CFAP53

cilia and flagella associated protein 53, the group of Cilia and flagella associated

Basic information

Region (hg38): 18:50227192-50266495

Previous symbols: [ "CCDC11" ]

Links

ENSG00000172361 ∙ NCBI:220136 ∙ OMIM:614759 ∙ HGNC:26530 ∙ Uniprot:Q96M91 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• heterotaxy, visceral, 6, autosomal (Strong), mode of inheritance: AR
• heterotaxy, visceral, 6, autosomal (Strong), mode of inheritance: AR
• situs inversus (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Heterotaxy, visceral, 6, autosomal recessive	AR	Allergy/Immunology/Infectious; Cardiovascular; Pulmonary	The condition can involve congenital cardiac anomalies, and awareness may allow early management; Pulmonary surveillance may be beneficial to assess respiratory function and institute early management; In order to facilitate mucus clearance, aggressive interventions (eg, chest percussion and oscillatory vest), as well as vaccinations and early and aggressive treatment of respiratory infections may be beneficial	Allergy/Immunology/Infectious; Cardiovascular; Gastrointestinal; Pulmonary	22577226; 25504577

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CFAP53 gene.

• Heterotaxy, visceral, 6, autosomal (60 variants)
• not provided (15 variants)
• not specified (13 variants)
• Inborn genetic diseases (8 variants)
• Dextrocardia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP53 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				17	3	20
missense			32	7	4	43
nonsense		1	2			3
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	3		4
non coding				1	2	3
Total	0	1	34	25	9

Highest pathogenic variant AF is 0.0000197

Variants in CFAP53

This is a list of pathogenic ClinVar variants found in the CFAP53 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-50227377-G-A		CFAP53-related disorder	Likely benign (Jun 28, 2019)
18-50227385-G-T		Heterotaxy, visceral, 6, autosomal	Uncertain significance (Sep 01, 2021)
18-50227405-T-C		Heterotaxy, visceral, 6, autosomal	Likely benign (Dec 29, 2021)
18-50227412-C-A		Heterotaxy, visceral, 6, autosomal	Uncertain significance (Jul 03, 2019)
18-50227412-C-T		Heterotaxy, visceral, 6, autosomal • Inborn genetic diseases	Uncertain significance (Dec 13, 2023)
18-50227413-G-A		Heterotaxy, visceral, 6, autosomal	Likely benign (Dec 07, 2022)
18-50227413-G-T		Heterotaxy, visceral, 6, autosomal • Inborn genetic diseases	Uncertain significance (Jan 31, 2023)
18-50227427-T-C		Inborn genetic diseases	Uncertain significance (Aug 30, 2021)
18-50227451-G-A		Heterotaxy, visceral, 6, autosomal	Uncertain significance (Jun 15, 2020)
18-50227481-A-G		Inborn genetic diseases	Uncertain significance (Nov 12, 2021)
18-50227515-G-A		Heterotaxy, visceral, 6, autosomal	Uncertain significance (May 05, 2020)
18-50227517-C-T		Inborn genetic diseases	Uncertain significance (Mar 25, 2022)
18-50227554-G-C		Inborn genetic diseases	Uncertain significance (Nov 27, 2023)
18-50227565-T-G		Inborn genetic diseases	Uncertain significance (Sep 07, 2022)
18-50227569-T-C		Heterotaxy, visceral, 6, autosomal	Uncertain significance (Dec 07, 2021)
18-50227608-G-A		Heterotaxy, visceral, 6, autosomal	Uncertain significance (Jun 17, 2023)
18-50238583-T-C		Heterotaxy, visceral, 6, autosomal	Likely benign (Jul 20, 2023)
18-50238637-C-A		Heterotaxy, visceral, 6, autosomal	Uncertain significance (May 29, 2022)
18-50238655-T-C		Inborn genetic diseases	Uncertain significance (Nov 17, 2022)
18-50238676-G-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Oct 10, 2023)
18-50238709-A-C			Likely benign (May 30, 2017)
18-50242883-G-T		Heterotaxy, visceral, 6, autosomal	Likely benign (Jan 06, 2024)
18-50242896-T-C		Heterotaxy, visceral, 6, autosomal	Uncertain significance (Aug 28, 2020)
18-50242899-C-T		Heterotaxy, visceral, 6, autosomal	Pathogenic (Jun 01, 2012)
18-50242927-T-C		Inborn genetic diseases	Uncertain significance (Mar 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP53	protein_coding	protein_coding	ENST00000398545	8	39330

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.70e-19	0.00450	124634	1	166	124801	0.000669

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.577	300	273	1.10	0.0000154	3435
Missense in Polyphen		95	74.709	1.2716		950
Synonymous	-0.749	102	92.8	1.10	0.00000461	852
Loss of Function	0.0973	28	28.6	0.980	0.00000177	327

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00135	0.00135
Ashkenazi Jewish	0.00200	0.00199
East Asian	0.000445	0.000445
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000613	0.000600
Middle Eastern	0.000445	0.000445
South Asian	0.000864	0.000850
Other	0.000848	0.000825

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the beating of primary cilia and thereby be involved in the establishment of organ laterality during embryogenesis. {ECO:0000269|PubMed:26531781}.

Recessive Scores

• pRec: 0.0718

Intolerance Scores

• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.58

Haploinsufficiency Scores

• pHI: 0.0586
• hipred: N
• hipred_score: 0.123
• ghis: 0.408

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Cfap53
• Phenotype: reproductive system phenotype; 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); embryo phenotype; liver/biliary system phenotype; respiratory system phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: cfap53
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: cilium movement;determination of left/right symmetry;cilium assembly;epithelial cilium movement involved in determination of left/right asymmetry
• Cellular component: cellular_component;cilium
• Molecular function: protein binding