CFAP61

Chr 20AR

cilia and flagella associated protein 61

Also known as: C20orf26, CaM-IP3, SPGF84, dJ1002M8.3, dJ1178H5.4

NCBI Gene: 26074 ENSG00000089101 UniProt: Q8NHU2 OMIM: 620381

The CFAP61 protein is involved in sperm flagellum assembly and plays an essential role in the formation of radial spokes in flagellum axoneme. Mutations cause spermatogenic failure 84, which follows autosomal recessive inheritance. This gene primarily affects male fertility rather than neurological development.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

Acts upstream of or within sperm mitochondrial sheath assembly. Located in axoneme and sperm flagellum. Implicated in spermatogenic failure 84. [provided by Alliance of Genome Resources, Jun 2026]

OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Spermatogenic failure 84MIM #620409

Clinical highlights

Gene–disease validity

Not independently assessedOMIM lists Spermatogenic failure 84; no ClinGen or GenCC tier

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.73

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.73LOEUF

pLI 0.000

Z-score 3.31

OE 0.55 (0.41–0.73)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.24Z-score

OE missense 0.97 (0.92–1.04)

700 obs / 718.4 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.55 (0.41–0.73)

0≤0.351.4

Missense OE?0.97 (0.92–1.04)

0≤0.61.4

Synonymous OE?0.97

0≤1.21.6

LoF obs/exp: 34 / 62.2Missense obs/exp: 700 / 718.4Syn Z: 0.45

Background carrier burden — how many people carry a rare variant somewhere in CFAP61?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 32

1,630 rare PASS variants

Rare truncating (LoF)

1 in 260

267 rare PASS variants

Rare synonymous (reference)

1 in 63

621 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for CFAP61. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 40	1 in 250
South Asian	~43k	1 in 28	1 in 260
Remaining (unassigned)	~30k	1 in 28	1 in 250
European (Finnish)	~27k	1 in 90	1 in 920
Admixed American	~22k	1 in 31	1 in 410
African / African American	~21k	1 in 33	1 in 580
East Asian	~20k	1 in 35	1 in 280
Ashkenazi Jewish	~13k	1 in 150	≈ 1 in 6,500
Middle Eastern	~2,884	1 in 29	1 in 570

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 23 of 26 coding exons well covered in gnomAD exomes; exons 9, 19, 24 marginal. Genomes: all 26.? see exons ↓