CFAP52

protein-coding

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

Gene summary

WD repeat-containing proteins, such as WDR16, play crucial roles in a wide range of physiologic functions, including signal transduction, RNA processing, remodeling the cytoskeleton, regulation of vesicular traffic, and cell division (Silva et al., 2005 [PubMed 15967112]).[supplied by OMIM, Mar 2008]

Previous symbols:

WDR16

MANE transcript

NM_145054.5

Inheritance

AR, AD

ClinVar variants

P:5U:114B:36

Top phenotype

Heterotaxy, visceral, 10, autosomal, with male infertility

gnomAD constraint

pLI —, LoF o/e 0.91

Max pathogenic AF

—

Genomic locus

chr17:9,576,627-9,643,447

External References & Databases

Ensembl (ENSG00000166596)

Transcript & Mutation Effects

hg38 • Region Span ~66.8 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

visceral heterotaxyLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0018677

Submitter: Ambry Genetics

situs inversusSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0010029

Submitter: Orphanet

Clinical Genomic Database (CGD)

Heterotaxy, visceral, 10, autosomal, with male infertilityAR

Manifestation: Cardiovascular; Genitourinary; Pulmonary

Intervention: Cardiovascular; Pulmonary

Rationale: 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

Refs: 25469542; 32111882; 33139725

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CFAP52 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 88

Situs inversusTotal: 57

not providedTotal: 33

CFAP52-related disorderTotal: 8

Heterotaxy, visceral, 10, autosomal, with male infertilityTotal: 5

Oculomotor apraxiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145054.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	21 clinvar	8 clinvar	30
missense			102 clinvar	7 clinvar		109
nonsense		2 clinvar	3 clinvar			5
start loss			1 clinvar			1
frameshift		2 clinvar	1 clinvar			3
splice donor/acceptor (+/-2bp)		1 clinvar	6 clinvar			7
Total	0	5	114	28	8	155

Highest pathogenic variant AF is 0.00007062934

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_145054.5	RefSeq	NP_659491.4	14	MANE Select
ENST00000352665.10	Ensembl	ENSP00000339449.5	14	MANE Select
NM_001080556.2	RefSeq	NP_001074025.1	13	Standard
ENST00000396219.7	Ensembl	ENSP00000379521.3	13	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
cfap52	Danio rerio	Structure: brain Quality: hydrocephalic abnormal

Gene / Model

Organism

Observed Phenotype

cfap52

Danio rerio

Structure: brain

Quality: hydrocephalic

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

cytoplasm
motile cilium

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000352665
Coding exons: 14
Length: 66833
Individuals with no LoFs: 125634
Homozygous LoFs: 0
Heterozygous LoFs: 114
Defined: 125748
p: 0.000453

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.178	355	365	0.974	0.0000199	4083
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0014	0.0014	notable
Latino/Admixed American	0.00043	0.00043	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00099	0.00098	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00041	0.00040	rare
South Asian	0.00036	0.00036	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (gene trap): N