CFAP61

cilia and flagella associated protein 61, the group of Cilia and flagella associated

Basic information

Region (hg38): 20:20052513-20360703

Previous symbols: [ "C20orf26" ]

Links

ENSG00000089101 ∙ NCBI:26074 ∙ ∙ HGNC:15872 ∙ Uniprot:Q8NHU2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 84	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	34792097; 35174165; 35387802

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CFAP61 gene.

• Inborn genetic diseases (60 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP61 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			55	6		61
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			1	1		2
Total	0	0	56	7	0

Variants in CFAP61

This is a list of pathogenic ClinVar variants found in the CFAP61 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-20052678-G-A			Likely benign (May 01, 2023)
20-20055992-A-G		not specified	Uncertain significance (Oct 18, 2021)
20-20056664-T-C		not specified	Uncertain significance (Sep 01, 2021)
20-20056690-G-A		not specified	Uncertain significance (Sep 14, 2022)
20-20056794-T-C			Likely benign (Oct 01, 2022)
20-20056801-G-A		Spermatogenic failure 84	Pathogenic (Jun 02, 2023)
20-20070852-A-G		Spermatogenic failure 84	Pathogenic (Sep 28, 2023)
20-20070895-A-G		not specified	Uncertain significance (Aug 17, 2022)
20-20070979-A-C			Likely benign (Jan 01, 2023)
20-20070984-G-A		not specified	Uncertain significance (Nov 17, 2023)
20-20074309-A-G		not specified	Uncertain significance (Jan 09, 2024)
20-20074321-T-C		not specified	Uncertain significance (Sep 22, 2023)
20-20074343-T-A		not specified	Uncertain significance (Jan 29, 2024)
20-20074346-G-C		not specified	Uncertain significance (Aug 09, 2021)
20-20075193-G-A		not specified	Uncertain significance (Aug 01, 2022)
20-20075250-A-T		not specified	Uncertain significance (Nov 27, 2023)
20-20075497-C-G		not specified	Uncertain significance (Jan 26, 2022)
20-20075499-CAT-C		Spermatogenic failure 84	Pathogenic (Jun 02, 2023)
20-20075512-G-A		not specified	Uncertain significance (Dec 19, 2023)
20-20075557-G-T		not specified	Uncertain significance (May 27, 2022)
20-20075606-G-A		not specified	Uncertain significance (Sep 30, 2021)
20-20090854-C-T		not specified	Uncertain significance (Feb 14, 2023)
20-20090855-A-C		not specified	Uncertain significance (Oct 26, 2021)
20-20090884-T-A		not specified	Uncertain significance (Feb 14, 2023)
20-20090902-G-A		not specified	Uncertain significance (Jun 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP61	protein_coding	protein_coding	ENST00000245957	26	308189

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.11e-15	1.00	125496	1	251	125748	0.00100

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.245	700	718	0.974	0.0000404	8196
Missense in Polyphen		196	220.14	0.89034		2553
Synonymous	0.449	274	284	0.966	0.0000177	2340
Loss of Function	3.31	34	62.2	0.547	0.00000330	724

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00440	0.00440
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00114	0.00114
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000874	0.000871
Middle Eastern	0.00114	0.00114
South Asian	0.00112	0.00108
Other	0.000979	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate cilium motility through its role in the assembly of the axonemal radial spokes. {ECO:0000250|UniProtKB:A8IF44, ECO:0000250|UniProtKB:Q23F13}.

Intolerance Scores

• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.87

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.332
• ghis: 0.514

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Cfap61
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: cilium movement;cilium organization
• Cellular component: radial spoke stalk;axoneme;motile cilium