CERK

ceramide kinase

Basic information

Region (hg38): 22:46684409-46738252

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.

• Inborn genetic diseases (38 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			35	3	1	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	3	3

Variants in CERK

This is a list of pathogenic ClinVar variants found in the CERK region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
22-46687156-G-A		not specified	Likely benign (Jan 30, 2024)
22-46689996-C-T		not specified	Uncertain significance (Mar 07, 2024)
22-46690006-A-T			Benign (Jun 21, 2018)
22-46690109-C-T		not specified	Likely benign (Mar 11, 2022)
22-46690119-G-A		not specified	Uncertain significance (Mar 22, 2022)
22-46690140-T-G		not specified	Uncertain significance (Aug 10, 2021)
22-46690151-G-A			Benign (Jun 21, 2018)
22-46690173-G-A		not specified	Uncertain significance (Jan 16, 2024)
22-46691633-C-T		not specified	Uncertain significance (Apr 17, 2023)
22-46691678-G-A		not specified	Uncertain significance (Feb 10, 2022)
22-46691699-C-T		not specified	Uncertain significance (Oct 13, 2023)
22-46691700-G-A		not specified	Uncertain significance (Oct 06, 2022)
22-46691703-G-A		not specified	Uncertain significance (Jul 06, 2022)
22-46691726-G-C		not specified	Uncertain significance (Jan 17, 2023)
22-46691753-A-G		not specified	Uncertain significance (Oct 05, 2021)
22-46691754-C-A		not specified	Uncertain significance (Mar 23, 2022)
22-46691754-C-T		not specified	Likely benign (Jul 14, 2021)
22-46693433-C-T		not specified	Uncertain significance (Feb 14, 2023)
22-46693467-C-G		not specified	Uncertain significance (Oct 27, 2022)
22-46695217-G-A		not specified	Uncertain significance (Oct 26, 2021)
22-46695232-C-A		not specified	Uncertain significance (Dec 20, 2023)
22-46695249-G-A		not specified	Uncertain significance (Nov 19, 2022)
22-46699376-C-T		not specified	Uncertain significance (Jan 04, 2022)
22-46699411-C-T		not specified	Uncertain significance (Jan 23, 2024)
22-46699412-G-A		not specified	Uncertain significance (Jun 24, 2022)

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