CFAP54
Basic information
Region (hg38): 12:96489571-96875555
Previous symbols: [ "C12orf63", "C12orf55" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
missense | 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) | |||
12-96630637-G-C | Likely benign (Nov 01, 2023) | |||
12-96644400-G-C | Likely benign (Nov 01, 2023) |
GnomAD
Source:
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:
- 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