CFAP100

protein-coding

cilia and flagella associated protein 100, the group of Cilia and flagella associated

Gene summary

Predicted to enable dynein complex binding activity. Predicted to be involved in several processes, including cilium movement; inner dynein arm assembly; and skin epidermis development. Located in ciliary basal body. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

CCDC37

MANE transcript

NM_182628.3

Inheritance

—

ClinVar variants

U:101B:11

Top phenotype

Primary ciliary dyskinesia

gnomAD constraint

pLI —, LoF o/e 0.84

Max pathogenic AF

—

Genomic locus

chr3:126,394,909-126,436,556

External References & Databases

Ensembl (ENSG00000163885)

Transcript & Mutation Effects

hg38 • Region Span ~41.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CFAP100 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 105

not providedTotal: 2

Primary ciliary dyskinesiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182628.3. 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				2 clinvar		2
missense			97 clinvar	9 clinvar		106
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	101	11	0	112

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182628.3	RefSeq	NP_872434.2	16	MANE Select
ENST00000352312.6	Ensembl	ENSP00000344749.1	16	MANE Select
ENST00000505024.1	Ensembl	ENSP00000423046.1	16	Standard
ENST00000505024.2	Ensembl	ENSP00000423046.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cilium movement
inner dynein arm assembly
regulation of microtubule motor activity

Molecular Function

dynein complex binding

Cellular Component

motile cilium
axonemal outer doublet

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000352312
Coding exons: 16
Length: 41618
Individuals with no LoFs: 124213
Homozygous LoFs: 18
Heterozygous LoFs: 1517
Defined: 125748
p: 0.00612

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0601	358	355	1.01	0.0000219	4006
Missense (PolyPhen)		91	97.103	0.93715		1190
Synonymous	-1.13	169	151	1.12	0.00000997	1110
Loss of Function	0.876	30	35.6	0.842	0.00000194	400

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0023	0.0022	notable
Latino/Admixed American	0.0022	0.0020	notable
Ashkenazi Jewish	0.0012	0.0011	notable
East Asian	0.0018	0.0017	notable
Finnish	0.033	0.029	notable
European (Non-Finnish)	0.0069	0.0061	notable
South Asian	0.0012	0.0011	notable
Other	0.0065	0.0060	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in ciliary/flagellar motility by regulating the assembly and the activity of axonemal inner dynein arm. {ECO:0000250|UniProtKB:A8I4E9}.;

Recessive Scores

pRec: 0.0884

Intolerance Scores

RVIS EVS: 1.34
RVIS percentile EVS: 94.3

Essentials

Essential (gene trap): N