CFAP298

cilia and flagella associated protein 298, the group of Cilia and flagella associated|Axonemal dynein assembly factors

Basic information

Region (hg38): 21:32592079-32612603

Previous symbols: [ "C21orf48", "C21orf59" ]

Links

ENSG00000159079 ∙ NCBI:56683 ∙ OMIM:615494 ∙ HGNC:1301 ∙ Uniprot:P57076 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• primary ciliary dyskinesia (Supportive), mode of inheritance: AD
• primary ciliary dyskinesia 26 (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ciliary dyskinesia, primary 26	AR	Allergy/Immunology/Infectious; Cardiovascular; Pulmonary	Pulmonary and audiologic surveillance may be beneficial to assess respiratory and hearing function and institute early management measures; 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, though measures including lobectomy or lung transplantation may be necessary; The condition can involve congenital cardiac anomalies, and awareness may allow early management	Allergy/Immunology/Infectious; Cardiovascular; Gastrointestinal; Pulmonary	24094744

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CFAP298 gene.

• not provided (5 variants)
• Primary ciliary dyskinesia 26 (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP298 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			2	29	2	33
missense			38	5		43
nonsense	4	1	1			6
start loss						0
frameshift	2		2			4
inframe indel			1			1
splice donor/acceptor (+/-2bp)		1				1
splice region			2	3		5
non coding			1	22	13	36
Total	6	2	45	56	15

Highest pathogenic variant AF is 0.000210

Variants in CFAP298

This is a list of pathogenic ClinVar variants found in the CFAP298 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-32601798-T-A			Benign (May 15, 2019)
21-32601870-G-A			Uncertain significance (Sep 28, 2019)
21-32601876-C-T			Uncertain significance (Nov 20, 2019)
21-32601880-TTA-T			Uncertain significance (Jul 14, 2021)
21-32601884-G-A			Likely benign (Apr 08, 2023)
21-32601901-A-G			Uncertain significance (Aug 24, 2021)
21-32601906-CT-C			Uncertain significance (Jul 21, 2023)
21-32601914-A-G			Likely benign (Jun 20, 2022)
21-32601927-G-A			Uncertain significance (Oct 17, 2022)
21-32601933-G-A			Uncertain significance (Aug 25, 2023)
21-32601940-TTAAA-T		Primary ciliary dyskinesia 26	Pathogenic (Oct 03, 2013)
21-32601955-C-T			Uncertain significance (Dec 06, 2021)
21-32601958-C-A			Uncertain significance (May 22, 2023)
21-32601984-G-T			Likely benign (Apr 19, 2023)
21-32601987-T-C			Likely benign (Nov 07, 2023)
21-32602012-G-A			Benign (Jan 16, 2019)
21-32602236-G-C		CFAP298-related disorder	Benign (Sep 25, 2019)
21-32602258-C-T			Likely benign (Nov 13, 2023)
21-32602266-T-C		CFAP298-related disorder	Benign (Jan 25, 2024)
21-32602299-G-C		Primary ciliary dyskinesia 26	Pathogenic (Aug 13, 2021)
21-32602300-T-C			Uncertain significance (Aug 27, 2021)
21-32602302-C-T			Likely benign (Nov 15, 2022)
21-32602313-G-A		Primary ciliary dyskinesia 26	Pathogenic (-)
21-32602346-G-A			Pathogenic (Aug 29, 2019)
21-32602360-T-C		Inborn genetic diseases	Uncertain significance (Jul 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP298	protein_coding	protein_coding	ENST00000290155	7	20788

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000112	0.811	125632	0	115	125747	0.000457

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.378	148	162	0.916	0.00000845	1898
Missense in Polyphen		38	44.634	0.85137		519
Synonymous	-0.990	76	65.8	1.16	0.00000414	526
Loss of Function	1.38	12	18.4	0.653	0.00000103	203

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000380	0.000380
Ashkenazi Jewish	0.00208	0.00209
East Asian	0.000217	0.000217
Finnish	0.000601	0.000601
European (Non-Finnish)	0.000485	0.000475
Middle Eastern	0.000217	0.000217
South Asian	0.000294	0.000294
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in motile cilium function, possibly by acting on outer dynein arm assembly (PubMed:24094744). Seems to be important for initiation rather than maintenance of cilium motility (By similarity). Required for correct positioning of the cilium at the apical cell surface, suggesting an additional role in the planar cell polarity (PCP) pathway (By similarity). May suppress canonical Wnt signaling activity (By similarity). {ECO:0000250|UniProtKB:Q6DRC3, ECO:0000269|PubMed:24094744}.
• Disease: DISEASE: Ciliary dyskinesia, primary, 26 (CILD26) [MIM:615500]: 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. Patients may 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:24094744}. Note=The disease is caused by mutations affecting the gene represented in this entry. Cilia in nasal epithelia show the absence of both outer and inner dynein- arm components and complete paralysis.

Intolerance Scores

• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.35

Haploinsufficiency Scores

• pHI: 0.166
• hipred: N
• hipred_score: 0.168
• ghis: 0.595

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Cfap298

Zebrafish Information Network

• Gene name: cfap298
• Affected structure: ciliated olfactory receptor neuron
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: regulation of cilium movement;cilium assembly
• Cellular component: nucleus;cytosol;cytoskeleton;cilium
• Molecular function: protein binding