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SCYL1 SCY1 like pseudokinase 1 [ Homo sapiens (human) ]

Gene ID: 57410, updated on 29-Mar-2023

Summary

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Official Symbol
SCYL1provided by HGNC
Official Full Name
SCY1 like pseudokinase 1provided by HGNC
Primary source
HGNC:HGNC:14372
See related
Ensembl:ENSG00000142186 MIM:607982; AllianceGenome:HGNC:14372
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
GKLP; NKTL; NTKL; P105; TAPK; TEIF; TRAP; HT019; SCAR21
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-terminal domain. It activates transcription of the telomerase reverse transcriptase and DNA polymerase beta genes. The protein has been localized to the nucleus, and also to the cytoplasm and centrosomes during mitosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 23.2), ovary (RPKM 22.4) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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See SCYL1 in Genome Data Viewer
Location:
11q13.1
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (65525083..65538704)
RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (65519285..65532904)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (65292554..65306175)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene TALAM1 transcript, MALAT1 antisense RNA Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:65274865-65275546 Neighboring gene small nuclear ribonucleoprotein polypeptide G pseudogene 19 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65305475-65305979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65305980-65306483 Neighboring gene Sharpr-MPRA regulatory region 4001 Neighboring gene latent transforming growth factor beta binding protein 3 Neighboring gene uncharacterized LOC124902823

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: 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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Related articles in PubMed

  1. Overexpression of SCYL1 Is Associated with Progression of Breast Cancer. Sun A, et al. Curr Oncol, 2022 Sep 24. PMID 36290821, Free PMC Article
  2. SCYL1 disease and liver transplantation diagnosed by reanalysis of exome sequencing and deletion/duplication analysis of SCYL1. McNiven V, et al. Am J Med Genet A, 2021 Apr. PMID 33442927
  3. Variant in SCYL1 gene causes aberrant splicing in a family with cerebellar ataxia, recurrent episodes of liver failure, and growth retardation. Shohet A, et al. Eur J Hum Genet, 2019 Feb. PMID 30258122, Free PMC Article
  4. SCYL1 variants cause a syndrome with low γ-glutamyl-transferase cholestasis, acute liver failure, and neurodegeneration (CALFAN). Lenz D, et al. Genet Med, 2018 Oct. PMID 29419818, Free PMC Article
  5. Overexpression of N-terminal kinase like gene promotes tumorigenicity of hepatocellular carcinoma by regulating cell cycle progression and cell motility. Wang J, et al. Oncotarget, 2015 Jan 30. PMID 25575811, Free PMC Article

See all (90) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Overexpression of SCYL1 Is Associated with Progression of Breast Cancer.
    Title: Overexpression of SCYL1 Is Associated with Progression of Breast Cancer.
  2. SCYL1 disease and liver transplantation diagnosed by reanalysis of exome sequencing and deletion/duplication analysis of SCYL1.
    Title: SCYL1 disease and liver transplantation diagnosed by reanalysis of exome sequencing and deletion/duplication analysis of SCYL1.
  3. SCYL1 arginine methylation by PRMT1 is essential for neurite outgrowth via Golgi morphogenesis.
    Title: SCYL1 arginine methylation by PRMT1 is essential for neurite outgrowth via Golgi morphogenesis.
  4. Mutations in NBAS and SCYL1, genetic causes of recurrent liver failure in children: Three case reports and a literature review.
    Title: Mutations in NBAS and SCYL1, genetic causes of recurrent liver failure in children: Three case reports and a literature review.
  5. SCYL1 splicing mutation causes cerebellar ataxia, recurrent episodes of liver failure, and growth retardation.
    Title: Variant in SCYL1 gene causes aberrant splicing in a family with cerebellar ataxia, recurrent episodes of liver failure, and growth retardation.
  6. SCYL1 deficiency can cause recurrent low-GGT cholestatic liver dysfunction in conjunction with a variable neurological phenotype
    Title: SCYL1 variants cause a syndrome with low γ-glutamyl-transferase cholestasis, acute liver failure, and neurodegeneration (CALFAN).
  7. findings indicate that SCYL1 does not contribute to REST turnover and thus do not support a previous study suggesting a role for SCYL1 in mediating REST degradation
    Title: SCYL1 does not regulate REST expression and turnover.
  8. Disruptive SCYL1 mutations underlie a syndrome characterized by recurrent episodes of liver failure, peripheral neuropathy, cerebellar atrophy, and ataxia.
    Title: Disruptive SCYL1 Mutations Underlie a Syndrome Characterized by Recurrent Episodes of Liver Failure, Peripheral Neuropathy, Cerebellar Atrophy, and Ataxia.
  9. Data identified the large GTPase dynamin2 as an interacting protein of NTKL, which might be responsible for the phenotype alterations caused by NTKL overexpression, such as cytokinesis failure, increased cell motility and abnormal of cell division.
    Title: Overexpression of N-terminal kinase like gene promotes tumorigenicity of hepatocellular carcinoma by regulating cell cycle progression and cell motility.
  10. Data reveal that Scyl1 is a key organizer of a subset of the COPI machinery.
    Title: Scyl1 scaffolds class II Arfs to specific subcomplexes of coatomer through the γ-COP appendage domain.
Submit: New GeneRIF Correction See all GeneRIFs (21)

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

Associated conditions

Description Tests
Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome
MedGen: C5569084 OMIM: 616719 GeneReviews: Not available
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EBI GWAS Catalog

Description
A genome-wide association study of optic disc parameters.
EBI GWAS Catalog
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC78454

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables cadherin binding HDA PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein tyrosine kinase activity NAS
Non-traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in inflammatory response IEA
Inferred from Electronic Annotation
more info
  
involved_in neuron development IEA
Inferred from Electronic Annotation
more info
  
involved_in protein localization IEA
Inferred from Electronic Annotation
more info
  
involved_in protein phosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in spinal cord motor neuron differentiation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of COPI vesicle coat IDA
Inferred from Direct Assay
more info
 PubMed 
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cis-Golgi network IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in endoplasmic reticulum-Golgi intermediate compartment IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane HDA PubMed 
located_in microtubule organizing center IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
N-terminal kinase-like protein
Names
SCY1-like protein 1
SCY1-like, kinase-like 1
coated vesicle-associated kinase of 90 kDa
likely ortholog of mouse N-terminal kinase-like protein
telomerase regulation-associated protein
telomerase transcriptional elements-interacting factor
teratoma-associated tyrosine kinase

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.

Genomic

  1. NG_047172.1 RefSeqGene

    Range
    5019..18640
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001048218.2 → NP_001041683.1  N-terminal kinase-like protein isoform B

    See identical proteins and their annotated locations for NP_001041683.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (B), also known as 1, uses an alternate in-frame splice site in the 3' coding region, compared to variant A. It encodes isoform B, which is shorter than isoform A.
    Source sequence(s)
    AB051428, BP281963, BU728709
    Consensus CDS
    CCDS44646.1
    UniProtKB/Swiss-Prot
    Q96KG9
    Related
    ENSP00000408192.2, ENST00000420247.6
    Conserved Domains (2) summary
    cd14011
    Location:20 → 296
    PK_SCY1_like; Pseudokinase domain of Scy1-like proteins
    sd00044
    Location:351 → 372
    HEAT; HEAT repeat [structural motif]

  2. NM_001411022.1 → NP_001397951.1  N-terminal kinase-like protein isoform C

    Status: REVIEWED

    Source sequence(s)
    AP000769
    Consensus CDS
    CCDS91507.1
    UniProtKB/TrEMBL
    E9PK59

  3. NM_020680.4 → NP_065731.3  N-terminal kinase-like protein isoform A

    See identical proteins and their annotated locations for NP_065731.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (A) represents the longer transcript and encodes the longer isoform (A).
    Source sequence(s)
    BC069233, BP281963
    Consensus CDS
    CCDS41672.1
    UniProtKB/Swiss-Prot
    Q96KG9, Q9NR53
    Related
    ENSP00000270176.5, ENST00000270176.10
    Conserved Domains (2) summary
    cd14011
    Location:20 → 296
    PK_SCY1_like; Pseudokinase domain of Scy1-like proteins
    sd00044
    Location:351 → 372
    HEAT; HEAT repeat [structural motif]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    65525083..65538704
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005274120.5 → XP_005274177.1  N-terminal kinase-like protein isoform X3

    See identical proteins and their annotated locations for XP_005274177.1

    UniProtKB/Swiss-Prot
    Q96KG9
    Conserved Domains (2) summary
    cd14011
    Location:20 → 296
    PK_SCY1_like; Pseudokinase domain of Scy1-like proteins
    sd00044
    Location:351 → 372
    HEAT; HEAT repeat [structural motif]

  2. XM_005274118.5 → XP_005274175.1  N-terminal kinase-like protein isoform X1

    Conserved Domains (2) summary
    cd14011
    Location:20 → 296
    PK_SCY1_like; Pseudokinase domain of Scy1-like proteins
    sd00044
    Location:351 → 372
    HEAT; HEAT repeat [structural motif]

  3. XM_017018031.3 → XP_016873520.1  N-terminal kinase-like protein isoform X4

  4. XM_017018030.3 → XP_016873519.1  N-terminal kinase-like protein isoform X2

  5. XM_047427316.1 → XP_047283272.1  N-terminal kinase-like protein isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    65519285..65532904
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054369448.1 → XP_054225423.1  N-terminal kinase-like protein isoform X3

  2. XM_054369446.1 → XP_054225421.1  N-terminal kinase-like protein isoform X1

  3. XM_054369449.1 → XP_054225424.1  N-terminal kinase-like protein isoform X4

  4. XM_054369447.1 → XP_054225422.1  N-terminal kinase-like protein isoform X2

  5. XM_054369450.1 → XP_054225425.1  N-terminal kinase-like protein isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96KG9.1 GenPept UniProtKB/Swiss-Prot:Q96KG9

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