CFAP20DC

CFAP20 domain containing

Basic information

Region (hg38): 3:58717365-59050084

Previous symbols: [ "C3orf67" ]

Links

ENSG00000163689 ∙ NCBI:200844 ∙ ∙ HGNC:24763 ∙ Uniprot:Q6ZVT6 ∙ 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 CFAP20DC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP20DC 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			6	2	1	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	6	2	2

Variants in CFAP20DC

This is a list of pathogenic ClinVar variants found in the CFAP20DC region.

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

Position	Type	Phenotype	Significance	ClinVar
3-58863617-C-T			Likely benign (Dec 01, 2022)
3-58863767-C-G		not specified	Uncertain significance (Nov 12, 2021)
3-58866572-G-C			Benign/Likely benign (Apr 01, 2022)
3-58867813-A-C			Likely benign (Sep 01, 2023)
3-58867852-T-C		not specified	Uncertain significance (Jul 20, 2021)
3-58867915-T-G		not specified	Uncertain significance (Aug 03, 2021)
3-58869477-A-G		not specified	Uncertain significance (Jul 20, 2021)
3-58870226-G-A		not specified	Uncertain significance (Oct 27, 2021)
3-58870245-G-A			Benign (Jan 22, 2019)
3-58884595-C-T			Benign (Apr 16, 2018)
3-58913851-C-A		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP20DC	protein_coding	protein_coding	ENST00000295966	12	332719

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.40e-11	0.901	125705	0	43	125748	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.363	292	310	0.942	0.0000161	3704
Missense in Polyphen		95	91.316	1.0403		1121
Synonymous	0.118	113	115	0.986	0.00000626	1049
Loss of Function	1.90	21	32.7	0.642	0.00000186	354

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000244	0.000242
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000194	0.000193
Middle Eastern	0.000218	0.000217
South Asian	0.000377	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.908
• rvis_EVS: 0.49
• rvis_percentile_EVS: 79.55

Haploinsufficiency Scores

• pHI: 0.378
• hipred: N
• hipred_score: 0.233

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: 4930452B06Rik

Zebrafish Information Network

• Gene name: zgc:162324
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: morphology