CEP164

centrosomal protein 164

Basic information

Region (hg38): 11:117314557-117413266

Links

ENSG00000110274 ∙ NCBI:22897 ∙ OMIM:614848 ∙ HGNC:29182 ∙ Uniprot:Q9UPV0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Senior-Loken syndrome (Supportive), mode of inheritance: AR
• nephronophthisis 15 (Strong), mode of inheritance: AR
• nephronophthisis 15 (Strong), mode of inheritance: AR
• nephronophthisis 15 (Definitive), mode of inheritance: AR
• ciliopathy (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Nephronophthisis 15	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	Gastrointestinal; Neurologic; Ophthalmologic; Pulmonary; Renal	22863007

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CEP164 gene.

• Nephronophthisis 15 (46 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEP164 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			3	285	8	296
missense		2	518	15	13	548
nonsense	19	9				28
start loss						0
frameshift	28	6	3		1	38
inframe indel			15			15
splice donor/acceptor (+/-2bp)		29			1	30
splice region			30	51	2	83
non coding			5	155	26	186
Total	47	46	544	455	49

Highest pathogenic variant AF is 0.0000394

Variants in CEP164

This is a list of pathogenic ClinVar variants found in the CEP164 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-117315542-G-A		not specified	Uncertain significance (Apr 19, 2023)
11-117315605-A-G		not specified	Uncertain significance (Aug 02, 2021)
11-117315678-C-G		not specified	Uncertain significance (Oct 29, 2021)
11-117315699-C-A		not specified	Uncertain significance (Aug 01, 2022)
11-117315762-T-C		not specified	Likely benign (Jan 08, 2024)
11-117338552-C-T			Benign (May 10, 2021)
11-117338578-A-T		CEP164-related disorder	Likely benign (Aug 23, 2024)
11-117338596-C-T		Nephronophthisis 15	Conflicting classifications of pathogenicity (Oct 11, 2023)
11-117338598-A-G		Nephronophthisis 15	Likely benign (Nov 01, 2022)
11-117338599-C-A		Nephronophthisis 15 • Inborn genetic diseases	Uncertain significance (Dec 12, 2023)
11-117338601-C-T		Nephronophthisis 15	Likely benign (Jul 05, 2022)
11-117338606-G-A		Nephronophthisis 15 • CEP164-related disorder	Uncertain significance (Oct 04, 2022)
11-117338614-G-C		Nephronophthisis 15	Uncertain significance (Jul 26, 2022)
11-117338618-A-C		Nephronophthisis 15	Pathogenic (Aug 03, 2012)
11-117338622-G-T		Nephronophthisis 15	Likely benign (Sep 13, 2022)
11-117338624-TTC-T		Nephronophthisis 15	Pathogenic (Dec 18, 2021)
11-117338631-A-T		Inborn genetic diseases	Uncertain significance (Sep 20, 2023)
11-117338636-A-G		Nephronophthisis 15	Uncertain significance (Apr 04, 2022)
11-117338639-A-C		Nephronophthisis 15	Uncertain significance (Nov 28, 2022)
11-117338645-A-C			Uncertain significance (Dec 05, 2022)
11-117338653-A-G		Nephronophthisis 15	Uncertain significance (Jul 25, 2022)
11-117338662-G-A		Nephronophthisis 15	Uncertain significance (Jul 04, 2018)
11-117338665-C-A		not specified • Nephronophthisis 15	Uncertain significance (Aug 16, 2022)
11-117338665-C-G		Nephronophthisis 15	Uncertain significance (Oct 13, 2022)
11-117338682-GA-G		Nephronophthisis 15	Likely benign (May 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEP164	protein_coding	protein_coding	ENST00000278935	31	98712

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.83e-27	0.933	125273	0	475	125748	0.00189

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.345	779	807	0.966	0.0000460	9488
Missense in Polyphen		175	202.28	0.86515		2693
Synonymous	-1.33	346	316	1.09	0.0000174	2829
Loss of Function	2.78	55	82.2	0.669	0.00000434	934

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00310	0.00310
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000436	0.000435
Finnish	0.00703	0.00653
European (Non-Finnish)	0.00200	0.00197
Middle Eastern	0.000436	0.000435
South Asian	0.000557	0.000555
Other	0.00181	0.00179

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in microtubule organization and/or maintenance for the formation of primary cilia (PC), a microtubule-based structure that protrudes from the surface of epithelial cells. Plays a critical role in G2/M checkpoint and nuclear divisions. A key player in the DNA damage-activated ATR/ATM signaling cascade since it is required for the proper phosphorylation of H2AX, RPA, CHEK2 and CHEK1. Plays a critical role in chromosome segregation, acting as a mediator required for the maintenance of genomic stability through modulation of MDC1, RPA and CHEK1. {ECO:0000269|PubMed:17954613, ECO:0000269|PubMed:18283122, ECO:0000269|PubMed:23348840}.
• Disease: DISEASE: Nephronophthisis 15 (NPHP15) [MIM:614845]: An autosomal recessive disorder characterized by the association of nephronophthisis with Leber congenital amaurosis and retinal degeneration, often resulting in blindness during childhood. Additional features include seizures, cerebellar vermis hypoplasia, facial dysmorphism, bronchiectasis and liver failure. Nephronophthisis is a chronic tubulo-interstitial nephritis that progresses to end-stage renal failure. {ECO:0000269|PubMed:22863007}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Regulation of PLK1 Activity at G2/M Transition;Recruitment of mitotic centrosome proteins and complexes;Loss of Nlp from mitotic centrosomes;Loss of proteins required for interphase microtubule organization from the centrosome;Centrosome maturation;AURKA Activation by TPX2;G2/M Transition;Mitotic G2-G2/M phases;Recruitment of NuMA to mitotic centrosomes;Mitotic Prometaphase;M Phase;Cell Cycle;Cell Cycle, Mitotic;Anchoring of the basal body to the plasma membrane;ATR signaling pathway;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.884
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.33

Haploinsufficiency Scores

• pHI: 0.401
• hipred: N
• hipred_score: 0.396
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.811

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cep164
• 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)

Zebrafish Information Network

• Gene name: cep164
• Affected structure: pronephric tubule
• Phenotype tag: abnormal
• Phenotype quality: cystic

Gene ontology

• Biological process: G2/M transition of mitotic cell cycle;DNA repair;regulation of G2/M transition of mitotic cell cycle;cell division;cilium assembly;ciliary basal body-plasma membrane docking
• Cellular component: extracellular space;nucleoplasm;cytoplasm;centrosome;centriole;cytosol;intracellular membrane-bounded organelle;ciliary transition fiber
• Molecular function: protein binding