CFAP299

cilia and flagella associated protein 299, the group of Cilia and flagella associated

Basic information

Region (hg38): 4:80335729-80963750

Previous symbols: [ "C4orf22" ]

Links

ENSG00000197826 ∙ NCBI:255119 ∙ ∙ HGNC:28554 ∙ Uniprot:Q6V702 ∙ 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 CFAP299 gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP299 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		1
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	1	0

Variants in CFAP299

This is a list of pathogenic ClinVar variants found in the CFAP299 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-80335780-A-T		not specified	Likely benign (Aug 04, 2021)
4-80583100-A-T		not specified	Uncertain significance (Sep 09, 2021)
4-80583137-C-T		not specified	Likely benign (Aug 17, 2021)
4-80944855-C-T			Likely benign (Jul 01, 2022)
4-80963591-C-G		not specified	Uncertain significance (Jul 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP299	protein_coding	protein_coding	ENST00000508675	7	628037

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.09e-9	0.0739	125295	2	451	125748	0.00180

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.571	148	130	1.14	0.00000644	1631
Missense in Polyphen		45	42.842	1.0504		543
Synonymous	0.239	46	48.1	0.956	0.00000246	466
Loss of Function	-0.158	13	12.4	1.05	5.24e-7	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00139	0.00139
Ashkenazi Jewish	0.00270	0.00238
East Asian	0.0149	0.0148
Finnish	0.00	0.00
European (Non-Finnish)	0.000595	0.000571
Middle Eastern	0.0149	0.0148
South Asian	0.00135	0.00131
Other	0.00221	0.00212

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.73

Haploinsufficiency Scores

• pHI: 0.0952
• hipred: N
• hipred_score: 0.177

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Cfap299
• Phenotype: normal phenotype; pigmentation phenotype; hearing/vestibular/ear phenotype; vision/eye phenotype