CERKL CERK like autophagy regulator [Homo sapiens (human)] - Gene

Summary

Official Symbol: CERKLprovided by HGNC
Official Full Name: CERK like autophagy regulatorprovided 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

Location:: 2q31.3

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (181536672..181657105, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (182026827..182147207, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (182401399..182521832, complement)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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?

CERKL-Associated Retinal Dystrophy: Genetics, Phenotype, and Natural History.
Title: CERKL-Associated Retinal Dystrophy: Genetics, Phenotype, and Natural History.
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.
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.
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.
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.
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.
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.
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.
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.
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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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	not available

EBI GWAS Catalog

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

RH69434 (e-PCR)
- UniSTS:46594

G35017 (e-PCR)
- UniSTS:17199

G66899 (e-PCR)
- UniSTS:166970

G62991 (e-PCR)
- UniSTS:140116

NoName (e-PCR)
- UniSTS:482739

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables lipid kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sphingolipid binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in negative regulation of apoptotic process	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
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

Names: ceramide kinase like

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_021178.2 RefSeqGene

Range

5003..125436

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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]
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
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
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
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

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
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