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

Summary

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

Location:: 11q13.1

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (65525083..65538704)
RS_2023_10	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_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Overexpression of SCYL1 Is Associated with Progression of Breast Cancer.
Title: Overexpression of SCYL1 Is Associated with Progression of Breast Cancer.
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.
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.
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.
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.
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).
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.
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.
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.
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	Compare labs

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S1209 (e-PCR)
- UniSTS:67341

RH65764 (e-PCR)
- UniSTS:9768

G38718 (e-PCR)
- UniSTS:9322

MARC_10501-10502:1000139918:1 (e-PCR)
- UniSTS:267156

WI-15382 (e-PCR)
- UniSTS:12183

RH78678 (e-PCR)
- UniSTS:64188

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 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 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 centrosome	IEA Inferred from Electronic Annotation more info
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 more info	PubMed
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

NG_047172.1 RefSeqGene

Range

5019..18640

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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]
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

Related

ENSP00000431635.1, ENST00000525364.5
NM_001425179.1 → NP_001412108.1 N-terminal kinase-like protein isoform 4

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425180.1 → NP_001412109.1 N-terminal kinase-like protein isoform 5

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425181.1 → NP_001412110.1 N-terminal kinase-like protein isoform 6

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425182.1 → NP_001412111.1 N-terminal kinase-like protein isoform 7

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425183.1 → NP_001412112.1 N-terminal kinase-like protein isoform 8

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425184.1 → NP_001412113.1 N-terminal kinase-like protein isoform 9

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425185.1 → NP_001412114.1 N-terminal kinase-like protein isoform 10

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425186.1 → NP_001412115.1 N-terminal kinase-like protein isoform 11

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425187.1 → NP_001412116.1 N-terminal kinase-like protein isoform 12

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425188.1 → NP_001412117.1 N-terminal kinase-like protein isoform 13

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425189.1 → NP_001412118.1 N-terminal kinase-like protein isoform 14

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425190.1 → NP_001412119.1 N-terminal kinase-like protein isoform 15

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425191.1 → NP_001412120.1 N-terminal kinase-like protein isoform 16

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425192.1 → NP_001412121.1 N-terminal kinase-like protein isoform 17

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425193.1 → NP_001412122.1 N-terminal kinase-like protein isoform 18

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425194.1 → NP_001412123.1 N-terminal kinase-like protein isoform 19

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425195.1 → NP_001412124.1 N-terminal kinase-like protein isoform 20

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425196.1 → NP_001412125.1 N-terminal kinase-like protein isoform 21

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425197.1 → NP_001412126.1 N-terminal kinase-like protein isoform 22

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425198.1 → NP_001412127.1 N-terminal kinase-like protein isoform 23

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425199.1 → NP_001412128.1 N-terminal kinase-like protein isoform 24

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425200.1 → NP_001412129.1 N-terminal kinase-like protein isoform 25

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425201.1 → NP_001412130.1 N-terminal kinase-like protein isoform 26

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425202.1 → NP_001412131.1 N-terminal kinase-like protein isoform 27

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425203.1 → NP_001412132.1 N-terminal kinase-like protein isoform 28

Status: REVIEWED

Source sequence(s)

AP000769

UniProtKB/TrEMBL

E9PPN3
NM_001425204.1 → NP_001412133.1 N-terminal kinase-like protein isoform 29

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425205.1 → NP_001412134.1 N-terminal kinase-like protein isoform 30

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425206.1 → NP_001412135.1 N-terminal kinase-like protein isoform 31

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425207.1 → NP_001412136.1 N-terminal kinase-like protein isoform 32

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425208.1 → NP_001412137.1 N-terminal kinase-like protein isoform 33

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425209.1 → NP_001412138.1 N-terminal kinase-like protein isoform 34

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425210.1 → NP_001412139.1 N-terminal kinase-like protein isoform 35

Status: REVIEWED

Source sequence(s)

AP000769
NM_001425211.1 → NP_001412140.1 N-terminal kinase-like protein isoform 36

Status: REVIEWED

Source sequence(s)

AP000769
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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

65525083..65538704

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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]
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]
XM_017018031.3 → XP_016873520.1 N-terminal kinase-like protein isoform X4
XM_017018030.3 → XP_016873519.1 N-terminal kinase-like protein isoform X2
XM_047427316.1 → XP_047283272.1 N-terminal kinase-like protein isoform X5