CFAP45

protein-coding

cilia and flagella associated protein 45, the group of Cilia and flagella associated

Gene summary

Enables AMP binding activity. Involved in establishment of left/right asymmetry and flagellated sperm motility. Located in axonemal microtubule and sperm flagellum. Implicated in visceral heterotaxy 11. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

CCDC19

MANE transcript

NM_012337.3

Inheritance

ClinVar variants

P:5U:113B:11

Top phenotype

Heterotaxy, visceral, 11, autosomal, with male infertility

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr1:159,872,364-159,900,165

External References & Databases

Ensembl (ENSG00000213085)

Transcript & Mutation Effects

hg38 • Region Span ~27.8 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

heterotaxy, visceral, 11, autosomal, with male infertilityMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0030475

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Heterotaxy, visceral, 11, autosomal, with male infertilityAR

Manifestation: Cardiovascular; Gastrointestinal; 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: 33139725

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CFAP45 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 111

not providedTotal: 9

Heterotaxy, visceral, 11, autosomal, with male infertilityTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012337.3. 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				5 clinvar		5
missense			111 clinvar	5 clinvar	1 clinvar	117
nonsense	2 clinvar	1 clinvar				3
start loss						0
frameshift	2 clinvar		1 clinvar			3
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	4	1	113	10	1	129

Highest pathogenic variant AF is 0.000053975447

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_012337.3	RefSeq	NP_036469.2	12	MANE Select
ENST00000368099.9	Ensembl	ENSP00000357079.4	12	MANE Select
ENST00000426543.6	Ensembl	ENSP00000403044.2	10	Standard
ENST00000426543.7	Ensembl	ENSP00000403044.2	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

nucleus
nucleoplasm
cilium

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368099
Coding exons: 12
Length: 27800
Individuals with no LoFs: 125638
Homozygous LoFs: 0
Heterozygous LoFs: 110
Defined: 125748
p: 0.000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.546	356	328	1.08	0.0000216	3655
Missense (PolyPhen)		118	104.2	1.1324		1113
Synonymous	1.18	98	114	0.859	0.00000610	988
Loss of Function	1.57	26	36.2	0.719	0.00000225	368

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00075	0.00075	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00054	0.00054	rare
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.00039	0.00039	rare
South Asian	0.00039	0.00039	rare
Other	0.0011	0.0011	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.120

Intolerance Scores

RVIS EVS: 0.36
RVIS percentile EVS: 74.66

Essentials

Essential (gene trap): N