CFAP47

cilia and flagella associated protein 47, the group of Cilia and flagella associated

Basic information

Region (hg38): X:35919734-36385317

Previous symbols: [ "CXorf59", "CXorf22", "CXorf30", "CHDC2" ]

Links

ENSG00000165164 ∙ NCBI:286464 ∙ OMIM:301057 ∙ HGNC:26708 ∙ Uniprot:Q6ZTR5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure, X-linked, 3 (Limited), mode of inheritance: XL
• spermatogenic failure, X-linked, 3 (Limited), mode of inheritance: XL
• polycystic kidney disease (Limited), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure, X-linked, 3	XL	Cardiovascular; Pulmonary	The condition can involve congenital cardiac anomalies, and awareness may allow early management; Though pulmonary manifestations have been described as relatively mild, awareness may allow management of respiratory sequelae	Cardiovascular; Genitourinary; Pulmonary	33472045

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CFAP47 gene.

• not_provided (23 variants)
• not_specified (11 variants)
• CFAP47-related_disorder (9 variants)
• Spermatogenic_failure,_X-linked,_3 (5 variants)
• Inborn_genetic_diseases (5 variants)
• Abnormality_of_neuronal_migration (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP47 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001304548.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				6		6
missense	3		24	17		44
nonsense				1		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	3	0	24	24	0

Highest pathogenic variant AF is 0.0000064414658

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP47	protein_coding	protein_coding	ENST00000297866	16	70419

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.989	0.0109	124917	20	79	125016	0.000396

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.101	338	343	0.985	0.0000249	6403
Missense in Polyphen		83	100.54	0.82555		2134
Synonymous	-1.42	140	120	1.17	0.00000878	1830
Loss of Function	4.26	3	26.8	0.112	0.00000199	546

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00731	0.00560
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000820	0.0000548
Finnish	0.00	0.00
European (Non-Finnish)	0.0000268	0.0000177
Middle Eastern	0.0000820	0.0000548
South Asian	0.00	0.00
Other	0.000468	0.000328

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.12

Haploinsufficiency Scores

• pHI: 0.0640
• hipred: N
• hipred_score: 0.316

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Cfap47