CCDC39 p.Glu144=
c.432G>A · rs990394869 · VCV2837181
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
primary ciliary dyskinesia
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.003 | GERP -3, phastCons 0.8 |
| Overall | ||
| CADD | 5.921 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CCDC39
- Protein
- p.Glu144=
- Coding
- c.432G>A
- MANE Select
- NM_181426
- dbSNP
- rs990394869
- Type
- single nucleotide variant
- Location
- chr3:180660654 (GRCh38)
- Gene constraint
- LOEUF 1.226 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 79.23 · 1 PDB
Disease context
primary ciliary dyskinesia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Primary ciliary dyskinesia (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive, X-linked recessive
- Onset
- Neonatal
- Prevalence
- 1-5 / 10 000 (Pakistan)
Similar variants
- CCDC39 p.Glu144fs Pathogenic ★ same residue
- CCDC39 c.1034+2T>A Pathogenic/Likely pathogenic ★★ same condition
- CCDC39 c.1167+1261A>G Pathogenic/Likely pathogenic ★★ same condition
- CCDC39 c.1362+1G>A Likely pathogenic ★★ same condition
- CCDC39 c.1999-2A>T Pathogenic/Likely pathogenic ★★ same condition
- CCDC39 c.210+2T>C Pathogenic ★★ same condition
- CCDC39 c.357+1G>C Pathogenic ★★ same condition
- CCDC39 c.516+1G>A Likely pathogenic ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ccdc39-p-glu144 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown