Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	7443
Gene name	VRK serine/threonine kinase 1
Gene symbol	VRK1
Synonyms (NCBI Gene)	HMNR10PCH1PCH1A
Chromosome	14
Chromosome location	14q32.2
Summary	This gene encodes a member of the vaccinia-related kinase (VRK) family of serine/threonine protein kinases. This gene is widely expressed in human tissues and has increased expression in actively dividing cells, such as those in testis, thymus, fetal live

Show/Hide all (19)

SNP ID	Visualize variation	Clinical significance	Consequence
rs61736727	T>G	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, missense variant
rs137853063	C>G,T	Pathogenic	Stop gained, coding sequence variant, missense variant, non coding transcript variant, genic downstream transcript variant
rs147853760	C>T	Conflicting-interpretations-of-pathogenicity, likely-benign	3 prime UTR variant, coding sequence variant, synonymous variant, non coding transcript variant
rs371295780	A>G	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs387906830	C>G,T	Pathogenic, uncertain-significance	Coding sequence variant, missense variant, non coding transcript variant
rs771364038	G>A,T	Pathogenic, uncertain-significance	Non coding transcript variant, coding sequence variant, missense variant
rs772146380	AAAA>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs772263867	C>T	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs772731615	C>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	3 prime UTR variant, non coding transcript variant, coding sequence variant, missense variant
rs773138218	G>A,C	Pathogenic, likely-pathogenic, uncertain-significance	Non coding transcript variant, coding sequence variant, missense variant
rs779282547	AAAC>-	Pathogenic	Frameshift variant, 3 prime UTR variant, non coding transcript variant, coding sequence variant
rs780789145	T>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs869312959	G>A	Pathogenic	Splice donor variant, 3 prime UTR variant
rs1172497555	G>T	Uncertain-significance, pathogenic	Intron variant, missense variant, coding sequence variant
rs1223645705	A>T	Pathogenic	Coding sequence variant, 3 prime UTR variant, non coding transcript variant, stop gained
rs1566696845	TCTTGGTA>-	Likely-pathogenic	Splice donor variant, non coding transcript variant, coding sequence variant, intron variant
rs1566713184	C>T	Pathogenic, likely-pathogenic	Non coding transcript variant, coding sequence variant, stop gained, 3 prime UTR variant
rs1595676477	T>C	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs1595676517	G>T	Uncertain-significance, pathogenic	Missense variant, non coding transcript variant, coding sequence variant

Show/Hide all (40)

miRTarBase ID	miRNA	Experiments	Reference
MIRT030361	hsa-miR-24-3p	Microarray	19748357
MIRT497971	hsa-miR-3662	PAR-CLIP	22291592
MIRT497970	hsa-miR-4694-3p	PAR-CLIP	22291592
MIRT497969	hsa-miR-4693-3p	PAR-CLIP	22291592
MIRT497971	hsa-miR-3662	PAR-CLIP	22291592
MIRT497970	hsa-miR-4694-3p	PAR-CLIP	22291592
MIRT497969	hsa-miR-4693-3p	PAR-CLIP	22291592
MIRT1487485	hsa-miR-1224-5p	CLIP-seq
MIRT1487486	hsa-miR-33a	CLIP-seq
MIRT1487487	hsa-miR-33b	CLIP-seq
MIRT1487488	hsa-miR-3609	CLIP-seq
MIRT1487489	hsa-miR-3682-5p	CLIP-seq
MIRT1487490	hsa-miR-3921	CLIP-seq
MIRT1487491	hsa-miR-4251	CLIP-seq
MIRT1487492	hsa-miR-4329	CLIP-seq
MIRT1487493	hsa-miR-4432	CLIP-seq
MIRT1487494	hsa-miR-4653-5p	CLIP-seq
MIRT1487495	hsa-miR-4696	CLIP-seq
MIRT1487496	hsa-miR-4714-5p	CLIP-seq
MIRT1487497	hsa-miR-4751	CLIP-seq
MIRT1487498	hsa-miR-496	CLIP-seq
MIRT1487499	hsa-miR-513a-5p	CLIP-seq
MIRT1487500	hsa-miR-539	CLIP-seq
MIRT1487501	hsa-miR-548ah	CLIP-seq
MIRT1487502	hsa-miR-548n	CLIP-seq
MIRT1487503	hsa-miR-548t	CLIP-seq
MIRT1487490	hsa-miR-3921	CLIP-seq
MIRT1487491	hsa-miR-4251	CLIP-seq
MIRT1487492	hsa-miR-4329	CLIP-seq
MIRT1487493	hsa-miR-4432	CLIP-seq
MIRT1487494	hsa-miR-4653-5p	CLIP-seq
MIRT1487495	hsa-miR-4696	CLIP-seq
MIRT1487496	hsa-miR-4714-5p	CLIP-seq
MIRT1487499	hsa-miR-513a-5p	CLIP-seq
MIRT1487500	hsa-miR-539	CLIP-seq
MIRT2660779	hsa-miR-3121-3p	CLIP-seq
MIRT2660780	hsa-miR-3671	CLIP-seq
MIRT2660781	hsa-miR-4428	CLIP-seq
MIRT1487499	hsa-miR-513a-5p	CLIP-seq
MIRT2660782	hsa-miR-607	CLIP-seq

Show/Hide all (48)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0000785	Component	Chromatin	IDA	35390161
GO:0004672	Function	Protein kinase activity	IDA	22194607
GO:0004672	Function	Protein kinase activity	IEA
GO:0004674	Function	Protein serine/threonine kinase activity	IBA
GO:0004674	Function	Protein serine/threonine kinase activity	IDA	21543316, 33076429
GO:0004674	Function	Protein serine/threonine kinase activity	IEA
GO:0004674	Function	Protein serine/threonine kinase activity	TAS	9344656
GO:0005515	Function	Protein binding	IPI	15105425, 15378002, 15542844, 18617507, 19103756, 21920476, 22194607, 22621922, 24492002, 25609649, 25923214, 26869104, 27334688, 29340707, 33076429, 37179361
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	22194607
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005730	Component	Nucleolus	IDA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005795	Component	Golgi stack	IDA	19103756
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	TAS
GO:0006338	Process	Chromatin remodeling	IMP	37179361
GO:0006468	Process	Protein phosphorylation	TAS	9344656
GO:0006974	Process	DNA damage response	IBA
GO:0006974	Process	DNA damage response	IDA	33076429
GO:0007077	Process	Mitotic nuclear membrane disassembly	TAS
GO:0007165	Process	Signal transduction	IBA
GO:0015030	Component	Cajal body	IDA	21920476
GO:0015030	Component	Cajal body	IEA
GO:0016301	Function	Kinase activity	IDA	21543316
GO:0016301	Function	Kinase activity	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0019901	Function	Protein kinase binding	IDA	22572157
GO:0030576	Process	Cajal body organization	IMP	31090908
GO:0031175	Process	Neuron projection development	IMP	31090908
GO:0031492	Function	Nucleosomal DNA binding	IDA	35390161
GO:0035175	Function	Histone H3S10 kinase activity	IDA	22194607
GO:0042393	Function	Histone binding	IPI	22194607, 35390161
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	33076429
GO:0046777	Process	Protein autophosphorylation	IDA	21543316
GO:0051301	Process	Cell division	IEA
GO:0072354	Function	Histone H3T3 kinase activity	IDA	22194607, 31527692
GO:0090166	Process	Golgi disassembly	IDA	19103756
GO:0106310	Function	Protein serine kinase activity	IEA
GO:0120187	Process	Positive regulation of protein localization to chromatin	IDA	33076429
GO:0141003	Function	Histone H2AX kinase activity	IDA	31527692
GO:2001222	Process	Regulation of neuron migration	IEA
GO:2001222	Process	Regulation of neuron migration	ISS

MIM	HGNC	e!Ensembl
602168	12718	ENSG00000100749

Q99986

Protein name

Serine/threonine-protein kinase VRK1 (EC 2.7.11.1) (Vaccinia-related kinase 1)

Protein function

Serine/threonine kinase involved in the regulation of key cellular processes including the cell cycle, nuclear condensation, transcription regulation, and DNA damage response (PubMed:14645249, PubMed:18617507, PubMed:19103756, PubMed:33076429).

PDB

2KTY , 2KUL , 2LAV , 2RSV , 3OP5 , 5UKF , 5UVF , 6AC9 , 6BP0 , 6BRU , 6BTW , 6BU6 , 6CFM , 6CMM , 6CNX , 6CQH , 6CSW , 6DD4 , 6NPN , 6VXU , 6VZH , 7M10 , 7TAN , 8F8Y , 8V42

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00069	Pkinase	37 → 324	Protein kinase domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Widely expressed. Highly expressed in fetal liver, testis and thymus. {ECO:0000269|PubMed:9344656}.

Sequence

MPRVKAAQAGRQSSAKRHLAEQFAVGEIITDMAKKEWKVGLPIGQGGFGCIYLADMNSSE
SVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHD
KNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKA
SNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKEYKEDPKRCHDGTIEFTSIDAHNGVAPSR
RGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPEKNKPGEIA
KYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITKKRKK
EIEESKEPGVEDTEWSNTQTEEAIQTRSRTRKRVQK

Sequence length

396

Interactions

View interactions

	Reactome
			Nuclear Envelope Breakdown Initiation of Nuclear Envelope (NE) Reformation

564

Show/Hide Causal Diseases (9)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormality of the musculature	Pathogenic	rs137853063	RCV001836703
Congenital pontocerebellar hypoplasia type 1	Pathogenic	rs137853063	RCV000690009
Distal spinal muscular atrophy	Likely pathogenic	rs1887280587	RCV002227297
Juvenile amyotrophic lateral sclerosis	Likely pathogenic; Pathogenic	rs772731615	RCV001095537
Neuronopathy, distal hereditary motor, autosomal recessive 10	Likely pathogenic; Pathogenic	rs2139845854, rs184887106, rs1566721633, rs2504252308, rs371295780, rs772731615, rs137853063, rs779282547, rs1420939606, rs762979613, rs774877872	RCV005008401 RCV004796691 RCV005010991 RCV005002878 RCV005008123 RCV005008124 RCV003387437 RCV005010506 RCV003387440 RCV005012487 RCV005235511
Pontocerebellar hypoplasia type 1A	Likely pathogenic; Pathogenic	rs2139804166, rs774518440, rs2139845849, rs2139748841, rs2139779014, rs2139795550, rs2139845854, rs2139796429, rs1200170208, rs2139845924, rs2139814734, rs1889019962, rs184887106, rs2139759363, rs2139801958 View all (49 more)	RCV001645020 RCV001836384 RCV002550963 RCV002550273 RCV003104064 RCV002551579 RCV002545462 RCV002554314 RCV002561409 RCV002571353 RCV002557619 RCV002568516 RCV002563635 RCV002563632 RCV002564383 RCV002579619 RCV002555342 RCV002564403 RCV002553454 RCV003065770 RCV003092789 RCV003073533 RCV002636991 RCV003117102 RCV002730532 RCV002811240 RCV000191143 RCV000191144 RCV002863646 RCV002899986 RCV002882026 RCV002953112 RCV003016872 RCV003034027 RCV003043515 RCV000007926 RCV003507492 RCV003778350 RCV003507556 RCV003507656 RCV003508368 RCV003508555 RCV003508952 RCV003506816 RCV003507082 RCV003620906 RCV003620836 RCV003621072 RCV003621418 RCV003836653 RCV003831271 RCV003867784 RCV005010506 RCV003103815 RCV002533248 RCV000758202 RCV002537997 RCV001809826 RCV002553233 RCV003103923 RCV002553209 RCV002553287 RCV002561763 RCV002561903 RCV002570361 RCV001290422
Pontocerebellar hypoplasia type 1B	Likely pathogenic	rs1566696845	RCV000762795
Pontoneocerebellar hypoplasia	Pathogenic	rs1174255706, rs2504252312	RCV003388412 RCV005429448
Spinal muscular atrophy	Pathogenic	rs1889019962	RCV001095536

Show/Hide Unknown Diseases (8)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Amyotrophic lateral sclerosis	Conflicting classifications of pathogenicity	rs139476915	RCV005862985
Distal hereditary motor neuropathy associated with upper motor neuron signs	Conflicting classifications of pathogenicity	rs1172497555, rs1595676517	RCV000791457 RCV000788106
EMG: neuropathic changes	Conflicting classifications of pathogenicity	rs1595676477	RCV001003373
Hereditary breast ovarian cancer syndrome	Conflicting classifications of pathogenicity	rs146113610	RCV001374508
Isolated microphthalmia 2	Benign	rs2145635	RCV001538074
Microcephaly-complex motor and sensory axonal neuropathy syndrome	Conflicting classifications of pathogenicity	rs1595676477	RCV001003373
Neuronopathy, distal hereditary motor, autosomal recessive	Conflicting classifications of pathogenicity	rs139476915	RCV005862985
VRK1-related disorder	Conflicting classifications of pathogenicity; Likely benign; Benign	rs139476915, rs371489397, rs528346065, rs368495945	RCV003952580 RCV003964771 RCV003955730 RCV004731050

Show/Hide Text Mining Associations (52)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Adenocarcinoma	Associate	27456229
Alcoholic Neuropathy	Associate	30847374
Amyotrophic Lateral Sclerosis	Associate	26583493, 30847374, 31527692, 31560180, 38017281, 38554151
Breast Neoplasms	Associate	21829721, 24731990, 30180179, 31970831
Carcinogenesis	Associate	27456229, 34071140
Carcinoma Hepatocellular	Associate	28927264, 38157278
Charcot Marie Tooth disease X linked recessive 2	Associate	31167812
Chromosome Deletion	Associate	32917334
Depression Postpartum	Associate	23284067
Distal Hereditary Motor Neuropathy Type II	Associate	30847374, 38554151
Drug Related Side Effects and Adverse Reactions	Associate	30937657
Drug Resistant Epilepsy	Inhibit	27319807
Ectodermal Dysplasia	Stimulate	38157278
Epileptic Encephalopathy Early Infantile 3	Associate	31527692
Fetal Growth Retardation	Associate	23284067
Genetic Diseases Inborn	Associate	32917334
Glioblastoma	Associate	26956052, 36069976
Glioma	Associate	36040810
Hereditary Sensory and Motor Neuropathy	Associate	31560180
Heredodegenerative Disorders Nervous System	Associate	26583493
Hyperplasia	Associate	35410639
Lung Neoplasms	Associate	23591868, 34071140
Lupus Erythematosus Systemic	Associate	31494269
Lymphatic Metastasis	Stimulate	30180179
Male Infertility with Large Headed Multiflagellar Polyploid Spermatozoa	Associate	36357561
Microcephaly	Associate	24126608, 31527692, 31560180
Motor Neuron Disease	Associate	26583493, 27281532, 31178479, 31527692, 31560180, 34990802, 38554151
Mouth Neoplasms	Associate	36052378
Multiple Myeloma	Associate	27319807
Muscular Atrophy Spinal	Associate	27281532, 30847374, 31527692, 31560180, 32365420, 38554151
Neointima	Stimulate	35410639
Neoplasm Metastasis	Associate	30180179
Neoplasms	Associate	21829721, 23591868, 24731990, 27319807, 27456229, 28790404, 31101118, 36040810, 36052378, 38157278
Neoplasms	Inhibit	31970831, 36069976
Neoplastic Syndromes Hereditary	Associate	31167812, 34990802
Nerve Degeneration	Associate	24524299
Neuroblastoma	Associate	36040810
Neurologic Manifestations	Associate	31527692
Osteosarcoma	Associate	31810390
Perinatal Death	Associate	23284067
Peripheral Nervous System Diseases	Associate	24126608
Pontocerebellar Hypoplasia	Associate	22452838, 27281532, 31527692, 31560180, 38017281
Pontocerebellar Hypoplasia Type 1	Associate	19646678, 23284067
Pre Eclampsia	Associate	33738906
Respiratory System Abnormalities	Associate	36040810
Schizophrenia	Associate	22234486
Sensorimotor neuropathy with ataxia autosomal dominant	Associate	30847374, 32365420
Spinal Muscular Atrophies of Childhood	Associate	19646678, 31560180
Spinal muscular atrophy Jerash type	Associate	32365420
Squamous Cell Carcinoma of Head and Neck	Associate	16547155
Syndrome	Associate	31527692
Vascular System Injuries	Stimulate	35410639

VRK1 (VRK serine/threonine kinase 1)