CFAP90

cilia and flagella associated protein 90

Basic information

Region (hg38): 5:7830378-7851151

Previous symbols: [ "C5orf49" ]

Links

ENSG00000215217 ∙ NCBI:134121 ∙ ∙ HGNC:27028 ∙ Uniprot:A4QMS7 ∙ 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 CFAP90 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP90 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						0
missense						0
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	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP90	protein_coding	protein_coding	ENST00000399810	3	21113

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0118	0.656	123270	37	1474	124781	0.00607

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.113	73	75.8	0.963	0.00000437	927
Missense in Polyphen		30	26.046	1.1518		307
Synonymous	0.815	25	30.8	0.813	0.00000174	285
Loss of Function	0.477	3	4.03	0.744	1.69e-7	65

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0181	0.0181
Ashkenazi Jewish	0.00	0.00
East Asian	0.0395	0.0390
Finnish	0.00649	0.00623
European (Non-Finnish)	0.000231	0.000230
Middle Eastern	0.0395	0.0390
South Asian	0.00135	0.00134
Other	0.00449	0.00446

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.344
• rvis_EVS: 0.82
• rvis_percentile_EVS: 87.87

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: 1700001L19Rik