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CERKL ceramide kinase like [ Homo sapiens (human) ]

Gene ID: 375298, updated on 5-Mar-2024

Summary

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Official Symbol
CERKLprovided by HGNC
Official Full Name
ceramide kinase likeprovided by HGNC
Primary source
HGNC:HGNC:21699
See related
Ensembl:ENSG00000188452 MIM:608381; AllianceGenome:HGNC:21699
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
RP26
Summary
This gene was initially identified as a locus (RP26) associated with an autosomal recessive form of retinitis pigmentosa (arRP) disease. This gene encodes a protein with ceramide kinase-like domains, however, the protein does not phosphorylate ceramide and its target substrate is currently unknown. This protein may be a negative regulator of apoptosis in photoreceptor cells. Mutations in this gene cause a form of retinitis pigmentosa characterized by autosomal recessive cone and rod dystrophy (arCRD). Alternative splicing of this gene results in multiple transcript variants encoding different isoforms and non-coding transcripts.[provided by RefSeq, May 2010]
Expression
Broad expression in lymph node (RPKM 16.6), appendix (RPKM 16.2) and 20 other tissues See more
Orthologs
mouse all
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Genomic context

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See CERKL in Genome Data Viewer
Location:
2q31.3
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (181536672..181657105, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (182026827..182147207, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (182401399..182521832, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1934 Neighboring gene MPRA-validated peak3959 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16825 Neighboring gene microRNA 4437 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16826 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16827 Neighboring gene uncharacterized LOC124907913 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16828 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16830 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16831 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16829 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16832 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16833 Neighboring gene integrin subunit alpha 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12157 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:182545894-182546470 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:182548197-182548772 Neighboring gene neuronal differentiation 1 Neighboring gene SAP18 pseudogene 2

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. Genetic and Clinical Findings in an Ethnically Diverse Cohort with Retinitis Pigmentosa Associated with Pathogenic Variants in CERKL. Downes SM, et al. Genes (Basel), 2020 Dec 12. PMID 33322828, Free PMC Article
  2. CERKL mutation causing retinitis pigmentosa(RP) in Indian population - a genotype and phenotype correlation study. Sen P, et al. Ophthalmic Genet, 2020 Dec. PMID 32865075
  3. CERKL regulates autophagy via the NAD-dependent deacetylase SIRT1. Hu X, et al. Autophagy, 2019 Mar. PMID 30205735, Free PMC Article
  4. A founder mutation in CERKL is a major cause of retinal dystrophy in Finland. Avela K, et al. Acta Ophthalmol, 2018 Mar. PMID 29068140
  5. Rod-Cone Dystrophy with Initially Preserved Visual Acuity Despite Early Macular Involvement Suggests Recessive CERKL Mutations. Khan AO, et al. Ophthalmic Genet, 2015. PMID 24547929

See all (38) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CERKL-Associated Retinal Dystrophy: Genetics, Phenotype, and Natural History.
    Title: CERKL-Associated Retinal Dystrophy: Genetics, Phenotype, and Natural History.
  2. Genetic and Clinical Findings in an Ethnically Diverse Cohort with Retinitis Pigmentosa Associated with Pathogenic Variants in CERKL.
    Title: Genetic and Clinical Findings in an Ethnically Diverse Cohort with Retinitis Pigmentosa Associated with Pathogenic Variants in CERKL.
  3. CERKL mutation causing retinitis pigmentosa(RP) in Indian population - a genotype and phenotype correlation study.
    Title: CERKL mutation causing retinitis pigmentosa(RP) in Indian population - a genotype and phenotype correlation study.
  4. CERKL is an important regulator of autophagy and it plays this role by stabilizing the deacetylase SIRT1.
    Title: CERKL regulates autophagy via the NAD-dependent deacetylase SIRT1.
  5. Our report indicates that the first diagnostic test for Finnish patients with sporadic or autosomal recessive retinal dystrophy should be a targeted test for founder mutations in the CERKL.
    Title: A founder mutation in CERKL is a major cause of retinal dystrophy in Finland.
  6. The initial presenting features of CERKL-related retinopathy are distinct and unusual. Recognition of this initial presenting phenotype can facilitate earlier molecular diagnosis and genetic counseling.
    Title: Rod-Cone Dystrophy with Initially Preserved Visual Acuity Despite Early Macular Involvement Suggests Recessive CERKL Mutations.
  7. pVHL interacts with CERKL and ubiquitinates it for oxygen dependent proteasomal degradation.
    Title: pVHL interacts with Ceramide kinase like (CERKL) protein and ubiquitinates it for oxygen dependent proteasomal degradation.
  8. CERKL interacts with TRX2 and plays a novel key role in the regulation of the TRX2 antioxidant pathway.
    Title: CERKL interacts with mitochondrial TRX2 and protects retinal cells from oxidative stress-induced apoptosis.
  9. An unexpected multiplicity of CERKL transcriptional start sites (four in each species) plus a high variety of alternative splicing events primarily affecting the 5' half of the gene generate >20 fully validated mRNA isoforms in human and 23 in mouse.
    Title: High transcriptional complexity of the retinitis pigmentosa CERKL gene in human and mouse.
  10. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Submit: New GeneRIF Correction See all GeneRIFs (25)

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
Retinitis pigmentosa 26
MedGen: C1842127 OMIM: 608380 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview
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EBI GWAS Catalog

Description
Gene network analysis in a pediatric cohort identifies novel lung function genes.
EBI GWAS Catalog
Multiple loci are associated with white blood cell phenotypes.
EBI GWAS Catalog
Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia.
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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables lipid kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables sphingolipid binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in phosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in sphingolipid biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in sphingolipid metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
located_in nucleolus IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in photoreceptor inner segment IEA
Inferred from Electronic Annotation
more info
  
located_in photoreceptor outer segment IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
ceramide kinase-like protein

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_021178.2 RefSeqGene

    Range
    5003..125436
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001030311.3 → NP_001025482.1  ceramide kinase-like protein isoform 2

    See identical proteins and their annotated locations for NP_001025482.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (2).
    Source sequence(s)
    AC020595, AK293844, AY690329, BM969366
    Consensus CDS
    CCDS42789.1
    UniProtKB/Swiss-Prot
    B2RPL2, B4DEY1, Q49MH9, Q49MI0, Q49MI1, Q49MI2, Q49MI3, Q5DVJ2, Q5DVJ4, Q5DVJ5, Q6UZF6, Q6ZP59
    Related
    ENSP00000341159.5, ENST00000339098.9
    Conserved Domains (2) summary
    PLN02204
    Location:148 → 553
    PLN02204; diacylglycerol kinase
    COG1597
    Location:167 → 550
    LCB5; Diacylglycerol kinase family enzyme [Lipid transport and metabolism, General function prediction only]

  2. NM_001030312.3 → NP_001025483.1  ceramide kinase-like protein isoform 3

    See identical proteins and their annotated locations for NP_001025483.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks four alternate in-frame exons in the central coding region, compared to variant 2. The resulting isoform (3) lacks an internal segment, compared to isoform 2.
    Source sequence(s)
    AC020595, AK293844, AY690330, BM969366
    Consensus CDS
    CCDS33340.1
    UniProtKB/Swiss-Prot
    Q49MI3
    Related
    ENSP00000364108.2, ENST00000374969.6
    Conserved Domains (1) summary
    cl01255
    Location:151 → 414
    DAGK_cat; Diacylglycerol kinase catalytic domain

  3. NM_001030313.3 → NP_001025484.1  ceramide kinase-like protein isoform 4

    See identical proteins and their annotated locations for NP_001025484.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks three alternate in-frame exons in the central coding region, compared to variant 2. The resulting isoform (4) lacks an internal segment, compared to isoform 2.
    Source sequence(s)
    AC020595, AK293844, AY690331, BM969366
    Consensus CDS
    CCDS33341.1
    UniProtKB/Swiss-Prot
    Q49MI3
    Related
    ENSP00000364109.2, ENST00000374970.6
    Conserved Domains (1) summary
    cl01255
    Location:206 → 458
    DAGK_cat; Diacylglycerol kinase catalytic domain

  4. NM_001160277.2 → NP_001153749.1  ceramide kinase-like protein isoform 7

    See identical proteins and their annotated locations for NP_001153749.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks one alternate in-frame exon in the central coding region, compared to variant 2. The resulting isoform (7) lacks an internal segment, compared to isoform 2.
    Source sequence(s)
    AC020595, AK293844, AY690329, BC137498, BM969366
    Consensus CDS
    CCDS54425.1
    UniProtKB/Swiss-Prot
    Q49MI3
    Related
    ENSP00000387080.3, ENST00000409440.7
    Conserved Domains (2) summary
    pfam00781
    Location:163 → 290
    DAGK_cat; Diacylglycerol kinase catalytic domain
    cl01255
    Location:250 → 509
    DAGK_cat; Diacylglycerol kinase catalytic domain

  5. NM_201548.5 → NP_963842.1  ceramide kinase-like protein isoform 1

    See identical proteins and their annotated locations for NP_963842.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks one alternate in-frame exon in the central coding region, compared to variant 2. The resulting isoform (1) lacks an internal segment, compared to isoform 2.
    Source sequence(s)
    AC020595, AK293844, AY690329, BC137498, BM969366
    Consensus CDS
    CCDS46466.1
    UniProtKB/Swiss-Prot
    Q49MI3
    Related
    ENSP00000386725.3, ENST00000410087.8
    Conserved Domains (1) summary
    PLN02204
    Location:148 → 527
    PLN02204; diacylglycerol kinase

RNA

  1. NR_027689.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks two alternate internal exons, compared to variant 2. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC020595, AK293844, AY690332, BM969366

  2. NR_027690.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks one alternate internal exon, compared to variant 2. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC020595, AK293844, AY690333, BM969366

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    181536672..181657105 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    182026827..182147207 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q49MI3.1 GenPept UniProtKB/Swiss-Prot:Q49MI3

Gene LinkOut

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