CFAP53

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

Basic information

Region (hg38): 18:50227193-50266495

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.

• Inborn_genetic_diseases (76 variants)
• Heterotaxy,_visceral,_6,_autosomal (68 variants)
• not_provided (22 variants)
• not_specified (10 variants)
• CFAP53-related_disorder (3 variants)
• Heterotaxy (2 variants)
• Dextrocardia (2 variants)
• Hypoplastic_left_heart_syndrome (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. These statistics are base on transcript: NM_000145020.5. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous		1		20	3	24
missense			87	10	2	99
nonsense	1	2	2			5
start loss						0
frameshift	1	2				3
splice donor/acceptor (+/-2bp)	1	4				5
Total	3	9	89	30	5

Highest pathogenic variant AF is 0.0000223054

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