CFAP44

protein-coding

cilia and flagella associated protein 44, the group of Cilia and flagella associated|MicroRNA protein coding host genes|WD repeat domain containing

Gene summary

Enables peptidase activity. Involved in sperm axoneme assembly. Acts upstream of or within microtubule cytoskeleton organization. Predicted to be located in cytoskeleton and motile cilium. Predicted to be active in axoneme. Implicated in spermatogenic failure 20. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

WDR52

MANE transcript

NM_001164496.2

Inheritance

ClinVar variants

P:20U:126B:68

Top phenotype

Spermatogenic failure 20

gnomAD constraint

pLI —, LoF o/e 0.43

Max pathogenic AF

—

Genomic locus

chr3:113,286,930-113,441,610

External References & Databases

Ensembl (ENSG00000206530)

Transcript & Mutation Effects

hg38 • Region Span ~154.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

non-syndromic male infertility due to sperm motility disorderSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0017173

Submitter: Orphanet

spermatogenic failure 20MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0054724

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Spermatogenic failure 20AR

Manifestation: Genitourinary

Intervention: General

Rationale: 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

Refs: 28552195

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CFAP44 variants in ClinVar

6 Conditions Cataloged

Inborn genetic diseasesTotal: 126

not providedTotal: 64

CFAP44-related disorderTotal: 23

Spermatogenic failure 20Total: 14

not specifiedTotal: 12

CFAP44 & WDR52-related disordersTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001164496.2. 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				30 clinvar	7 clinvar	37
missense	1 clinvar		121 clinvar	22 clinvar	7 clinvar	151
nonsense	3 clinvar	4 clinvar	1 clinvar	1 clinvar		9
start loss						0
frameshift	3 clinvar	6 clinvar		1 clinvar		10
splice donor/acceptor (+/-2bp)	1 clinvar	2 clinvar	4 clinvar			7
Total	8	12	126	54	14	214

Highest pathogenic variant AF is 0.00015613736

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001164496.2	RefSeq	NP_001157968.1	34	MANE Select
ENST00000393845.9	Ensembl	ENSP00000377428.2	34	MANE Select
NM_018338.3	RefSeq	NP_060808.2	20	Standard
ENST00000295868.6	Ensembl	ENSP00000295868.2	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

sperm axoneme assembly
cilium-dependent cell motility

Cellular Component

cytoplasm
cytoskeleton
motile cilium

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000393845
Coding exons: 34
Length: 154681
Individuals with no LoFs: 125576
Homozygous LoFs: 0
Heterozygous LoFs: 172
Defined: 125748
p: 0.000684

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.37	801	918	0.873	0.0000462	12303
Missense (PolyPhen)		168	208.86	0.80436		2844
Synonymous	1.41	284	316	0.899	0.0000162	3306
Loss of Function	5.12	41	94.8	0.432	0.00000547	1221

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0012	0.0012	notable
Latino/Admixed American	0.00039	0.00038	rare
Ashkenazi Jewish	0.0062	0.0062	notable
East Asian	0.0016	0.0015	notable
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00034	0.00033	rare
South Asian	0.00013	0.00013	rare
Other	0.00099	0.00098	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Flagellar protein involved in sperm flagellum axoneme organization and function. {ECO:0000250|UniProtKB:E9Q5M6}.;

Intolerance Scores

RVIS EVS: 2.43
RVIS percentile EVS: 98.54

Essentials

Essential (gene trap): N