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

ENSG00000188596NCBI:144535HGNC:26456Uniprot:Q96N23AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

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
1
clinvar
1
missense
2
clinvar
2
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 0 3 0

Variants in CFAP54

This is a list of pathogenic ClinVar variants found in the CFAP54 region.

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

Position Type Phenotype Significance ClinVar
12-96489675-A-G Likely benign (Feb 01, 2023)2643224
12-96630637-G-C Likely benign (Nov 01, 2023)2672515
12-96644400-G-C Likely benign (Nov 01, 2023)2672516

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CFAP54protein_codingprotein_codingENST00000524981 67385985
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
3.74e-411.0012564701011257480.000402
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.4511941.34e+30.8890.000067020173
Missense in Polyphen191228.660.83533606
Synonymous2.744144910.8430.00002515765
Loss of Function4.12881410.6260.000007022208

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001320.00129
Ashkenazi Jewish0.000.00
East Asian0.0003540.000326
Finnish0.00004740.0000462
European (Non-Finnish)0.0005120.000501
Middle Eastern0.0003540.000326
South Asian0.0004020.000392
Other0.0001960.000163

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
ghis

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
Molecular function