CFAP47

Chr XXLR

cilia and flagella associated protein 47

Also known as: CHDC2, CXorf22, CXorf30, CXorf59, SPGF52, SPGFX3

NCBI Gene: 286464ENSG00000165164UniProt: Q6ZTR5OMIM: 301057

This protein plays a role in flagellar formation and sperm motility. Mutations cause X-linked recessive spermatogenic failure, which primarily affects male fertility rather than causing pediatric neurological disease. The gene is highly constrained against loss-of-function variants (pLI 0.99, LOEUF 0.29), suggesting it may have additional undiscovered functions beyond reproduction.

OMIMResearchSummary from RefSeq, OMIM, UniProt
XLRLOEUF 0.291 OMIM phenotype
Clinical Summary— CFAP47
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Gene-Disease Validity (ClinGen)
spermatogenic failure, X-linked, 3 · XLLimited

Limited evidence — not for standalone diagnostic reporting

2 total gene-disease associations curated

⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.99). One damaged copy is likely sufficient to cause disease.
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ClinVar Variants
54 unique Pathogenic / Likely Pathogenic· 26 VUS of 214 total submissions
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.29LOEUF
pLI 0.989
Z-score 4.26
OE 0.11 (0.05–0.29)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
0.10Z-score
OE missense 0.98 (0.90–1.08)
338 obs / 343.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.11 (0.05–0.29)
0≤0.351.4
Missense OE0.98 (0.90–1.08)
0≤0.61.4
Synonymous OE1.17
0≤1.21.6
LoF obs/exp: 3 / 26.8Missense obs/exp: 338 / 343.3Syn Z: -1.42

ClinVar Variant Classifications

214 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic52
Likely Pathogenic2
VUS26
Likely Benign27
52
Pathogenic
2
Likely Pathogenic
26
VUS
27
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
2
50
0
52
Likely Pathogenic
0
0
2
0
2
VUS
0
23
3
0
26
Likely Benign
1
18
2
6
27
Benign
0
0
0
0
0
Total143576107

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CFAP47 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 4 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients