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CDKAL1 CDK5 regulatory subunit associated protein 1 like 1 [ Homo sapiens (human) ]

Gene ID: 54901, updated on 5-Mar-2024

Summary

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Official Symbol
CDKAL1provided by HGNC
Official Full Name
CDK5 regulatory subunit associated protein 1 like 1provided by HGNC
Primary source
HGNC:HGNC:21050
See related
Ensembl:ENSG00000145996 MIM:611259; AllianceGenome:HGNC:21050
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
Summary
The protein encoded by this gene is a member of the methylthiotransferase family. The function of this gene is not known. Genome-wide association studies have linked single nucleotide polymorphisms in an intron of this gene with susceptibilty to type 2 diabetes. [provided by RefSeq, May 2010]
Expression
Ubiquitous expression in thyroid (RPKM 1.8), endometrium (RPKM 1.4) and 25 other tissues See more
Orthologs
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Genomic context

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See CDKAL1 in Genome Data Viewer
Location:
6p22.3
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (20534457..21232404)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (20406474..21104535)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (20534688..21232635)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:20467153-20467794 Neighboring gene E2F3 intronic transcript 1 Neighboring gene RNA, U6 small nuclear 141, pseudogene Neighboring gene E2F transcription factor 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24131 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24130 Neighboring gene uncharacterized LOC124901273 Neighboring gene MPRA-validated peak5719 silencer Neighboring gene uncharacterized LOC105374968 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:20629440-20630213 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:20630214-20630986 Neighboring gene NANOG hESC enhancer GRCh37_chr6:20686272-20686773 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16981 Neighboring gene MPRA-validated peak5720 silencer Neighboring gene ribosomal protein L36a pseudogene 25 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:20798064-20798254 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:20810592-20811186 Neighboring gene MPRA-validated peak5721 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr6:20834311-20834850 Neighboring gene VISTA enhancer hs1340 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:20877312-20878511 Neighboring gene Sharpr-MPRA regulatory region 659 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24134 Neighboring gene MPRA-validated peak5723 silencer Neighboring gene RNA, U6 small nuclear 150, pseudogene Neighboring gene uncharacterized LOC105374966 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:21150224 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:21163919 Neighboring gene melanoma risk locus-associated MPRA allelic enhancers 6:21164131 and 6:21164145 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:21166705 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24135 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:21186041-21186767 Neighboring gene NANOG hESC enhancer GRCh37_chr6:21223372-21223889 Neighboring gene uncharacterized LOC107986578 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:21230452-21231651 Neighboring gene Sharpr-MPRA regulatory region 5810 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:21263602-21264102 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24137 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:21275814-21276318 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:21276319-21276823 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21327213-21328056 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21361231-21362046 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:21362047-21362861 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21367138-21367689 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21367690-21368242 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21368243-21368793 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:21393485-21394340 Neighboring gene MPRA-validated peak5728 silencer Neighboring gene uncharacterized LOC107986579 Neighboring gene long intergenic non-protein coding RNA 581

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. Association of the CDKAL1 gene polymorphism with gestational diabetes mellitus in Chinese women. Huang C, et al. BMJ Open Diabetes Res Care, 2023 Apr. PMID 37055162, Free PMC Article
  2. Association of CDKAL1 gene polymorphism (rs10946398) with gestational diabetes mellitus in Pakistani population. Asghar A, et al. Mol Biol Rep, 2023 Jan. PMID 36301463
  3. The CDKAL1 rs7747752-Bile Acids Interaction Increased Risk of Gestational Diabetes Mellitus: A Nested Case-Control Study. Wang H, et al. Front Endocrinol (Lausanne), 2022. PMID 35360068, Free PMC Article
  4. Sex Differences in the Effects of CDKAL1 Variants on Glycemic Control in Diabetic Patients: Findings from the Korean Genome and Epidemiology Study. Lee HA, et al. Diabetes Metab J, 2022 Nov. PMID 35130687, Free PMC Article
  5. Association of CDKAL1 RS10946398 Gene Polymorphism with Susceptibility to Diabetes Mellitus Type 2: A Meta-Analysis. Xu N, et al. J Diabetes Res, 2021. PMID 34977253, Free PMC Article

See all (257) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CDC123 promotes Hepatocellular Carcinoma malignant progression by regulating CDKAL1.
    Title: CDC123 promotes Hepatocellular Carcinoma malignant progression by regulating CDKAL1.
  2. TCF7L2 (rs7903146) But Not CDKAL1 (rs7754840) Gene Polymorphisms Increase the Risk of New-Onset Diabetes After Kidney Transplant.
    Title: TCF7L2 (rs7903146) But Not CDKAL1 (rs7754840) Gene Polymorphisms Increase the Risk of New-Onset Diabetes After Kidney Transplant.
  3. CDKAL1 Drives the Maintenance of Cancer Stem-Like Cells by Assembling the eIF4F Translation Initiation Complex.
    Title: CDKAL1 Drives the Maintenance of Cancer Stem-Like Cells by Assembling the eIF4F Translation Initiation Complex.
  4. The Association between CDKAL1 Gene rs10946398 Polymorphism and Post-Transplant Diabetes in Kidney Allograft Recipients Treated with Tacrolimus.
    Title: The Association between CDKAL1 Gene rs10946398 Polymorphism and Post-Transplant Diabetes in Kidney Allograft Recipients Treated with Tacrolimus.
  5. Common and Distinct Genetic Architecture of Age at Diagnosis of Diabetes in South Indian and European Populations.
    Title: Common and Distinct Genetic Architecture of Age at Diagnosis of Diabetes in South Indian and European Populations.
  6. Hepatic Cdkal1 deletion regulates HDL catabolism and promotes reverse cholesterol transport.
    Title: Hepatic Cdkal1 deletion regulates HDL catabolism and promotes reverse cholesterol transport.
  7. Association of the CDKAL1 gene polymorphism with gestational diabetes mellitus in Chinese women.
    Title: Association of the CDKAL1 gene polymorphism with gestational diabetes mellitus in Chinese women.
  8. The triglyceride glucose index and CDKAL1 gene rs10946398 SNP are associated with NAFLD in Chinese adults.
    Title: The triglyceride glucose index and CDKAL1 gene rs10946398 SNP are associated with NAFLD in Chinese adults.
  9. FTO demethylates m6A modifications in CDKAL1 mRNA and promotes gastric cancer chemoresistance by altering mitochondrial dynamics.
    Title: FTO demethylates m6A modifications in CDKAL1 mRNA and promotes gastric cancer chemoresistance by altering mitochondrial dynamics.
  10. Association of CDKAL1 gene polymorphism (rs10946398) with gestational diabetes mellitus in Pakistani population.
    Title: Association of CDKAL1 gene polymorphism (rs10946398) with gestational diabetes mellitus in Pakistani population.
Submit: New GeneRIF Correction See all GeneRIFs (118)

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

EBI GWAS Catalog

Description
A genome-wide association study identifies GRK5 and RASGRP1 as type 2 diabetes loci in Chinese Hans.
EBI GWAS Catalog
A genome-wide association study of gestational diabetes mellitus in Korean women.
EBI GWAS Catalog
A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants.
EBI GWAS Catalog
A pilot genome-wide association study shows genomic variants enriched in the non-tumor cells of patients with well-differentiated neuroendocrine tumors of the ileum.
EBI GWAS Catalog
A variant in CDKAL1 influences insulin response and risk of type 2 diabetes.
EBI GWAS Catalog
Adiposity-related heterogeneity in patterns of type 2 diabetes susceptibility observed in genome-wide association data.
EBI GWAS Catalog
Association of glycosylated hemoglobin with the gene encoding CDKAL1 in the Korean Association Resource (KARE) study.
EBI GWAS Catalog
Common variants at CDKAL1 and KLF9 are associated with body mass index in east Asian populations.
EBI GWAS Catalog
Confirmation of multiple risk Loci and genetic impacts by a genome-wide association study of type 2 diabetes in the Japanese population.
EBI GWAS Catalog
Genetic variant near IRS1 is associated with type 2 diabetes, insulin resistance and hyperinsulinemia.
EBI GWAS Catalog
Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels.
EBI GWAS Catalog
Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease.
EBI GWAS Catalog
Genome-wide association meta-analysis identifies novel variants associated with fasting plasma glucose in East Asians.
EBI GWAS Catalog
Genome-wide association study identifies multiple loci associated with bladder cancer risk.
EBI GWAS Catalog
Genome-wide association study identifies three novel loci for type 2 diabetes.
EBI GWAS Catalog
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
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
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
EBI GWAS Catalog
Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
EBI GWAS Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog
Meta-analysis identifies common variants associated with body mass index in east Asians.
EBI GWAS Catalog
Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies in East Asian-ancestry populations identifies four new loci for body mass index.
EBI GWAS Catalog
Multiple nonglycemic genomic loci are newly associated with blood level of glycated hemoglobin in East Asians.
EBI GWAS Catalog
New loci associated with birth weight identify genetic links between intrauterine growth and adult height and metabolism.
EBI GWAS Catalog
New susceptibility loci in MYL2, C12orf51 and OAS1 associated with 1-h plasma glucose as predisposing risk factors for type 2 diabetes in the Korean population.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog
Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes.
EBI GWAS Catalog
SNPs in KCNQ1 are associated with susceptibility to type 2 diabetes in East Asian and European populations.
EBI GWAS Catalog
Stratifying type 2 diabetes cases by BMI identifies genetic risk variants in LAMA1 and enrichment for risk variants in lean compared to obese cases.
EBI GWAS Catalog
Transferability of type 2 diabetes implicated loci in multi-ethnic cohorts from Southeast Asia.
EBI GWAS Catalog
Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.
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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Nef nef Messenger RNAs for three proteins AATK, SLC27A1, and CDKAL1 are preferentially secreted out in exosomes from HIV-1 Nef-expressing cells, and their targeting miRNAs (miR-32 and miR-93*) are retained in these cells PubMed
Vif vif HIV-1 Vif interacts with CDKAL1 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ20342, FLJ46705, MGC75469

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 4 iron, 4 sulfur cluster binding IEA
Inferred from Electronic Annotation
more info
  
enables N6-threonylcarbomyladenosine methylthiotransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables tRNA (N(6)-L-threonylcarbamoyladenosine(37)-C(2))-methylthiotransferase IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
involved_in maintenance of translational fidelity IEA
Inferred from Electronic Annotation
more info
  
involved_in tRNA methylthiolation IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
located_in membrane HDA PubMed 
located_in rough endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
threonylcarbamoyladenosine tRNA methylthiotransferase
Names
tRNA-t(6)A37 methylthiotransferase
NP_060244.2
XP_011513020.1
XP_011513021.1
XP_016866475.1
XP_024302249.1
XP_047274903.1
XP_047274904.1
XP_047274905.1
XP_047274906.1
XP_047274907.1
XP_047274908.1
XP_047274909.1
XP_047274910.1
XP_047274911.1
XP_047274912.1
XP_047274913.1
XP_047274914.1
XP_054211725.1
XP_054211726.1
XP_054211727.1
XP_054211728.1
XP_054211729.1
XP_054211730.1
XP_054211731.1
XP_054211732.1

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_021195.2 RefSeqGene

    Range
    5001..702948
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_017774.3 → NP_060244.2  threonylcarbamoyladenosine tRNA methylthiotransferase

    See identical proteins and their annotated locations for NP_060244.2

    Status: REVIEWED

    Source sequence(s)
    AK128546, AL451080, BC121020
    Consensus CDS
    CCDS4546.1
    UniProtKB/Swiss-Prot
    A8K6S0, Q5VV42, Q6P385, Q6ZR27, Q9NXB3
    Related
    ENSP00000274695.4, ENST00000274695.8
    Conserved Domains (1) summary
    cl27627
    Location:65 → 445
    UPF0004; Uncharacterized protein family UPF0004

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

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    20534457..21232404
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047418949.1 → XP_047274905.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X1

    UniProtKB/Swiss-Prot
    A8K6S0, Q5VV42, Q6P385, Q6ZR27, Q9NXB3

  2. XM_047418952.1 → XP_047274908.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X2

  3. XM_011514718.1 → XP_011513020.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X2

    Conserved Domains (3) summary
    cd01335
    Location:208 → 416
    Radical_SAM; Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. ...
    TIGR01578
    Location:65 → 481
    MiaB-like-B; MiaB-like tRNA modifying enzyme, archaeal-type
    pfam00919
    Location:65 → 146
    UPF0004; Uncharacterized protein family UPF0004

  4. XM_047418947.1 → XP_047274903.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X8

  5. XM_047418948.1 → XP_047274904.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X8

  6. XM_024446481.2 → XP_024302249.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X8

    Conserved Domains (1) summary
    cl27627
    Location:65 → 445
    UPF0004; Uncharacterized protein family UPF0004

  7. XM_047418950.1 → XP_047274906.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X9

  8. XM_017010986.2 → XP_016866475.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X4

    Conserved Domains (1) summary
    TIGR01578
    Location:65 → 423
    MiaB-like-B; MiaB-like tRNA modifying enzyme, archaeal-type

  9. XM_011514719.3 → XP_011513021.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X3

    Conserved Domains (3) summary
    cd01335
    Location:208 → 406
    Radical_SAM; Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. ...
    smart00729
    Location:207 → 420
    Elp3; Elongator protein 3, MiaB family, Radical SAM
    pfam00919
    Location:65 → 146
    UPF0004; Uncharacterized protein family UPF0004

  10. XM_047418958.1 → XP_047274914.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X7

  11. XM_047418951.1 → XP_047274907.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X9

  12. XM_047418954.1 → XP_047274910.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X5

  13. XM_047418955.1 → XP_047274911.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X6

  14. XM_047418953.1 → XP_047274909.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X10

  15. XM_047418956.1 → XP_047274912.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X11

  16. XM_047418957.1 → XP_047274913.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X11

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    20406474..21104535
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054355750.1 → XP_054211725.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X1

    UniProtKB/Swiss-Prot
    A8K6S0, Q5VV42, Q6P385, Q6ZR27, Q9NXB3

  2. XM_054355752.1 → XP_054211727.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X2

  3. XM_054355751.1 → XP_054211726.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X2

  4. XM_054355754.1 → XP_054211729.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X4

  5. XM_054355753.1 → XP_054211728.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X3

  6. XM_054355757.1 → XP_054211732.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X7

  7. XM_054355756.1 → XP_054211731.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X6

  8. XM_054355755.1 → XP_054211730.1  threonylcarbamoyladenosine tRNA methylthiotransferase isoform X5

RNA

  1. XR_008487355.1 RNA Sequence

  2. XR_008487356.1 RNA Sequence

  3. XR_008487354.1 RNA Sequence

  4. XR_008487357.1 RNA Sequence

  5. XR_008487358.1 RNA Sequence

  6. XR_008487359.1 RNA Sequence

  7. XR_008487360.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5VV42.1 GenPept UniProtKB/Swiss-Prot:Q5VV42

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