GeneBe

CLYBL

citramalyl-CoA lyase, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 13:99606669-99909459

Links

ENSG00000125246 ∙ NCBI:171425 ∙ OMIM:609686 ∙ HGNC:18355 ∙ Uniprot:Q8N0X4 ∙ 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 CLYBL gene.

  • not_specified (56 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLYBL gene is commonly pathogenic or not. These statistics are base on transcript: NM_000206808.5. 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.

EffectPLPVUSLBBSum
synonymous
0
missense
55
clinvar
1
clinvar
 56
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 55 1 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CLYBLprotein_codingprotein_codingENST00000376360 8290469
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.64e-90.22211866112169661257480.0286
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.07881831801.020.000009472181
Missense in Polyphen6161.3050.99503723
Synonymous-0.8338071.11.130.00000396701
Loss of Function0.5821517.60.8500.00000102198

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.03270.0326
Ashkenazi Jewish0.04980.0502
East Asian0.04970.0500
Finnish0.03580.0356
European (Non-Finnish)0.02720.0271
Middle Eastern0.04970.0500
South Asian0.02370.0231
Other0.03380.0341

dbNSFP

Source: dbNSFP

Function
FUNCTION: Mitochondrial citramalyl-CoA lyase indirectly involved in the vitamin B12 metabolism (PubMed:29056341). Converts citramalyl-CoA into acetyl-CoA and pyruvate in the C5- dicarboxylate catabolism pathway (PubMed:29056341). The C5- dicarboxylate catabolism pathway is required to detoxify itaconate, a vitamin B12-poisoning metabolite (PubMed:29056341). Also acts as a malate synthase in vitro, converting glyoxylate and acetyl-CoA to malate (PubMed:24334609, PubMed:29056341). Also acts as a beta-methylmalate synthase in vitro, by mediating conversion of glyoxylate and propionyl-CoA to beta-methylmalate (PubMed:24334609, PubMed:29056341). Also has very weak citramalate synthase activity in vitro (PubMed:24334609, PubMed:29056341). {ECO:0000269|PubMed:24334609, ECO:0000269|PubMed:29056341}.;
Pathway
TCA cycle (Consensus)

Recessive Scores

pRec
0.323

Intolerance Scores

loftool
0.889
rvis_EVS
0.77
rvis_percentile_EVS
87.06

Haploinsufficiency Scores

pHI
0.195
hipred
N
hipred_score
0.345
ghis
0.396

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.848

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Clybl
Phenotype

Gene ontology

Biological process
protein homotrimerization;regulation of cobalamin metabolic process
Cellular component
mitochondrion
Molecular function
magnesium ion binding;malate synthase activity;(3S)-citramalyl-CoA lyase activity