CFAP52

cilia and flagella associated protein 52, the group of WD repeat domain containing|Cilia and flagella associated

Basic information

Region (hg38): 17:9576626-9643447

Previous symbols: [ "WDR16" ]

Links

ENSG00000166596 ∙ NCBI:146845 ∙ OMIM:609804 ∙ HGNC:16053 ∙ Uniprot:Q8N1V2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• situs inversus (Supportive), mode of inheritance: AD
• visceral heterotaxy (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Heterotaxy, visceral, 10, autosomal, with male infertility	AR	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	25469542; 32111882; 33139725

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CFAP52 gene.

• Situs inversus (52 variants)
• Inborn genetic diseases (25 variants)
• not provided (14 variants)
• CFAP52-related condition (2 variants)
• Oculomotor apraxia;Situs inversus (1 variants)
• Heterotaxy, visceral, 10, autosomal, with male infertility (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CFAP52 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	14	10	25
missense			43	5	1	49
nonsense						0
start loss			1			1
frameshift		1				1
inframe indel			1			1
splice donor/acceptor (+/-2bp)		1				1
splice region				2	2	4
non coding				1	1	2
Total	0	2	46	20	12

Highest pathogenic variant AF is 0.000381

Variants in CFAP52

This is a list of pathogenic ClinVar variants found in the CFAP52 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-9576698-G-A		CFAP52-related disorder	Uncertain significance (Jul 23, 2023)
17-9576738-G-A		not specified	Uncertain significance (Dec 13, 2022)
17-9585806-A-G		not specified	Uncertain significance (Jun 22, 2023)
17-9585823-T-C		Situs inversus	Uncertain significance (Aug 10, 2023)
17-9585840-A-G		Situs inversus	Likely benign (Dec 08, 2019)
17-9585865-A-G		not specified	Uncertain significance (Nov 23, 2021)
17-9585891-T-AGCA		Situs inversus	Uncertain significance (May 09, 2023)
17-9585901-G-A		Situs inversus	Uncertain significance (Nov 08, 2017)
17-9585915-C-T		Situs inversus	Benign/Likely benign (Jul 17, 2023)
17-9585916-A-G		Situs inversus	Likely benign (Aug 01, 2021)
17-9585937-A-T		CFAP52-related disorder	Uncertain significance (Feb 09, 2024)
17-9585939-C-T			Likely benign (Nov 15, 2017)
17-9585945-C-T		Situs inversus	Likely benign (Sep 24, 2019)
17-9585946-G-A		Situs inversus	Uncertain significance (Aug 16, 2022)
17-9585966-G-T			Likely benign (Jan 01, 2024)
17-9586735-T-C		not specified	Uncertain significance (May 31, 2022)
17-9586743-C-T		not specified	Uncertain significance (Mar 21, 2022)
17-9586744-G-A		not specified	Uncertain significance (Dec 21, 2022)
17-9586774-C-T		not specified	Uncertain significance (Apr 07, 2022)
17-9586826-T-C			Likely benign (Jun 13, 2018)
17-9586830-G-A		not specified	Uncertain significance (Jun 29, 2022)
17-9594213-C-A		not specified	Uncertain significance (Feb 17, 2024)
17-9594224-G-A		Situs inversus • not specified	Uncertain significance (Apr 27, 2023)
17-9594243-C-T		Situs inversus	Likely benign (Aug 04, 2023)
17-9594248-G-A		not specified	Uncertain significance (Aug 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CFAP52	protein_coding	protein_coding	ENST00000352665	14	66833

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.12e-18	0.0157	125634	0	114	125748	0.000453

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.178	355	365	0.974	0.0000199	4083
Missense in Polyphen		83	97.548	0.85086		1066
Synonymous	0.335	138	143	0.964	0.00000883	1187
Loss of Function	0.484	28	30.9	0.906	0.00000160	352

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00179	0.00179
Ashkenazi Jewish	0.00	0.00
East Asian	0.000985	0.000979
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000406	0.000404
Middle Eastern	0.000985	0.000979
South Asian	0.000362	0.000359
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in cell growth and/or survival. {ECO:0000269|PubMed:15967112}.

Recessive Scores

• pRec: 0.0979

Intolerance Scores

• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.45

Haploinsufficiency Scores

• pHI: 0.0480
• hipred: N
• hipred_score: 0.317
• ghis: 0.433

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Cfap52

Zebrafish Information Network

• Gene name: cfap52
• Affected structure: brain
• Phenotype tag: abnormal
• Phenotype quality: hydrocephalic

Gene ontology

• Cellular component: cytoplasm;motile cilium
• Molecular function: protein binding