CFAP69

cilia and flagella associated protein 69, the group of Armadillo like helical domain containing|Cilia and flagella associated

Basic information

Region (hg38): 7:90245174-90311063

Previous symbols: [ "C7orf63" ]

Links

ENSG00000105792 ∙ NCBI:79846 ∙ OMIM:617949 ∙ HGNC:26107 ∙ Uniprot:A5D8W1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 24 (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 24	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	29606301

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CFAP69 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP69 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	5	6
missense			65	7	6	78
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	1	65	8	13

Variants in CFAP69

This is a list of pathogenic ClinVar variants found in the CFAP69 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-90245418-A-C		CFAP69-related disorder	Likely benign (Mar 06, 2019)
7-90245430-G-C		not specified	Uncertain significance (May 24, 2023)
7-90245448-G-T		CFAP69-related disorder	Benign (Dec 31, 2019)
7-90245460-C-T		CFAP69-related disorder	Benign (Dec 31, 2019)
7-90245473-A-G		CFAP69-related disorder	Likely benign (Aug 30, 2024)
7-90245497-A-C		not specified	Likely benign (Dec 17, 2023)
7-90255438-A-G		CFAP69-related disorder	Likely benign (Jan 11, 2023)
7-90255468-G-A		not specified	Uncertain significance (Sep 20, 2023)
7-90258119-C-G		not specified	Uncertain significance (Oct 31, 2022)
7-90258128-G-C		not specified	Uncertain significance (Nov 30, 2021)
7-90258145-G-C		not specified	Uncertain significance (Dec 19, 2022)
7-90258161-C-T		not specified	Likely benign (Apr 13, 2022)
7-90262016-C-A		not specified	Uncertain significance (Mar 16, 2022)
7-90262017-G-A		CFAP69-related disorder	Benign (Nov 15, 2018)
7-90262037-GAT-G		Susceptibility to severe COVID-19	Likely pathogenic (Jul 22, 2024)
7-90262038-A-G		not specified	Uncertain significance (Oct 03, 2023)
7-90268342-G-A		not specified	Uncertain significance (Sep 26, 2024)
7-90268354-C-T		not specified	Uncertain significance (Aug 02, 2024)
7-90271539-G-A		CFAP69-related disorder	Benign (Dec 31, 2019)
7-90271549-T-C		not specified	Uncertain significance (Dec 07, 2022)
7-90271587-A-T		not specified	Uncertain significance (Nov 08, 2021)
7-90271592-T-C		not specified	Uncertain significance (May 24, 2023)
7-90271630-G-C			Uncertain significance (Sep 01, 2024)
7-90271640-G-A		Spermatogenic failure 24	Pathogenic (May 03, 2019)
7-90271642-G-A		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP69	protein_coding	protein_coding	ENST00000389297	23	65890

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.33e-8	1.00	124691	0	102	124793	0.000409

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.371	430	452	0.951	0.0000215	6168
Missense in Polyphen		131	152.58	0.85857		2159
Synonymous	0.594	145	154	0.939	0.00000747	1679
Loss of Function	3.82	21	50.2	0.418	0.00000246	684

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00110	0.00109
Ashkenazi Jewish	0.00215	0.00209
East Asian	0.000408	0.000389
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000405	0.000362
Middle Eastern	0.000408	0.000389
South Asian	0.000139	0.000131
Other	0.000764	0.000660

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.25
• rvis_percentile_EVS: 69.62

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.462
• ghis: 0.450

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Cfap69
• Phenotype: growth/size/body region phenotype; taste/olfaction phenotype; reproductive system phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype

Gene ontology

• Biological process: spermatogenesis;sensory perception of smell;cell differentiation;olfactory behavior;positive regulation of flagellated sperm motility;positive regulation of fertilization;response to odorant
• Cellular component: cytoplasm;sperm midpiece;non-motile cilium