DNAAF5 p.Gln540=
c.1620G>A · VCV3675103
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. | ||
| REVEL | 0.084 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.4 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 1.511 | 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
- DNAAF5
- Protein
- p.Gln540=
- Coding
- c.1620G>A
- MANE Select
- NM_017802
- Type
- single nucleotide variant
- Location
- chr7:763811 (GRCh38)
- Gene constraint
- LOEUF 1.12 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.80
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
- DNAAF5 c.1470+1G>A Likely pathogenic ★★ same condition
- DNAAF5 c.1615-2A>G Likely pathogenic ★★ same condition
- DNAAF5 p.Arg253Ter Pathogenic/Likely pathogenic ★★ same condition
- DNAAF5 p.Cys500Phe Pathogenic/Likely pathogenic ★★ ⚠ same condition
- DNAAF5 p.Leu795Pro Pathogenic/Likely pathogenic ★★ same condition
- DNAAF5 p.Trp309Ter Pathogenic/Likely pathogenic ★★ same condition
- DNAAF5 c.780+6T>A Uncertain significance ★★ same condition
- DNAAF5 c.905+4C>T Uncertain significance ★★ 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/dnaaf5-p-gln540 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown