ATAD3A p.Ala541=
c.1623G>A · rs147003509 · VCV2638041
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0331%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.01 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -12 | GERP -2.5 |
| Overall | ||
| CADD | 0.129 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0331%
Middle Eastern · 2/6,038 alleles
Filtering AF
0.013%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0123%
Overall
0.0145%
234/1,612,958 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0331% | 3,019 |
| Remaining individualsnot grpmax-eligible | 0.024% | 4,165 |
| Admixed American | 0.0217% | 4,614 |
| South Asian | 0.0187% | 5,356 |
| European (non-Finnish) | 0.0148% | 6,742 |
| African / African-American | 0.00936% | 10,688 |
| East Asian | 0.00669% | 14,943 |
| Finnishnot grpmax-eligible | 0.00315% | 31,708 |
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.Ala541=
- Coding
- c.1623G>A
- MANE Select
- NM_001170535
- dbSNP
- rs147003509
- Type
- single nucleotide variant
- Location
- chr1:1533934 (GRCh38)
- Gene constraint
- LOEUF 0.861 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.35
- Residue 541
- a UniProt-annotated variant site (in phrinl)
Similar variants
- ATAD3A p.Ala541Val 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-ala541 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown