ATAD3A p.Phe409=
c.1227T>C · rs575132198 · VCV1675335
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.076%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.321 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -3.9 | GERP -3.1 |
| Overall | ||
| CADD | 0.066 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.076%
African / African-American · 57/75,012 alleles
Filtering AF
0.0601%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0545%
Overall
0.00626%
101/1,613,846 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.076% | 1,316 |
| Admixed American | 0.0167% | 6,001 |
| Middle Eastern | 0.0166% | 6,042 |
| Finnishnot grpmax-eligible | 0.00626% | 15,985 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,831 |
| South Asian | 0.0022% | 45,529 |
| European (non-Finnish) | 0.00203% | 49,164 |
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
- ATAD3A
- Protein
- p.Phe409=
- Coding
- c.1227T>C
- MANE Select
- NM_001170535
- dbSNP
- rs575132198
- Type
- single nucleotide variant
- Location
- chr1:1525252 (GRCh38)
- Gene constraint
- LOEUF 0.861 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.35
- Residue 409
- a UniProt-annotated variant site (in phrinl)
Similar variants
- ATAD3A p.Phe409Leu Uncertain significance ★ ⚠ same residue
- ATAD3A c.1266+1G>A Likely pathogenic ★★ same type
- ATAD3A c.384+1G>A Likely pathogenic ★★ same type
- ATAD3A p.Arg528Gln Likely pathogenic ★★ ⚠ same type
- ATAD3A p.Arg528Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
- ATAD3A c.282+5G>A Uncertain significance ★★ same type
- ATAD3A c.283-3C>T Uncertain significance ★★ same type
- ATAD3A c.385-3C>G 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/atad3a-p-phe409 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown