CFAP46

cilia and flagella associated protein 46, the group of Cilia and flagella associated|Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 10:132808392-132942823

Previous symbols: [ "C10orf123", "C10orf124", "C10orf93", "C10orf92", "TTC40" ]

Links

ENSG00000171811 ∙ NCBI:54777 ∙ OMIM:618543 ∙ HGNC:25247 ∙ Uniprot:Q8IYW2 ∙ 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 CFAP46 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP46 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				14		14
missense			63	11		74
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	64	25	0

Variants in CFAP46

This is a list of pathogenic ClinVar variants found in the CFAP46 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-132808450-T-C		not specified	Likely benign (Dec 09, 2023)
10-132808498-C-T		not specified	Uncertain significance (Apr 15, 2024)
10-132808515-C-T		not specified	Uncertain significance (Feb 26, 2024)
10-132808571-A-G			Likely benign (Aug 01, 2022)
10-132808600-G-A			Likely benign (Feb 01, 2024)
10-132808672-C-G		not specified	Uncertain significance (Jan 18, 2023)
10-132808672-C-T		not specified	Uncertain significance (Apr 29, 2024)
10-132808711-G-T		not specified	Uncertain significance (Jul 17, 2023)
10-132808783-A-G		not specified	Uncertain significance (Jan 26, 2022)
10-132808785-G-A		not specified	Uncertain significance (Nov 20, 2023)
10-132808786-C-T		not specified	Uncertain significance (Aug 02, 2022)
10-132808798-G-A		not specified	Likely benign (Nov 09, 2021)
10-132808837-C-T		not specified	Uncertain significance (Jun 07, 2023)
10-132808854-C-T		not specified	Uncertain significance (Aug 04, 2021)
10-132810415-T-C		not specified	Uncertain significance (Jun 12, 2023)
10-132810960-C-T		not specified	Uncertain significance (Feb 21, 2024)
10-132810967-C-A		not specified	Uncertain significance (Jun 04, 2024)
10-132810999-G-C		not specified	Uncertain significance (Jun 03, 2024)
10-132811017-C-T		not specified	Uncertain significance (May 09, 2022)
10-132812800-C-T		not specified	Uncertain significance (Jan 24, 2024)
10-132812814-A-G		not specified	Uncertain significance (Dec 02, 2022)
10-132812877-G-A		not specified	Uncertain significance (Nov 10, 2022)
10-132812889-T-C		not specified	Uncertain significance (Mar 15, 2024)
10-132814223-G-T		not specified	Likely benign (May 13, 2024)
10-132814242-G-A		not specified	Uncertain significance (Apr 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP46	protein_coding	protein_coding	ENST00000368586	58	134432

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.06e-33	1.00	125040	0	708	125748	0.00282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.91	1333	1.54e+3	0.863	0.0000975	17484
Missense in Polyphen		361	443.66	0.81368		5291
Synonymous	0.512	674	691	0.975	0.0000497	5397
Loss of Function	4.62	76	134	0.569	0.00000672	1614

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00207	0.00207
Ashkenazi Jewish	0.0122	0.0121
East Asian	0.000403	0.000381
Finnish	0.00302	0.00296
European (Non-Finnish)	0.00365	0.00355
Middle Eastern	0.000403	0.000381
South Asian	0.000960	0.000948
Other	0.00411	0.00408

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As part of the central apparatus of the cilium axoneme plays a role in cilium movement. {ECO:0000250|UniProtKB:A8ICS9}.

Haploinsufficiency Scores

• pHI: 0.138
• hipred: N
• hipred_score: 0.180
• ghis: 0.384

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Cfap46

Gene ontology

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