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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Morbid obesity and spermatogenic failure	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	Endocrine; Genitourinary	24268657

ClinVar

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

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.

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			1	19	2	22
missense			61		1	62
nonsense			4			4
start loss			1			1
frameshift			3			3
inframe indel			2			2
splice donor/acceptor (+/-2bp)						0
splice region			1	2		3
non coding				3	2	5
Total	0	0	72	22	5

Variants in CEP19

This is a list of pathogenic ClinVar variants found in the CEP19 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-196707553-A-C			Uncertain significance (Nov 08, 2022)
3-196707569-C-A			Uncertain significance (Dec 31, 2019)
3-196707572-T-C			Benign/Likely benign (Jan 29, 2024)
3-196707577-C-T			Uncertain significance (Aug 28, 2021)
3-196707578-C-T			Uncertain significance (Sep 27, 2022)
3-196707582-C-G			Uncertain significance (Jun 01, 2022)
3-196707582-C-T			Uncertain significance (Mar 23, 2022)
3-196707586-AGGACTGCAGTTGATC-A			Uncertain significance (Sep 01, 2021)
3-196707602-G-A			Likely benign (Oct 30, 2023)
3-196707616-C-T			Uncertain significance (Aug 19, 2021)
3-196707618-A-C			Uncertain significance (Mar 10, 2022)
3-196707624-A-G			Uncertain significance (Jan 28, 2022)
3-196707629-A-G			Likely benign (Apr 18, 2023)
3-196707630-T-C			Uncertain significance (Oct 13, 2022)
3-196707643-G-A			Uncertain significance (Dec 01, 2021)
3-196707649-CCTT-C			Uncertain significance (Aug 22, 2022)
3-196707650-C-T			Likely benign (Jul 01, 2022)
3-196707669-T-C			Uncertain significance (Aug 19, 2021)
3-196707673-A-G			Uncertain significance (Nov 08, 2022)
3-196707681-T-C			Uncertain significance (Nov 29, 2022)
3-196707682-C-T		not specified	Uncertain significance (Jan 23, 2024)
3-196707684-A-T			Uncertain significance (Jul 19, 2022)
3-196707686-G-T			Likely benign (Nov 01, 2023)
3-196707697-T-C		not specified	Uncertain significance (Aug 13, 2021)
3-196707711-T-C			Uncertain significance (Oct 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEP19	protein_coding	protein_coding	ENST00000409690	2	6017

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0157	0.890	124774	0	18	124792	0.0000721

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.136	94	90.4	1.04	0.00000477	1116
Missense in Polyphen		28	25.891	1.0815		359
Synonymous	0.0882	30	30.6	0.980	0.00000151	287
Loss of Function	1.40	4	8.39	0.477	6.03e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.000371	0.000371
European (Non-Finnish)	0.0000536	0.0000530
Middle Eastern	0.000111	0.000111
South Asian	0.0000327	0.0000327
Other	0.00	0.00

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

• 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

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

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