CFAP74

cilia and flagella associated protein 74, the group of Cilia and flagella associated

Basic information

Region (hg38): 1:1921951-2003837

Previous symbols: [ "C1orf222", "KIAA1751" ]

Links

ENSG00000142609 ∙ NCBI:85452 ∙ OMIM:620187 ∙ HGNC:29368 ∙ Uniprot:Q9C0B2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• ciliary dyskinesia, primary, 49, without situs inversus (Limited), mode of inheritance: AR
• primary ciliary dyskinesia (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ciliary dyskinesia, primary, 49, without situs inversus	AR	Allergy/Immunology/Infectious; Pulmonary	Early and aggressive treatment of respiratory infections may be beneficial; Pulmonary surveillance may be beneficial to assess respiratory function and institute early management measures	Allergy/Immunology/Infectious; Genitourinary; Pulmonary	32555313; 36047773

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CFAP74 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP74 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	1	3
missense			97	10	1	108
nonsense						0
start loss						0
frameshift		4				4
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding			2			2
Total	0	4	100	12	2

Variants in CFAP74

This is a list of pathogenic ClinVar variants found in the CFAP74 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-1922598-C-T			Likely benign (Feb 01, 2023)
1-1923416-G-A			Benign (Feb 01, 2025)
1-1923782-A-AAG		Ciliary dyskinesia, primary, 49, without situs inversus	Likely pathogenic (Jan 05, 2024)
1-1923833-C-G		Ciliary dyskinesia, primary, 49, without situs inversus	Pathogenic (Jan 12, 2023)
1-1925836-C-T			Uncertain significance (Feb 01, 2023)
1-1927024-C-T		Ciliary dyskinesia, primary, 49, without situs inversus	Pathogenic (Jan 12, 2023)
1-1928875-A-C			Uncertain significance (Feb 01, 2023)
1-1930142-C-A			Benign (Oct 01, 2024)
1-1930304-A-G		CFAP74-related disorder	Likely pathogenic (Oct 07, 2024)
1-1938941-CA-C		Ciliary dyskinesia, primary, 49, without situs inversus	Likely pathogenic (Aug 01, 2024)
1-1944365-G-A		CFAP74-related disorder	Likely pathogenic (Oct 07, 2024)
1-1946378-A-C		Ciliary dyskinesia, primary, 49, without situs inversus	Uncertain significance (Jul 17, 2023)
1-1955657-G-A		not specified	Uncertain significance (Jul 05, 2023)
1-1955661-A-C		not specified	Uncertain significance (Dec 06, 2021)
1-1955730-C-T		not specified	Uncertain significance (Sep 08, 2024)
1-1955732-A-C		not specified	Uncertain significance (Feb 01, 2025)
1-1955756-G-T		not specified	Uncertain significance (Jan 27, 2022)
1-1955777-T-G		not specified	Uncertain significance (Jun 22, 2023)
1-1956676-A-G		not specified	Uncertain significance (Sep 25, 2024)
1-1956703-C-A		not specified	Uncertain significance (Apr 06, 2024)
1-1956703-C-T		not specified	Uncertain significance (May 16, 2024)
1-1956723-C-T		not specified	Uncertain significance (May 07, 2024)
1-1956729-G-A		not specified	Uncertain significance (Jan 03, 2022)
1-1956745-C-T		not specified	Uncertain significance (Nov 10, 2024)
1-1956751-T-C		not specified	Uncertain significance (Jul 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP74	protein_coding	protein_coding	ENST00000493964	21	81881

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.78e-11	0.994	123624	0	360	123984	0.00145

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	436	509	0.856	0.0000316	5587
Missense in Polyphen		152	175.43	0.86646		1965
Synonymous	1.41	212	240	0.884	0.0000172	1789
Loss of Function	2.61	23	41.1	0.560	0.00000229	455

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000771	0.000771
Ashkenazi Jewish	0.00449	0.00421
East Asian	0.0000559	0.0000544
Finnish	0.00171	0.00171
European (Non-Finnish)	0.00216	0.00216
Middle Eastern	0.0000559	0.0000544
South Asian	0.000235	0.000229
Other	0.00204	0.00197

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As part of the central apparatus of the cilium axoneme may play a role in cilium movement. {ECO:0000250|UniProtKB:D4P3R7}.

Recessive Scores

• pRec: 0.0984

Haploinsufficiency Scores

• pHI: 0.126
• ghis: 0.440

Mouse Genome Informatics

• Gene name: Cfap74

Gene ontology

• Biological process: axoneme assembly
• Cellular component: axoneme