CFAP54

cilia and flagella associated protein 54, the group of Cilia and flagella associated

Basic information

Region (hg38): 12:96489571-96875555

Previous symbols: [ "C12orf63", "C12orf55" ]

Links

ENSG00000188596 ∙ NCBI:144535 ∙ ∙ HGNC:26456 ∙ Uniprot:Q96N23 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CFAP54 gene.

• not_provided (10 variants)
• Spermatogenic_failure_98 (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP54 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001306084.2. 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		1
missense	4		2	4		10
nonsense	1					1
start loss						0
frameshift	1	1				2
splice donor/acceptor (+/-2bp)						0
Total	6	1	2	5	0

Highest pathogenic variant AF is 0.000378243

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP54	protein_coding	protein_coding	ENST00000524981	67	385985

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.74e-41	1.00	125647	0	101	125748	0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.45	1194	1.34e+3	0.889	0.0000670	20173
Missense in Polyphen		191	228.66	0.8353		3606
Synonymous	2.74	414	491	0.843	0.0000251	5765
Loss of Function	4.12	88	141	0.626	0.00000702	2208

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00132	0.00129
Ashkenazi Jewish	0.00	0.00
East Asian	0.000354	0.000326
Finnish	0.0000474	0.0000462
European (Non-Finnish)	0.000512	0.000501
Middle Eastern	0.000354	0.000326
South Asian	0.000402	0.000392
Other	0.000196	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for assembly and function of cilia and flagella. {ECO:0000250|UniProtKB:Q8C6S9}.

Haploinsufficiency Scores

• pHI: 0.314
• hipred: N
• hipred_score: 0.233

Mouse Genome Informatics

• Gene name: Cfap54
• Phenotype: craniofacial phenotype; cellular 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); reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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); skeleton phenotype; respiratory system phenotype

Gene ontology

• Biological process: spermatogenesis;cell differentiation;cilium assembly;cilium movement involved in cell motility
• Cellular component: axoneme