CFAP65

cilia and flagella associated protein 65, the group of Cilia and flagella associated

Basic information

Region (hg38): 2:219002846-219041527

Previous symbols: [ "CCDC108" ]

Links

ENSG00000181378 ∙ NCBI:255101 ∙ OMIM:614270 ∙ HGNC:25325 ∙ Uniprot:Q6ZU64 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 40 (Limited), mode of inheritance: AR
• non-syndromic male infertility due to sperm motility disorder (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 40	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	30686508; 31413122; 31571197

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CFAP65 gene.

• not provided (1 variants)
• Spermatogenic failure 40 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP65 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				10	5	15
missense		1	26	8	4	39
nonsense	2	1				3
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	2	2	26	19	9

Highest pathogenic variant AF is 0.00000658

Variants in CFAP65

This is a list of pathogenic ClinVar variants found in the CFAP65 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-219002940-C-T			Benign (Nov 15, 2018)
2-219002952-A-G			Likely benign (Mar 01, 2023)
2-219002997-C-T			Benign (Mar 01, 2022)
2-219003989-C-A		Susceptibility to severe COVID-19	Likely pathogenic (Jul 22, 2024)
2-219004022-G-T			Uncertain significance (-)
2-219004065-G-A			Benign (Nov 15, 2018)
2-219004092-C-T			Likely benign (Mar 01, 2022)
2-219004166-C-A		Spermatogenic failure 40	Pathogenic (Aug 14, 2019)
2-219004321-G-C			Likely benign (Apr 16, 2018)
2-219004354-A-C		CFAP65-related disorder	Likely benign (Jan 13, 2023)
2-219005519-A-G			Benign (Nov 15, 2018)
2-219005543-C-T		not specified	Uncertain significance (Jun 18, 2021)
2-219009087-C-T			Benign (Apr 16, 2018)
2-219009154-G-A			Benign (Dec 31, 2019)
2-219009381-T-C		not specified	Uncertain significance (Sep 16, 2021)
2-219009965-G-A		Spermatogenic failure 40	Uncertain significance (Nov 24, 2023)
2-219010021-C-T		not specified	Uncertain significance (Jun 11, 2021)
2-219010669-C-T			Likely benign (Jan 01, 2024)
2-219010812-G-A		not specified	Uncertain significance (Jul 13, 2021)
2-219013277-G-A			Likely benign (Mar 01, 2022)
2-219013323-T-A			Uncertain significance (Feb 01, 2020)
2-219013929-T-C		not specified	Uncertain significance (Oct 06, 2021)
2-219013946-T-C			Likely benign (Apr 01, 2022)
2-219013954-G-A			Benign (Dec 31, 2019)
2-219014044-C-T		CFAP65-related disorder	Likely pathogenic (Jul 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP65	protein_coding	protein_coding	ENST00000341552	33	38682

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.72e-27	0.997	125465	0	283	125748	0.00113

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.315	1069	1.10e+3	0.973	0.0000621	12612
Missense in Polyphen		292	305.12	0.957		3548
Synonymous	0.00275	463	463	1.00	0.0000283	3770
Loss of Function	3.29	57	90.8	0.628	0.00000439	1022

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00238	0.00237
Ashkenazi Jewish	0.000312	0.000298
East Asian	0.000613	0.000598
Finnish	0.000519	0.000508
European (Non-Finnish)	0.00144	0.00142
Middle Eastern	0.000613	0.000598
South Asian	0.00123	0.00108
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in sperm motility. {ECO:0000250|UniProtKB:I6WQT8}.

Intolerance Scores

• rvis_EVS: -1.85
• rvis_percentile_EVS: 2.04

Haploinsufficiency Scores

• pHI: 0.0766
• hipred: N
• hipred_score: 0.369
• ghis: 0.547

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Cfap65

Gene ontology

• Cellular component: plasma membrane;integral component of membrane;motile cilium
• Molecular function: RNA binding