SCYL1 (SCY1 like pseudokinase 1)

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
SNPs SNP information provided by dbSNP.
14
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
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
miRNA miRNA information provided by mirtarbase database.
34
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
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
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
25
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
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
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
MIM HGNC e!Ensembl
607982 14372 ENSG00000142186
Protein Protein information from UniProt database.
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
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
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
9
Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Show/Hide Causal Diseases (2)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
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
View all (1 more)		 RCV001329770
RCV003997056
RCV003997057
RCV003997556
RCV003997557
View all (12 more)
★★★★★
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
SCYL1-related disorder Likely pathogenic; Pathogenic rs535912271 RCV003424376
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Show/Hide Unknown Diseases (7)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
ATAXIA, SPINOCEREBELLAR — Disgenet
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
HYPERURICEMIA — GWAS catalog
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
PSORIATIC ARTHRITIS — GWAS catalog
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 21 — HPO
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Show/Hide Text Mining Associations (144)
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome Liver Failure-Cerebellar Ataxia-Peripheral Sensory Motor Neuropathy Syndrome Orphanet
★★★★★
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Acute lymphocytic leukemia Lymphocytic Leukemia BEFREE 1612589
★★★★★
★☆☆☆☆
Found in Text Mining only
Acute Promyelocytic Leukemia Promyelocytic Leukemia BEFREE 23589495, 25769384
★★★★★
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Of Esophagus Esophageal Cancer BEFREE 31809243
★★★★★
★☆☆☆☆
Found in Text Mining only
Arthritis Arthritis BEFREE 29339199, 31508794
★★★★★
★☆☆☆☆
Found in Text Mining only
Asthma Asthma BEFREE 17913447
★★★★★
★☆☆☆☆
Found in Text Mining only
Ataxia Ataxia Pubtator 26581903, 29419818 Associate
★★★★★
★☆☆☆☆
Found in Text Mining only
Ataxia, Spinocerebellar Spinocerebellar Ataxia CTD_human_DG
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Atrial Fibrillation Atrial Fibrillation BEFREE 29437577
★★★★★
★☆☆☆☆
Found in Text Mining only
Bernard-Soulier Syndrome Bernard Soulier Syndrome BEFREE 14987917
★★★★★
★☆☆☆☆
Found in Text Mining only