GeneBe

CEP19

centrosomal protein 19

Basic information

Region (hg38): 3:196706277-196712250

Previous symbols: [ "C3orf34" ]

Links

ENSG00000174007 ∙ NCBI:84984 ∙ OMIM:615586 ∙ HGNC:28209 ∙ Uniprot:Q96LK0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • obesity due to CEP19 deficiency (Strong), mode of inheritance: AR
  • Bardet-Biedl syndrome (Supportive), mode of inheritance: AR
  • obesity due to CEP19 deficiency (Supportive), mode of inheritance: AR
  • obesity due to CEP19 deficiency (Strong), mode of inheritance: AR
  • obesity due to CEP19 deficiency (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Morbid obesity and spermatogenic failureARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingEndocrine; Genitourinary24268657

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CEP19 gene.

  • not_provided (100 variants)
  • not_specified (19 variants)
  • Obesity_due_to_CEP19_deficiency (2 variants)
  • CEP19-related_disorder (1 variants)
  • Optic_atrophy (1 variants)
  • Bardet-Biedl_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEP19 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000032898.5. 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
22
clinvar
2
clinvar
 24
missense
65
clinvar
1
clinvar
 66
nonsense
1
clinvar
1
clinvar
3
clinvar
 5
start loss
1
 1
frameshift
1
clinvar
4
clinvar
 5
splice donor/acceptor (+/-2bp)
0
Total 2 1 73 22 3

Highest pathogenic variant AF is 0.0000117718055

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CEP19protein_codingprotein_codingENST00000409690 26017
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.01570.8901247740181247920.0000721
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.1369490.41.040.000004771116
Missense in Polyphen2825.8911.0815359
Synonymous0.08823030.60.9800.00000151287
Loss of Function1.4048.390.4776.03e-784

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002900.0000290
Ashkenazi Jewish0.000.00
East Asian0.0001110.000111
Finnish0.0003710.000371
European (Non-Finnish)0.00005360.0000530
Middle Eastern0.0001110.000111
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Required for ciliation (PubMed:28625565, PubMed:28428259, PubMed:28659385). Recruits the RABL2B GTPase to the ciliary base to initiate ciliation. After specifically capturing the activated GTP-bound RABL2B, the CEP19-RABL2B complex binds intraflagellar transport (IFT) complex B from the large pool pre-docked at the base of the cilium and thus triggers its entry into the cilia (PubMed:28625565, PubMed:28428259). Involved in the early steps in cilia formation by recruiting the ciliary vesicles (CVs) to the distal end of the mother centriole where they fuse to initiate cilium assembly. Involved in microtubule (MT) anchoring to the centrosomes (PubMed:28659385). {ECO:0000269|PubMed:28428259, ECO:0000269|PubMed:28625565, ECO:0000269|PubMed:28659385}.;
Disease
DISEASE: Morbid obesity and spermatogenic failure (MOSPGF) [MIM:615703]: An autosomal recessive morbid obesity syndrome characterized by hypertension, fatty liver disease, insulin resistance, and decreased sperm counts. Variable clinical manifestations are early coronary artery disease with myocardial infarction before 45 years of age, type II diabetes mellitus, and intellectual disability. Morbid obese individuals are defined as having a BMI greater than 40. {ECO:0000269|PubMed:24268657}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.0926

Intolerance Scores

loftool
rvis_EVS
0.01
rvis_percentile_EVS
54.95

Haploinsufficiency Scores

pHI
0.137
hipred
N
hipred_score
0.292
ghis
0.515

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.114

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cep19
Phenotype
homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process
microtubule anchoring at centrosome;cilium assembly;vesicle targeting, trans-Golgi to periciliary membrane compartment
Cellular component
spindle pole;centrosome;centriole;cilium;ciliary basal body
Molecular function
protein binding