CFAP126

protein-coding

cilia and flagella associated protein 126, the group of Cilia and flagella associated

Gene summary

Predicted to be involved in cilium organization and flagellated sperm motility. Located in axonemal microtubule. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C1orf192

MANE transcript

NM_001013625.4

Inheritance

—

ClinVar variants

P:2U:29B:2

Top phenotype

Pheochromocytoma/paraganglioma syndrome 3

gnomAD constraint

pLI —, LoF o/e 0.98

Max pathogenic AF

—

Genomic locus

chr1:161,364,733-161,367,876

External References & Databases

Ensembl (ENSG00000188931)

Transcript & Mutation Effects

hg38 • Region Span ~3.1 kb

Loading mutation effect viewer...

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 CFAP126 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 27

not providedTotal: 1

Pheochromocytoma/paraganglioma syndrome 3Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001013625.4. 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						0
missense			28 clinvar	2 clinvar		30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)	2 clinvar		1 clinvar			3
Total	2	0	29	2	0	33

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001013625.4	RefSeq	NP_001013647.2	5	MANE Select
ENST00000367974.2	Ensembl	ENSP00000356951.1	5	MANE Select
ENST00000906331.1	Ensembl	ENSP00000576390.1	3	Standard
ENST00000906331.2	Ensembl	ENSP00000576390.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cilium organization

Cellular Component

cytoplasm
cilium
apical plasma membrane
ciliary basal body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000367974
Coding exons: 5
Length: 3144
Individuals with no LoFs: 125663
Homozygous LoFs: 0
Heterozygous LoFs: 84
Defined: 125747
p: 0.000334

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.713	78	97.9	0.797	0.00000489	1142
Missense (PolyPhen)		41	41.582	0.986		467
Synonymous	1.81	20	33.3	0.601	0.00000152	367
Loss of Function	0.0555	8	8.17	0.979	3.46e-7	97

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00043	0.00027	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00053	0.00053	rare
South Asian	0.00020	0.00020	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a regulator of cilium basal body docking and positioning in mono- and multiciliated cells. Regulates basal body docking and cilia formation in multiciliated lung cells. Regulates kinocilium positioning and stereocilia bundle morphogenesis in the inner ear. {ECO:0000250|UniProtKB:Q6P8X9}.;

Intolerance Scores

RVIS EVS: 0.41
RVIS percentile EVS: 76.67

Essentials

Essential (gene trap): N