CFAP77

protein-coding

cilia and flagella associated protein 77, the group of Cilia and flagella associated

Gene summary

Predicted to be involved in flagellated sperm motility. Located in axonemal microtubule. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C9orf171

MANE transcript

NM_001282957.2

Inheritance

—

ClinVar variants

U:62B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr9:132,410,043-132,573,319

External References & Databases

Ensembl (ENSG00000188523)

Transcript & Mutation Effects

hg38 • Region Span ~163.3 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 CFAP77 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 68

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001282957.2. 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						0
missense			61 clinvar	4 clinvar		65
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	62	4	0	66

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001282957.2	RefSeq	NP_001269886.1	6	MANE Select
ENST00000393216.3	Ensembl	ENSP00000376909.2	6	MANE Select
NM_207417.3	RefSeq	NP_997300.1	7	Standard
ENST00000343036.6	Ensembl	ENSP00000343290.2	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

cilium

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000343036
Coding exons: 7
Length: 163275
Individuals with no LoFs: 125701
Homozygous LoFs: 0
Heterozygous LoFs: 47
Defined: 125748
p: 0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.161	213	207	1.03	0.0000136	2029
Missense (PolyPhen)		67	68.394	0.97961		640
Synonymous	-0.123	88	86.5	1.02	0.00000549	656
Loss of Function	0.736	12	15.1	0.796	7.27e-7	167

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00045	0.00043	rare
Latino/Admixed American	0.00027	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00099	0.00098	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00010	0.000097	rare
South Asian	0.000069	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: -0.31
RVIS percentile EVS: 32.15

Essentials

Essential (gene trap): N