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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	57410
Gene name	SCY1 like pseudokinase 1
Gene symbol	SCYL1
Synonyms (NCBI Gene)	GKLPHT019NKTLNTKLP105SCAR21TAPKTEIFTRAP
Chromosome	11
Chromosome location	11q13.1
Summary	This gene encodes a transcriptional regulator belonging to the SCY1-like family of kinase-like proteins. The protein has a divergent N-terminal kinase domain that is thought to be catalytically inactive, and can bind specific DNA sequences through its C-t

Show/Hide all (14)

SNP ID	Visualize variation	Clinical significance	Consequence
rs535912271	A>T	Pathogenic	Coding sequence variant, stop gained
rs755131489	C>-	Likely-pathogenic	Frameshift variant, 5 prime UTR variant, coding sequence variant
rs759830598	CA>-	Pathogenic	Coding sequence variant, frameshift variant
rs864309664	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs864309665	TG>-	Pathogenic	Frameshift variant, coding sequence variant
rs864309666	G>A	Pathogenic	Splice donor variant
rs864309667	C>T	Pathogenic	Stop gained, coding sequence variant
rs942522644	C>T	Pathogenic	5 prime UTR variant, missense variant, coding sequence variant
rs1554967681	C>T	Pathogenic	Coding sequence variant, stop gained, 5 prime UTR variant
rs1554967761	G>T	Pathogenic	Coding sequence variant, stop gained, 5 prime UTR variant
rs1554969894	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1554969925	A>C,G	Pathogenic	Coding sequence variant, missense variant
rs1554970375	C>T	Pathogenic	Coding sequence variant, stop gained
rs1590740858	->T	Pathogenic	Coding sequence variant, frameshift variant

Show/Hide all (34)

miRTarBase ID	miRNA	Experiments	Reference
MIRT001596	hsa-let-7b-5p	pSILAC	18668040
MIRT028426	hsa-miR-30a-5p	Proteomics	18668040
MIRT001596	hsa-let-7b-5p	Proteomics;Other	18668040
MIRT051600	hsa-let-7e-5p	CLASH	23622248
MIRT043006	hsa-miR-324-3p	CLASH	23622248
MIRT041975	hsa-miR-484	CLASH	23622248
MIRT1330979	hsa-miR-1273f	CLIP-seq
MIRT1330980	hsa-miR-143	CLIP-seq
MIRT1330981	hsa-miR-3064-5p	CLIP-seq
MIRT1330982	hsa-miR-3652	CLIP-seq
MIRT1330983	hsa-miR-3920	CLIP-seq
MIRT1330984	hsa-miR-3924	CLIP-seq
MIRT1330985	hsa-miR-4284	CLIP-seq
MIRT1330986	hsa-miR-4430	CLIP-seq
MIRT1330987	hsa-miR-4437	CLIP-seq
MIRT1330988	hsa-miR-4474-3p	CLIP-seq
MIRT1330989	hsa-miR-4505	CLIP-seq
MIRT1330990	hsa-miR-4708-5p	CLIP-seq
MIRT1330991	hsa-miR-4717-3p	CLIP-seq
MIRT1330992	hsa-miR-4770	CLIP-seq
MIRT1330993	hsa-miR-760	CLIP-seq
MIRT1330979	hsa-miR-1273f	CLIP-seq
MIRT1330980	hsa-miR-143	CLIP-seq
MIRT1330981	hsa-miR-3064-5p	CLIP-seq
MIRT1330982	hsa-miR-3652	CLIP-seq
MIRT1330983	hsa-miR-3920	CLIP-seq
MIRT1330984	hsa-miR-3924	CLIP-seq
MIRT1330986	hsa-miR-4430	CLIP-seq
MIRT1330988	hsa-miR-4474-3p	CLIP-seq
MIRT1330989	hsa-miR-4505	CLIP-seq
MIRT1330990	hsa-miR-4708-5p	CLIP-seq
MIRT1330991	hsa-miR-4717-3p	CLIP-seq
MIRT1330992	hsa-miR-4770	CLIP-seq
MIRT1330993	hsa-miR-760	CLIP-seq

Show/Hide all (25)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003677	Function	DNA binding	IEA
GO:0004672	Function	Protein kinase activity	IEA
GO:0005515	Function	Protein binding	IPI	26871637, 32296183, 32707033, 33961781, 35271311
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	ISS	12783284
GO:0005793	Component	Endoplasmic reticulum-Golgi intermediate compartment	IDA	18556652
GO:0005793	Component	Endoplasmic reticulum-Golgi intermediate compartment	IEA
GO:0005794	Component	Golgi apparatus	IDA	18556652
GO:0005794	Component	Golgi apparatus	IEA
GO:0005801	Component	Cis-Golgi network	IDA	18556652
GO:0005813	Component	Centrosome	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005856	Component	Cytoskeleton	IEA
GO:0006890	Process	Retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	IDA	18556652
GO:0006954	Process	Inflammatory response	IEA
GO:0008104	Process	Intracellular protein localization	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016192	Process	Vesicle-mediated transport	IEA
GO:0021522	Process	Spinal cord motor neuron differentiation	IEA
GO:0030126	Component	COPI vesicle coat	IDA	18556652
GO:0030126	Component	COPI vesicle coat	IEA
GO:0045296	Function	Cadherin binding	HDA	25468996
GO:0048666	Process	Neuron development	IEA

MIM	HGNC	e!Ensembl
607982	14372	ENSG00000142186

Q96KG9

Protein name

N-terminal kinase-like protein (Coated vesicle-associated kinase of 90 kDa) (SCY1-like protein 1) (Telomerase regulation-associated protein) (Telomerase transcriptional element-interacting factor) (Teratoma-associated tyrosine kinase)

Protein function

Regulates COPI-mediated retrograde protein traffic at the interface between the Golgi apparatus and the endoplasmic reticulum (PubMed:18556652). Involved in the maintenance of the Golgi apparatus morphology (PubMed:26581903). {ECO:0000269|PubMed

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00069	Pkinase	31 → 256	Protein kinase domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:12036289}.

Sequence

MWFFARDPVRDFPFELIPEPPEGGLPGPWALHRGRKKATGSPVSIFVYDVKPGAEEQTQV
AKAAFKRFKTLRHPNILAYIDGLETEKCLHVVTEAVTPLGIYLKARVEAGGLKELEISWG
LHQIVKALSFLVNDCSLIHNNVCMAAVFVDRAGEWKLGGLDYMYSAQGNGGGPPRKGIPE
LEQYDPPELADSSGRVVREKWSADMWRLGCLIWEVFNGPLPRAAALRNPGKIPKTLVPHY
CELVGANPKVRPNPARFLQNCRAPGGFMSNRFVETNLFLEEIQIKEPAEKQKFFQELSKS
LDAFPEDFCRHKVLPQLLTAFEFGNAGAVVLTPLFKVGKFLSAEEYQQKIIPVVVKMFSS
TDRAMRIRLLQQMEQFIQYLDEPTVNTQIFPHVVHGFLDTNPAIREQTVKSMLLLAPKLN
EANLNVELMKHFARLQAKDEQGPIRCNTTVCLGKIGSYLSASTRHRVLTSAFSRATRDPF
APSRVAGVLGFAATHNLYSMNDCAQKILPVLCGLTVDPEKSVRDQAFKAIRSFLSKLESV
SEDPTQLEEVEKDVHAASSPGMGGAAASWAGWAVTGVSSLTSKLIRSHPTTAPTETNIPQ
RPTPEGVPAPAPTPVPATPTTSGHWETQEEDKDTAEDSSTADRWDDEDWGSLEQEAESVL
AQQDDWSTGGQVSRASQVSNSDHKSSKSPESDWSSWEAEGSWEQGWQEPSSQEPPPDGTR
LASEYNWGGPESSDKGDPFATLSARPSTQPRPDSWGEDNWEGLETDSRQVKAELARKKRE
ERRREMEAKRAERKVAKGPMKLGARKLD

Sequence length

808

Interactions

View interactions

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome	Pathogenic; Likely pathogenic	rs1320473430, rs864309664, rs864309665, rs864309666, rs864309667, rs201581270, rs2496024369, rs2495967037, rs1554967681, rs1554967761, rs942522644, rs1554969925, rs1554970375, rs1554969894, rs1590740858, rs535912271 View all (1 more)	RCV001329770 RCV003997056 RCV003997057 RCV003997556 RCV003997557 RCV003152858 RCV003153151 RCV004595237 RCV000853082 RCV005414504 RCV000853083 RCV000853081 RCV000853080 RCV000661920 RCV004002907 RCV000853313 RCV001251097
SCYL1-related disorder	Likely pathogenic; Pathogenic	rs535912271	RCV003424376

Show/Hide Text Mining Associations (19)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Ataxia	Associate	26581903, 29419818
Breast Neoplasms	Associate	35948564
Breast Neoplasms	Stimulate	36290821
Cerebellar Ataxia	Associate	30258122
Cerebellar Diseases	Associate	26581903, 29419818
Cholestasis	Associate	29419818
Gait Ataxia	Associate	26581903
Genetic Diseases Inborn	Associate	35948564
Growth Disorders	Associate	30258122
Liver Failure	Associate	26581903, 29419818, 30258122
Liver Failure Acute	Associate	26581903, 29419818, 30959346
Muscular Atrophy	Associate	26581903
Nervous System Diseases	Associate	26581903
Neurodegenerative Diseases	Associate	20209057, 29419818, 30959346
Oculocerebrorenal Syndrome	Associate	30959346
Peripheral Nervous System Diseases	Associate	26581903, 29419818, 30258122
Spinocerebellar Ataxia 29	Associate	26581903
Spinocerebellar Ataxias	Associate	29419818, 30258122, 35948564
Tremor	Associate	26581903

SCYL1 (SCY1 like pseudokinase 1)