CFAP276

cilia and flagella associated protein 276

Basic information

Region (hg38): 1:109105951-109113857

Previous symbols: [ "C1orf194" ]

Links

ENSG00000179902 ∙ NCBI:127003 ∙ OMIM:618682 ∙ HGNC:32331 ∙ Uniprot:Q5T5A4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Charcot-Marie-Tooth disease (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CFAP276 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP276 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			2			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	2	0	0

Variants in CFAP276

This is a list of pathogenic ClinVar variants found in the CFAP276 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-109106547-G-C			Uncertain significance (Mar 17, 2022)
1-109106609-A-T			Uncertain significance (Sep 15, 2021)
1-109107982-C-T		not specified	Uncertain significance (Oct 06, 2021)
1-109108036-T-A			Uncertain significance (Oct 26, 2021)
1-109112908-C-A			Likely benign (Mar 01, 2023)
1-109113650-G-T			Uncertain significance (Aug 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP276	protein_coding	protein_coding	ENST00000369949	5	7907

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000398	0.222	123919	6	665	124590	0.00270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.961	62	87.3	0.711	0.00000430	1017
Missense in Polyphen		23	26.838	0.85699		323
Synonymous	-0.172	33	31.8	1.04	0.00000154	297
Loss of Function	-0.133	8	7.60	1.05	3.19e-7	98

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0374	0.0375
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000223
Finnish	0.00	0.00
European (Non-Finnish)	0.000160	0.000159
Middle Eastern	0.000223	0.000223
South Asian	0.000329	0.000327
Other	0.000666	0.000660

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.556
• rvis_EVS: 0.99
• rvis_percentile_EVS: 90.52

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.188

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: 1700013F07Rik