CFAP95

protein-coding

cilia and flagella associated protein 95

Gene summary

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

Previous symbols:

C9orf135

MANE transcript

NM_001010940.3

Inheritance

—

ClinVar variants

U:5B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.9

Max pathogenic AF

—

Genomic locus

chr9:69,820,817-69,906,227

External References & Databases

Ensembl (ENSG00000204711)

Transcript & Mutation Effects

hg38 • Region Span ~85.4 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 CFAP95 variants in ClinVar

2 Conditions Cataloged

not providedTotal: 3

not specifiedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001010940.3. 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			1 clinvar	1 clinvar	1 clinvar	3
missense			4 clinvar			4
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	5	1	1	7

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001010940.3	RefSeq	NP_001010940.1	6	MANE Select
ENST00000377197.8	Ensembl	ENSP00000366402.3	6	MANE Select
NM_001308084.2	RefSeq	NP_001295013.1	5	Standard
NM_001308085.2	RefSeq	NP_001295014.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

cytoplasm
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000377197
Coding exons: 6
Length: 85440
Individuals with no LoFs: 125590
Homozygous LoFs: 2
Heterozygous LoFs: 154
Defined: 125746
p: 0.000620

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.299	137	128	1.07	0.00000666	1487
Missense (PolyPhen)		48	43.168	1.1119		509
Synonymous	0.0311	46	46.3	0.994	0.00000235	411
Loss of Function	0.325	12	13.3	0.904	6.45e-7	165

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000062	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.0040	0.0040	notable
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.370
RVIS EVS: 0
RVIS percentile EVS: 53.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium