CERKL

ceramide kinase like

Basic information

Region (hg38): 2:181535041-181680665

Previous symbols: [ "RP26" ]

Links

ENSG00000188452

∙ NCBI:375298 ∙ OMIM:608381 ∙ HGNC:21699 ∙ Uniprot:Q49MI3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

retinitis pigmentosa (Supportive), mode of inheritance: AD
retinitis pigmentosa 26 (Definitive), mode of inheritance: AR
retinitis pigmentosa 26 (Strong), mode of inheritance: AR
CERKL-related retinopathy (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinitis pigmentosa 26	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	14681825

ClinVar

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

not_provided (819 variants)
Retinitis_pigmentosa_26 (249 variants)
Retinal_dystrophy (71 variants)
Inborn_genetic_diseases (67 variants)
Retinitis_pigmentosa (60 variants)
not_specified (15 variants)
CERKL-related_disorder (8 variants)
Cone-rod_dystrophy (6 variants)
Autosomal_recessive_retinitis_pigmentosa (6 variants)
See_cases (2 variants)
Retinal_pigment_epithelial_atrophy (2 variants)
Cone_dystrophy (2 variants)
Macular_dystrophy (1 variants)
Stargardt_disease (1 variants)
CERKL-related_retinopathy (1 variants)
Severe_photosensitivity (1 variants)
Retinitis_Pigmentosa,_Recessive (1 variants)
Isolated_macular_dystrophy (1 variants)
Adult-onset_night_blindness (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CERKL gene is commonly pathogenic or not. These statistics are base on transcript: NM_000201548.5. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			11 clinvar	243 clinvar	1 clinvar	255
missense	3 clinvar	19 clinvar	219 clinvar	16 clinvar	1 clinvar	258
nonsense	22 clinvar	21 clinvar	2 clinvar			45
start loss	4					4
frameshift	44 clinvar	40 clinvar	6 clinvar			90
splice donor/acceptor (+/-2bp)	4 clinvar	41 clinvar	1 clinvar			46
Total	77	121	239	259	2

Highest pathogenic variant AF is 0.0005930632

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CERKL	protein_coding	protein_coding	ENST00000339098	14	143990

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.84e-25	0.0000676	125553	0	195	125748	0.000776

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.266	316	303	1.04	0.0000148	3626
Missense in Polyphen		83	92.682	0.89553		1137
Synonymous	0.173	107	109	0.979	0.00000549	1061
Loss of Function	-0.797	34	29.3	1.16	0.00000147	352

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00113	0.00113
Ashkenazi Jewish	0.00	0.00
East Asian	0.000550	0.000544
Finnish	0.00132	0.00129
European (Non-Finnish)	0.000888	0.000862
Middle Eastern	0.000550	0.000544
South Asian	0.000794	0.000784
Other	0.000494	0.000489

dbNSFP

Source: dbNSFP

Function: FUNCTION: Has no detectable ceramide-kinase activity. Overexpression of CERKL protects cells from apoptosis in oxidative stress conditions. {ECO:0000269|PubMed:15708351, ECO:0000269|PubMed:19158957}.;
Disease: DISEASE: Retinitis pigmentosa 26 (RP26) [MIM:608380]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:14681825, ECO:0000269|PubMed:18978954}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec: 0.0976

Intolerance Scores

loftool: 0.988
rvis_EVS: 0.71
rvis_percentile_EVS: 85.73

Haploinsufficiency Scores

pHI: 0.345
hipred: N
hipred_score: 0.264
ghis: 0.467

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.224

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cerkl
Phenotype: cellular phenotype; vision/eye phenotype;

Zebrafish Information Network

Gene name: cerkl
Affected structure: retinal rod cell
Phenotype tag: abnormal
Phenotype quality: decreased amount

Gene ontology

Biological process: phosphorylation;sphingolipid biosynthetic process
Cellular component: photoreceptor outer segment;photoreceptor inner segment;nucleus;nucleolus;endoplasmic reticulum;Golgi apparatus;cytosol;perinuclear region of cytoplasm
Molecular function: NAD+ kinase activity;sphingolipid binding