CFAP91

protein-coding

cilia and flagella associated protein 91

Gene summary

Involved in axonemal central apparatus assembly and spermatogenesis. Predicted to be located in motile cilium and radial spoke stalk. Implicated in spermatogenic failure 51. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C3orf15
MAATS1

MANE transcript

NM_033364.4

Inheritance

ClinVar variants

P:5U:138B:13

Top phenotype

Spermatogenic failure 51

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr3:119,703,022-119,767,102

External References & Databases

Ensembl (ENSG00000183833)

Transcript & Mutation Effects

hg38 • Region Span ~64.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

Clinical Genomic Database (CGD)

Spermatogenic failure 51AR

Manifestation: Genitourinary

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 32161152

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CFAP91 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 140

Spermatogenic failure 51Total: 5

not providedTotal: 3

CFAP91-related conditionTotal: 2

Primary ciliary dyskinesiaTotal: 2

Male infertility with teratozoospermia due to single gene mutationTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033364.4. 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			2 clinvar	1 clinvar		3
missense			133 clinvar	11 clinvar	1 clinvar	145
nonsense		1 clinvar	1 clinvar			2
start loss						0
frameshift		2 clinvar				2
splice donor/acceptor (+/-2bp)	1 clinvar	1 clinvar	2 clinvar			4
Total	1	4	138	12	1	156

Highest pathogenic variant AF is 0.00029823062

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033364.4	RefSeq	NP_203528.3	17	MANE Select
ENST00000273390.9	Ensembl	ENSP00000273390.5	17	MANE Select
NM_001320316.2	RefSeq	NP_001307245.2	17	Standard
NM_001320317.2	RefSeq	NP_001307246.2	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cilium movement

Molecular Function

protein binding

Cellular Component

radial spoke stalk
mitochondrion
axoneme
motile cilium

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000273390
Coding exons: 17
Length: 64081
Individuals with no LoFs: 125596
Homozygous LoFs: 0
Heterozygous LoFs: 152
Defined: 125748
p: 0.000605

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0888	424	429	0.988	0.0000241	5019
Missense (PolyPhen)		126	128.75	0.97867		1380
Synonymous	0.292	146	151	0.970	0.00000778	1413
Loss of Function	2.14	27	42.0	0.643	0.00000205	531

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.0013	0.0013	notable
Ashkenazi Jewish	0.0012	0.0011	notable
East Asian	0.00072	0.00071	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00057	0.00056	rare
South Asian	0.00020	0.00020	rare
Other	0.00099	0.00098	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in spermatogenesis (PubMed:12223483). May regulate cilium motility through its role in the assembly of the axonemal radial spokes (By similarity). {ECO:0000250|UniProtKB:A8IH47, ECO:0000269|PubMed:12223483}.;

Recessive Scores

pRec: 0.0951

Intolerance Scores

RVIS EVS: 0.87
RVIS percentile EVS: 88.87

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