DDX54 p.Phe246=
c.738C>T · VCV3500654
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0223%, eas)
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 -3.3 | GERP -3.9 |
| Overall | ||
| CADD | 4.621 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0223%
East Asian · 10/44,892 alleles
Filtering AF
0.012%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00916%
Overall
0.00266%
43/1,614,000 alleles · ultra-rare
exomes 38/1,461,866 · genomes 5/152,134 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0223% | 4,489 |
| South Asian | 0.00329% | 30,361 |
| European (non-Finnish) | 0.00246% | 40,691 |
| Finnishnot grpmax-eligible | 0.00156% | 64,010 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- DDX54
- Protein
- p.Phe246=
- Coding
- c.738C>T
- MANE Select
- NM_024072
- Type
- single nucleotide variant
- Location
- chr12:113176854 (GRCh38)
- Gene constraint
- LOEUF 0.821 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.89 · 6 PDB
- Residue 246
- the helicase atp-binding domain; a β-strand
Similar variants
- DDX54 p.Gln608His Uncertain significance ★★ ⚠ same type
- DDX54 p.Ser71Leu Uncertain significance ★★ ⚠ same type
- DDX54 c.937-5C>T Benign/Likely benign ★★ same type
- DDX54 p.Asp132= Benign ★★ same type
- DDX54 p.Ala148Thr Uncertain significance ★ ⚠ same type
- DDX54 p.Ala169Ser Uncertain significance ★ ⚠ same type
- DDX54 p.Ala169Val Uncertain significance ★ ⚠ same type
- DDX54 p.Ala258Thr Uncertain significance ★ ⚠ same type
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/ddx54-p-phe246 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown