breast cancer cells.
Nek3 insertion/deletion polymorphism with alterations at 13q14 is associated with cancers
Title: Is there any association between nek3 and cancers with frequent 13q14 deletion?
Molecular cloning and characterization of the human NIMA-related protein kinase 3 gene (NEK3).
Title: Molecular cloning and characterization of the human NIMA-related protein kinase 3 gene (NEK3).

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH68007 (e-PCR)
- UniSTS:15627

D1S3693 (e-PCR)
- UniSTS:474271

G43267 (e-PCR)
- UniSTS:94911

G59593 (e-PCR)
- UniSTS:136897

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 3-phosphoinositide-dependent protein kinase activity	IEA Inferred from Electronic Annotation more info
enables AMP-activated protein kinase activity	IEA Inferred from Electronic Annotation more info
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables DNA-dependent protein kinase activity	IEA Inferred from Electronic Annotation more info
enables Rho-dependent protein serine/threonine kinase activity	IEA Inferred from Electronic Annotation more info
enables eukaryotic translation initiation factor 2alpha kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AS1 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AS121 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AT120 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AXS139 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2BS14 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2BS36 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3S10 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3S28 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3S57 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T11 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T3 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T45 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T6 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H4S1 kinase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein serine kinase activity	IEA Inferred from Electronic Annotation more info
enables protein serine/threonine kinase activity	NAS Non-traceable Author Statement more info	PubMed
enables ribosomal protein S6 kinase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in establishment of cell polarity	IEA Inferred from Electronic Annotation more info
involved_in mitotic cell cycle	NAS Non-traceable Author Statement more info	PubMed
involved_in neuron projection morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in protein phosphorylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of tubulin deacetylation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in axon	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: serine/threonine-protein kinase Nek3

Names: HSPK 36; NIMA (never in mitosis gene a)-related kinase 3; glycogen synthase A kinase; hydroxyalkyl-protein kinase; never in mitosis A-related kinase 3; nimA-related protein kinase 3; phosphorylase B kinase kinase

NP_001139571.1

EC 2.7.11.1

NP_001411183.1

EC 2.7.11.1

NP_001411184.1

EC 2.7.11.1

NP_001411186.1

EC 2.7.11.1

NP_001411188.1

EC 2.7.11.1

NP_001411193.1

EC 2.7.11.1

NP_001411194.1

EC 2.7.11.1

NP_001411195.1

EC 2.7.11.1

NP_001411197.1

EC 2.7.11.1

NP_001411198.1

EC 2.7.11.1

NP_001411199.1

EC 2.7.11.1

NP_001411200.1

EC 2.7.11.1

NP_002489.1

EC 2.7.11.1

NP_689933.1

EC 2.7.11.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001146099.2 → NP_001139571.1 serine/threonine-protein kinase Nek3 isoform b

See identical proteins and their annotated locations for NP_001139571.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) represents the splice pattern of variant 5 but without the extra 'A' found in the GRCh38 haplotype.

Source sequence(s)

CP068265

UniProtKB/TrEMBL

Q6ZN64

Conserved Domains (1) summary

cd08219
Location:3 → 257

STKc_Nek3; Catalytic domain of the Protein Serine/Threonine Kinase, Never In Mitosis gene A (NIMA)-related kinase 3
NM_001424254.1 → NP_001411183.1 serine/threonine-protein kinase Nek3 isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (7) represents the splice pattern of variant 19 but with the extra 'A' found in the GRCh38 haplotype.

Source sequence(s)

AL139082, KF459684
NM_001424255.1 → NP_001411184.1 serine/threonine-protein kinase Nek3 isoform d

Status: REVIEWED

Source sequence(s)

AL139082, KF459684
NM_001424257.1 → NP_001411186.1 serine/threonine-protein kinase Nek3 isoform d

Status: REVIEWED

Source sequence(s)

AL139082, KF459684
NM_001424259.1 → NP_001411188.1 serine/threonine-protein kinase Nek3 isoform e

Status: REVIEWED

Source sequence(s)

AL139082, KF459684
NM_001424264.1 → NP_001411193.1 serine/threonine-protein kinase Nek3 isoform f

Status: REVIEWED

Source sequence(s)

AL139082, KF459684
NM_001424265.1 → NP_001411194.1 serine/threonine-protein kinase Nek3 isoform a

Status: REVIEWED

Source sequence(s)

AL139082, KF459684

UniProtKB/Swiss-Prot

A8K2J4, P51956, Q5TAP2, Q8J023, Q8WUN5
NM_001424266.1 → NP_001411195.1 serine/threonine-protein kinase Nek3 isoform a

Status: REVIEWED

Source sequence(s)

AL139082, KF459684

UniProtKB/Swiss-Prot

A8K2J4, P51956, Q5TAP2, Q8J023, Q8WUN5
NM_001424268.1 → NP_001411197.1 serine/threonine-protein kinase Nek3 isoform b

Status: REVIEWED

Source sequence(s)

CP068265
NM_001424269.1 → NP_001411198.1 serine/threonine-protein kinase Nek3 isoform b

Status: REVIEWED

Source sequence(s)

CP068265
NM_001424270.1 → NP_001411199.1 serine/threonine-protein kinase Nek3 isoform g

Status: REVIEWED

Source sequence(s)

CP068265
NM_001424271.1 → NP_001411200.1 serine/threonine-protein kinase Nek3 isoform h

Status: REVIEWED

Source sequence(s)

CP068265
NM_002498.3 → NP_002489.1 serine/threonine-protein kinase Nek3 isoform a

See identical proteins and their annotated locations for NP_002489.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the splice pattern of variant 4 but with the extra 'A' found in the GRCh38 haplotype.

Source sequence(s)

AL139082, BC019916

Consensus CDS

CCDS73576.1

UniProtKB/Swiss-Prot

A8K2J4, P51956, Q5TAP2, Q8J023, Q8WUN5

UniProtKB/TrEMBL

Q5JPB0

Related

ENSP00000480328.1, ENST00000610828.5

Conserved Domains (1) summary

cd08219
Location:3 → 257

STKc_Nek3; Catalytic domain of the Protein Serine/Threonine Kinase, Never In Mitosis gene A (NIMA)-related kinase 3
NM_152720.3 → NP_689933.1 serine/threonine-protein kinase Nek3 isoform a

See identical proteins and their annotated locations for NP_689933.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) represents the splice pattern of variant 6 but with the extra 'A' found in the GRCh38 haplotype.

Source sequence(s)

AI209040, AK131359, AK290259, AL139082, H15146

Consensus CDS

CCDS73576.1

UniProtKB/Swiss-Prot

A8K2J4, P51956, Q5TAP2, Q8J023, Q8WUN5

UniProtKB/TrEMBL

Q5JPB0

Related

ENSP00000484443.1, ENST00000618534.4

Conserved Domains (1) summary

cd08219
Location:3 → 257

STKc_Nek3; Catalytic domain of the Protein Serine/Threonine Kinase, Never In Mitosis gene A (NIMA)-related kinase 3

RNA

NR_027415.3 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) represents the splice pattern of variant 1 but without the extra 'A' found in the GRCh38 haplotype. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

CP068265
NR_164641.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) represents the splice pattern of variant 3 but with the extra 'A' found in the GRCh38 haplotype. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AL139082, KF459684
NR_172104.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (6) represents the splice pattern of variant 2 but without the extra 'A' found in the GRCh38 haplotype. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AL139082, KF459684
NR_188248.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (19) represents the splice pattern of variant 7 but without the extra 'A' found in the GRCh38 haplotype. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

CP068265