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

Gene ID: 57410, updated on 3-May-2025
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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See SCYL1 in Genome Data Viewer
Location:
11q13.1
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (65525083..65538704)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (65519285..65532904)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (65292554..65306175)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene metastasis associated lung adenocarcinoma transcript 1 Neighboring gene TALAM1 transcript, MALAT1 antisense RNA Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4984 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:65274865-65275546 Neighboring gene MALAT1-associated small cytoplasmic RNA Neighboring gene small nuclear ribonucleoprotein polypeptide G pseudogene 19 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3529 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:65297753-65297921 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65305475-65305979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65305980-65306483 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3530 Neighboring gene Sharpr-MPRA regulatory region 4001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4987 Neighboring gene latent transforming growth factor beta binding protein 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3532 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3533 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3534 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3535 Neighboring gene uncharacterized LOC124902823 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65319617-65320292 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:65320293-65320968 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3537 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:65328600-65329263 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4988 Neighboring gene ZNRD2 divergent transcript

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Related articles in PubMed

  1. 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
  2. Localization of TEIF in the centrosome and its functional association with centrosome amplification in DNA damage, telomere dysfunction and human cancers. Gong Y, et al. Oncogene, 2009 Mar 26. PMID 19198626
  3. 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
  4. [Expression of TEIF protein in colorectal tumors and its correlation with centrosome abnormality]. Gao Y, et al. Ai Zheng, 2009 Dec. PMID 19958622
  5. Expression of a telomerase-associated gene in normal, atrophic, and tumorous testes. Mei F, et al. Chin Med Sci J, 2005 Sep. PMID 16261899

See all (107) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SCYL1-mediated regulation of the mTORC1 signaling pathway inhibits autophagy and promotes gastric cancer metastasis.
    Title: SCYL1-mediated regulation of the mTORC1 signaling pathway inhibits autophagy and promotes gastric cancer metastasis.
  2. Overexpression of SCYL1 Is Associated with Progression of Breast Cancer.
    Title: Overexpression of SCYL1 Is Associated with Progression of Breast Cancer.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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).
  8. 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.
  9. 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.
  10. 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.
Submit: New GeneRIF Correction See all GeneRIFs (22)

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
Compare labs

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

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Products Interactant Other Gene Complex Source Pubs Description

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 kinase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within inflammatory response IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within neuron development IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within protein localization 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 
acts_upstream_of_or_within spinal cord motor neuron differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in vesicle-mediated transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of COPI vesicle coat IDA
Inferred from Direct Assay
more info
 PubMed 
part_of COPI vesicle coat IEA
Inferred from Electronic Annotation
more info
  
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in Golgi apparatus IEA
Inferred from Electronic Annotation
more info
  
located_in centrosome IEA
Inferred from Electronic Annotation
more info
  
located_in cis-Golgi network IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
located_in cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
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 endoplasmic reticulum-Golgi intermediate compartment IEA
Inferred from Electronic Annotation
more info
  
located_in membrane HDA PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
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

NEW Try the new Transcript table

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/TrEMBL
    E9PS17
    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, E9PS17
    Related
    ENSP00000431635.1, ENST00000525364.5

  3. NM_001425179.1 → NP_001412108.1  N-terminal kinase-like protein isoform 4

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  4. NM_001425180.1 → NP_001412109.1  N-terminal kinase-like protein isoform 5

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  5. NM_001425181.1 → NP_001412110.1  N-terminal kinase-like protein isoform 6

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  6. NM_001425182.1 → NP_001412111.1  N-terminal kinase-like protein isoform 7

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  7. NM_001425183.1 → NP_001412112.1  N-terminal kinase-like protein isoform 8

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  8. NM_001425184.1 → NP_001412113.1  N-terminal kinase-like protein isoform 9

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  9. NM_001425185.1 → NP_001412114.1  N-terminal kinase-like protein isoform 10

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17
    Related
    ENSP00000437254.1, ENST00000533862.5

  10. NM_001425186.1 → NP_001412115.1  N-terminal kinase-like protein isoform 11

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  11. NM_001425187.1 → NP_001412116.1  N-terminal kinase-like protein isoform 12

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  12. NM_001425188.1 → NP_001412117.1  N-terminal kinase-like protein isoform 13

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  13. NM_001425189.1 → NP_001412118.1  N-terminal kinase-like protein isoform 14

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  14. NM_001425190.1 → NP_001412119.1  N-terminal kinase-like protein isoform 15

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  15. NM_001425191.1 → NP_001412120.1  N-terminal kinase-like protein isoform 16

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  16. NM_001425192.1 → NP_001412121.1  N-terminal kinase-like protein isoform 17

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  17. NM_001425193.1 → NP_001412122.1  N-terminal kinase-like protein isoform 18

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  18. NM_001425194.1 → NP_001412123.1  N-terminal kinase-like protein isoform 19

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  19. NM_001425195.1 → NP_001412124.1  N-terminal kinase-like protein isoform 20

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  20. NM_001425196.1 → NP_001412125.1  N-terminal kinase-like protein isoform 21

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17
    Related
    ENSP00000432175.1, ENST00000524944.5

  21. NM_001425197.1 → NP_001412126.1  N-terminal kinase-like protein isoform 22

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  22. NM_001425198.1 → NP_001412127.1  N-terminal kinase-like protein isoform 23

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  23. NM_001425199.1 → NP_001412128.1  N-terminal kinase-like protein isoform 24

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  24. NM_001425200.1 → NP_001412129.1  N-terminal kinase-like protein isoform 25

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  25. NM_001425201.1 → NP_001412130.1  N-terminal kinase-like protein isoform 26

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  26. NM_001425202.1 → NP_001412131.1  N-terminal kinase-like protein isoform 27

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  27. NM_001425203.1 → NP_001412132.1  N-terminal kinase-like protein isoform 28

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PPN3, E9PS17
    Related
    ENSP00000436993.1, ENST00000527009.5

  28. NM_001425204.1 → NP_001412133.1  N-terminal kinase-like protein isoform 29

    Status: REVIEWED

    Source sequence(s)
    AP000769
    UniProtKB/TrEMBL
    E9PS17

  29. NM_001425205.1 → NP_001412134.1  N-terminal kinase-like protein isoform 30

    Status: REVIEWED

    Source sequence(s)
    AP000769

  30. NM_001425206.1 → NP_001412135.1  N-terminal kinase-like protein isoform 31

    Status: REVIEWED

    Source sequence(s)
    AP000769

  31. NM_001425207.1 → NP_001412136.1  N-terminal kinase-like protein isoform 32

    Status: REVIEWED

    Source sequence(s)
    AP000769

  32. NM_001425208.1 → NP_001412137.1  N-terminal kinase-like protein isoform 33

    Status: REVIEWED

    Source sequence(s)
    AP000769

  33. NM_001425209.1 → NP_001412138.1  N-terminal kinase-like protein isoform 34

    Status: REVIEWED

    Source sequence(s)
    AP000769

  34. NM_001425210.1 → NP_001412139.1  N-terminal kinase-like protein isoform 35

    Status: REVIEWED

    Source sequence(s)
    AP000769

  35. NM_001425211.1 → NP_001412140.1  N-terminal kinase-like protein isoform 36

    Status: REVIEWED

    Source sequence(s)
    AP000769

  36. 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
    A6NJF1, Q96G50, Q96KG8, Q96KG9, Q96KH1, Q9HAW5, Q9HBL3, Q9NR53
    UniProtKB/TrEMBL
    E9PS17
    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_2024_08

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)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    65519285..65532904
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96KG9.1 GenPept UniProtKB/Swiss-Prot:Q96KG9

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