CEP43

centrosomal protein 43

Basic information

Region (hg38): 6:166999173-167052718

Previous symbols: [ "FGFR1OP" ]

Links

ENSG00000213066 ∙ NCBI:11116 ∙ OMIM:605392 ∙ HGNC:17012 ∙ Uniprot:O95684 ∙ 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 CEP43 gene.

• Inborn genetic diseases (5 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEP43 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						0
missense			5		1	6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	1

Variants in CEP43

This is a list of pathogenic ClinVar variants found in the CEP43 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-166999429-C-T		not specified	Uncertain significance (Jan 19, 2024)
6-166999445-G-T		not specified	Uncertain significance (Mar 03, 2022)
6-166999461-C-T		not specified	Uncertain significance (Aug 02, 2021)
6-166999497-G-T		not specified	Uncertain significance (Jan 22, 2024)
6-167000109-T-G		not specified	Uncertain significance (Oct 07, 2022)
6-167003199-A-T		not specified	Uncertain significance (Aug 20, 2023)
6-167003224-A-G		not specified	Uncertain significance (Jul 05, 2022)
6-167003243-A-C		not specified	Uncertain significance (Dec 01, 2022)
6-167003778-T-G		not specified	Uncertain significance (Dec 06, 2022)
6-167003779-A-T		not specified	Uncertain significance (May 09, 2022)
6-167004276-G-A		not specified	Uncertain significance (Sep 06, 2022)
6-167004287-G-T		not specified	Uncertain significance (Sep 06, 2022)
6-167004298-G-A		not specified	Uncertain significance (Aug 17, 2021)
6-167004363-C-T		not specified	Uncertain significance (Jan 08, 2024)
6-167004399-G-A		not specified	Uncertain significance (Jun 27, 2022)
6-167010879-A-G		not specified	Uncertain significance (Dec 21, 2023)
6-167013530-G-A		not specified	Uncertain significance (Jan 17, 2024)
6-167013534-G-C		not specified	Uncertain significance (Dec 06, 2022)
6-167022453-G-C		not specified	Uncertain significance (Aug 02, 2021)
6-167022463-A-C		not specified	Uncertain significance (Dec 01, 2022)
6-167022533-T-C		not specified	Uncertain significance (Mar 27, 2023)
6-167022574-G-A		not specified	Uncertain significance (Jun 16, 2023)
6-167022622-A-G		not specified	Uncertain significance (Dec 07, 2023)
6-167024804-G-C			Benign (Dec 31, 2019)
6-167024826-C-T		not specified	Uncertain significance (Jun 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEP43	protein_coding	protein_coding	ENST00000366847	13	53532

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000628	0.995	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.192	199	192	1.04	0.00000932	2567
Missense in Polyphen		39	38.854	1.0038		559
Synonymous	0.218	68	70.3	0.967	0.00000357	756
Loss of Function	2.50	9	21.5	0.418	0.00000106	291

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000182	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000559	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000977	0.0000967
Middle Eastern	0.0000559	0.0000544
South Asian	0.0000656	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for anchoring microtubules to the centrosomes (PubMed:16314388, PubMed:28659385). Required for ciliation (PubMed:28625565, PubMed:28659385). {ECO:0000269|PubMed:16314388, ECO:0000269|PubMed:28625565, ECO:0000269|PubMed:28659385}.
• Pathway: VEGF Signaling Pathway;Disease;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;Signaling by FGFR in disease;Cell Cycle;Signaling by cytosolic FGFR1 fusion mutants;FGFR1 mutant receptor activation;Signaling by FGFR1 in disease;Cell Cycle, Mitotic;Anchoring of the basal body to the plasma membrane;Diseases of signal transduction;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.252

Intolerance Scores

• loftool: 0.707
• rvis_EVS: 1.06
• rvis_percentile_EVS: 91.58

Haploinsufficiency Scores

• pHI: 0.628
• hipred: Y
• hipred_score: 0.783
• ghis: 0.504

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.840

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fgfr1op
• Phenotype: immune system phenotype; homeostasis/metabolism 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); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); vision/eye phenotype

Gene ontology

• Biological process: G2/M transition of mitotic cell cycle;negative regulation of protein kinase activity;positive regulation of cell population proliferation;regulation of G2/M transition of mitotic cell cycle;peptidyl-tyrosine phosphorylation;positive regulation of cell growth;positive regulation of cell migration;microtubule anchoring;negative regulation of protein tyrosine kinase activity;ciliary basal body-plasma membrane docking
• Cellular component: nucleus;centrosome;centriole;cytosol;cell projection;perinuclear region of cytoplasm
• Molecular function: protein tyrosine kinase activity;protein binding;protein kinase binding;protein tyrosine kinase inhibitor activity;protein homodimerization activity