CFAP300

cilia and flagella associated protein 300, the group of Cilia and flagella associated

Basic information

Region (hg38): 11:102047436-102084554

Previous symbols: [ "C11orf70" ]

Links

ENSG00000137691 ∙ NCBI:85016 ∙ OMIM:618058 ∙ HGNC:28188 ∙ Uniprot:Q9BRQ4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• primary ciliary dyskinesia (Supportive), mode of inheritance: AD
• ciliary dyskinesia, primary, 38 (Strong), mode of inheritance: AR
• ciliary dyskinesia, primary, 38 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ciliary dyskinesia, primary, 38	AR	Audiologic/Otolaryngologic; Cardiovascular; Pulmonary	Among other findings, patients can manifest with early-onset respiratory disease, including upper respiratory infections, and awareness may allow early interventions related to these sequelae; The condition can involve congenital cardiac anomalies, and awareness may allow early management	Audiologic/Otolaryngologic; Cardiovascular; Gastrointestinal; Genitourinary; Pulmonary	29727692; 29727693

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CFAP300 gene.

• not provided (7 variants)
• Ciliary dyskinesia, primary, 38 (4 variants)
• Primary ciliary dyskinesia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP300 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				18	4	22
missense			22	3	2	27
nonsense	6			1		7
start loss						0
frameshift	2					2
inframe indel			1			1
splice donor/acceptor (+/-2bp)		1				1
splice region		2		5		7
non coding				10	4	14
Total	8	1	23	32	10

Highest pathogenic variant AF is 0.0000132

Variants in CFAP300

This is a list of pathogenic ClinVar variants found in the CFAP300 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-102047477-A-G		CFAP300-related disorder	Benign (Jan 29, 2024)
11-102047486-C-T		CFAP300-related disorder	Benign/Likely benign (Jan 22, 2024)
11-102047491-G-A			Likely benign (May 09, 2021)
11-102047493-A-ACTTGGG			Uncertain significance (May 19, 2022)
11-102047500-T-C			Likely benign (Mar 06, 2023)
11-102047511-T-G		Inborn genetic diseases	Uncertain significance (Aug 13, 2021)
11-102047547-G-C			Uncertain significance (Sep 13, 2022)
11-102047558-A-G			Likely benign (Jul 27, 2023)
11-102047572-C-T			Likely benign (Sep 30, 2022)
11-102047581-G-T			Likely pathogenic (Oct 23, 2023)
11-102047590-C-T			Likely benign (Mar 24, 2023)
11-102047596-A-G		Ciliary dyskinesia, primary, 38	Benign (Jan 31, 2024)
11-102047596-A-T			Likely benign (Dec 22, 2023)
11-102047598-A-C			Likely benign (Apr 18, 2021)
11-102047801-C-T			Likely benign (Jun 09, 2022)
11-102047803-C-T			Likely benign (Dec 18, 2022)
11-102047809-C-T			Likely benign (Feb 04, 2023)
11-102047811-C-A			Likely benign (Sep 06, 2023)
11-102047824-G-A			Likely benign (Jan 22, 2024)
11-102047838-C-T			Likely benign (Dec 27, 2023)
11-102047839-G-T			Likely benign (Mar 27, 2022)
11-102047858-C-T		Ciliary dyskinesia, primary, 38	Pathogenic (Jul 31, 2018)
11-102047872-C-T		CFAP300-related disorder	Benign (Jan 25, 2024)
11-102047878-G-A			Likely benign (Dec 16, 2023)
11-102047879-A-T		Ciliary dyskinesia, primary, 38	Likely pathogenic (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP300	protein_coding	protein_coding	ENST00000434758	7	37118

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000207	0.715	125569	0	178	125747	0.000708

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.102	137	140	0.976	0.00000684	1745
Missense in Polyphen		41	41.131	0.99681		553
Synonymous	0.142	47	48.3	0.974	0.00000228	487
Loss of Function	1.15	11	16.0	0.689	9.34e-7	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000314	0.000314
Ashkenazi Jewish	0.00	0.00
East Asian	0.000222	0.000217
Finnish	0.00548	0.00542
European (Non-Finnish)	0.000372	0.000360
Middle Eastern	0.000222	0.000217
South Asian	0.000237	0.000229
Other	0.000517	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cilium- and flagellum-specific protein that plays a role in axonemal structure organization and motility. May play a role in outer and inner dynein arm assembly. {ECO:0000250|UniProtKB:A0CY51}.
• Disease: DISEASE: Note=Defects in CFAP300 are a cause of primary ciliary dyskinesia (PCD), a disorder characterized by abnormalities of motile cilia. Respiratory infections leading to chronic inflammation and bronchiectasis are recurrent, due to defects in the respiratory cilia; reduced fertility is often observed in male patients due to abnormalities of sperm tails. Half of the patients exhibit randomization of left-right body asymmetry and situs inversus, due to dysfunction of monocilia at the embryonic node. Primary ciliary dyskinesia associated with situs inversus is referred to as Kartagener syndrome. {ECO:0000269|PubMed:29727692, ECO:0000269|PubMed:29727693}.

Recessive Scores

• pRec: 0.0947

Intolerance Scores

• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.196
• hipred: N
• hipred_score: 0.251
• ghis: 0.534

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Cfap300

Gene ontology

• Cellular component: cytoplasm;cytoskeleton;motile cilium
• Molecular function: protein binding