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

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.

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.

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				6		6
missense			22	9		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	2		3
non coding						0
Total	0	0	22	15	0

Variants in CFAP47

This is a list of pathogenic ClinVar variants found in the CFAP47 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-35919809-C-T		CFAP47-related disorder	Likely benign (Nov 01, 2021)
X-35919953-A-T		not specified	Uncertain significance (Jun 11, 2021)
X-35926032-A-T		not specified	Uncertain significance (Aug 12, 2021)
X-35951180-G-A		-	no classification for the single variant (-)
X-35951276-A-G		not specified	Likely benign (Oct 20, 2021)
X-35951279-C-T			Uncertain significance (Dec 01, 2021)
X-35951890-A-T		not specified	Uncertain significance (Jun 18, 2021)
X-35953715-C-G			Likely benign (Feb 01, 2023)
X-35956071-C-T		not specified	Uncertain significance (Nov 12, 2021)
X-35956102-A-C		not specified	Uncertain significance (Jul 06, 2021)
X-35956104-T-C			Likely benign (Feb 01, 2024)
X-35956123-C-T		-	no classification for the single variant (-)
X-35966601-G-T			Uncertain significance (Oct 01, 2023)
X-35966646-G-A		not specified	Uncertain significance (Aug 23, 2021)
X-35967714-G-T		not specified	Uncertain significance (Nov 09, 2021)
X-35970837-A-G			Likely benign (Mar 01, 2023)
X-35975194-A-T		CFAP47-related disorder	Likely benign (May 26, 2022)
X-35975293-G-A		not specified	Uncertain significance (Aug 13, 2021)
X-35975701-C-T		not specified	Uncertain significance (Aug 10, 2021)
X-35975808-C-T			Likely benign (Aug 01, 2022)
X-35975809-G-A		CFAP47-related disorder	Likely benign (May 16, 2023)
X-35991866-A-G			Uncertain significance (Feb 01, 2022)
X-35993205-C-G			Likely benign (Apr 01, 2023)
X-36035691-G-C			Uncertain significance (Dec 01, 2021)
X-36039133-A-G		CFAP47-related disorder	Likely benign (May 16, 2024)

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