CERK

protein-coding

ceramide kinase

Gene summary

CERK converts ceramide to ceramide 1-phosphate (C1P), a sphingolipid metabolite. Both CERK and C1P have been implicated in various cellular processes, including proliferation, apoptosis, phagocytosis, and inflammation (Kim et al., 2006 [PubMed 16488390]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_022766.6

Inheritance

—

ClinVar variants

U:114B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr22:46,684,410-46,738,252

External References & Databases

Ensembl (ENSG00000100422)

Transcript & Mutation Effects

hg38 • Region Span ~53.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CERK variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 109

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022766.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	1 clinvar	2 clinvar	6
missense			109 clinvar	6 clinvar	1 clinvar	116
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	114	7	3	124

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022766.6	RefSeq	NP_073603.2	13	MANE Select
ENST00000216264.13	Ensembl	ENSP00000216264.8	13	MANE Select
ENST00000443629.5	Ensembl	ENSP00000400859.1	5	Standard
ENST00000918417.1	Ensembl	ENSP00000588476.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Sphingolipid metabolism - Homo sapiens (human)
Sphingolipid Metabolism
Gaucher Disease
Globoid Cell Leukodystrophy
Metachromatic Leukodystrophy (MLD)

Biological Process

ceramide metabolic process
glycosphingolipid metabolic process
lipid phosphorylation

Molecular Function

magnesium ion binding
ceramide kinase activity
NAD+ kinase activity
protein binding
ATP binding

Cellular Component

cytoplasm
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000216264
Coding exons: 13
Length: 53851
Individuals with no LoFs: 125695
Homozygous LoFs: 0
Heterozygous LoFs: 53
Defined: 125748
p: 0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.764	276	314	0.879	0.0000198	3488
Missense (PolyPhen)		70	97.69	0.71655		973
Synonymous	0.00667	125	125	0.999	0.00000850	1020
Loss of Function	2.58	12	26.2	0.457	0.00000121	320

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00018	0.00018	rare
European (Non-Finnish)	0.00027	0.00027	rare
South Asian	0.00016	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalyzes specifically the phosphorylation of ceramide to form ceramide 1-phosphate. Acts efficiently on natural and analog ceramides (C6, C8, C16 ceramides, and C8-dihydroceramide), to a lesser extent on C2-ceramide and C6-dihydroceramide, but not on other lipids, such as various sphingosines. Binds phosphoinositides. {ECO:0000269|PubMed:19168031}.;

Recessive Scores

pRec: 0.157

Intolerance Scores

LoFtool: 0.773
RVIS EVS: 0.27
RVIS percentile EVS: 70.69

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.991

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium