CERK

ceramide kinase

Basic information

Region (hg38): 22:46684410-46738252

Links

ENSG00000100422 ∙ NCBI:64781 ∙ OMIM:610307 ∙ HGNC:19256 ∙ Uniprot:Q8TCT0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CERK gene.

• not_specified (96 variants)
• not_provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CERK gene is commonly pathogenic or not. These statistics are base on transcript: NM_000022766.6. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	2	3
missense			90	5	1	96
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	90	6	3

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CERK	protein_coding	protein_coding	ENST00000216264	13	53851

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000259	0.997	125695	0	53	125748	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.764	276	314	0.879	0.0000198	3488
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000449	0.000448
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000273	0.000273
Middle Eastern	0.000109	0.000109
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Sphingolipid metabolism - Homo sapiens (human);Sphingolipid Metabolism;Gaucher Disease;Globoid Cell Leukodystrophy;Metachromatic Leukodystrophy (MLD);Fabry disease;Krabbe disease;Sphingolipid Metabolism;Integrated Breast Cancer Pathway;Metabolism of lipids;Metabolism;Glycosphingolipid metabolism;Sphingolipid metabolism (Consensus)

Recessive Scores

• pRec: 0.157

Intolerance Scores

• loftool: 0.773
• rvis_EVS: 0.27
• rvis_percentile_EVS: 70.69

Haploinsufficiency Scores

• pHI: 0.217
• hipred: N
• hipred_score: 0.394
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cerk
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; digestive/alimentary phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: ceramide metabolic process;glycosphingolipid metabolic process;lipid phosphorylation
• Cellular component: cytoplasm;plasma membrane;integral component of membrane
• Molecular function: magnesium ion binding;ceramide kinase activity;NAD+ kinase activity;protein binding;ATP binding;dihydroceramide kinase activity