CFAP58

cilia and flagella associated protein 58, the group of Cilia and flagella associated

Basic information

Region (hg38): 10:104353832-104455102

Previous symbols: [ "C10orf80", "CCDC147" ]

Links

ENSG00000120051 ∙ NCBI:159686 ∙ OMIM:619129 ∙ HGNC:26676 ∙ Uniprot:Q5T655 ∙ 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 49	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	32791035

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CFAP58 gene.

• Inborn genetic diseases (34 variants)
• not provided (5 variants)
• Spermatogenic failure 49 (2 variants)
• CFAP58-related condition (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP58 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			35	3	1	39
nonsense	1	1				2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	1	1	35	4	1

Highest pathogenic variant AF is 0.000348

Variants in CFAP58

This is a list of pathogenic ClinVar variants found in the CFAP58 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-104358419-C-A		not specified	Uncertain significance (Feb 12, 2024)
10-104358495-A-G		not specified	Uncertain significance (Jul 19, 2023)
10-104358552-A-G		not specified	Uncertain significance (May 05, 2023)
10-104358558-C-T		not specified	Uncertain significance (Dec 28, 2023)
10-104358566-G-A		not specified	Uncertain significance (Jan 05, 2022)
10-104364733-C-T		not specified	Likely benign (Dec 17, 2023)
10-104364768-C-G		not specified	Uncertain significance (Mar 05, 2024)
10-104364821-G-C		not specified	Uncertain significance (Sep 28, 2022)
10-104365863-G-A		not specified	Uncertain significance (Jan 16, 2024)
10-104365922-C-A		not specified	Uncertain significance (Feb 06, 2023)
10-104368457-A-G		not specified	Uncertain significance (Aug 17, 2021)
10-104368481-T-G		not specified	Uncertain significance (Nov 10, 2022)
10-104370895-G-A		not specified	Uncertain significance (Aug 02, 2023)
10-104370934-G-A		not specified	Uncertain significance (Oct 27, 2023)
10-104370938-A-C		not specified	Uncertain significance (Aug 28, 2023)
10-104376855-A-G		not specified	Uncertain significance (May 04, 2022)
10-104380042-C-T		not specified	Uncertain significance (Mar 31, 2022)
10-104380048-A-G		not specified	Likely benign (Mar 29, 2022)
10-104380050-G-A		not specified	Uncertain significance (Jul 15, 2021)
10-104380051-C-T		not specified	Uncertain significance (Jul 05, 2023)
10-104380092-G-A		CFAP58-related disorder	Uncertain significance (May 15, 2023)
10-104380118-C-A			Likely benign (Feb 01, 2023)
10-104380180-G-A		not specified	Uncertain significance (Aug 10, 2021)
10-104380183-A-G		not specified	Uncertain significance (Feb 03, 2022)
10-104380186-G-A		not specified	Uncertain significance (Aug 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP58	protein_coding	protein_coding	ENST00000369704	18	101327

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.43e-23	0.0943	125393	1	354	125748	0.00141

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.161	466	456	1.02	0.0000247	5793
Missense in Polyphen		99	105.96	0.93434		1400
Synonymous	0.0881	169	170	0.991	0.00000915	1501
Loss of Function	1.53	41	53.0	0.773	0.00000286	646

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00270	0.00269
Ashkenazi Jewish	0.0115	0.0115
East Asian	0.000602	0.000598
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000716	0.000712
Middle Eastern	0.000602	0.000598
South Asian	0.00185	0.00177
Other	0.00213	0.00212

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.59

Haploinsufficiency Scores

• pHI: 0.104
• hipred: N
• hipred_score: 0.251
• ghis: 0.493

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Cfap58

Gene ontology

• Cellular component: extracellular space;cilium
• Molecular function: protein binding