ATAD1 p.Pro260=
c.780T>A · rs114428714 · VCV1605669
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.375%, afr)
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 0.47 | GERP -3.5, phastCons 0.9 |
| Overall | ||
| CADD | 10.22 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.375%
African / African-American · 281/75,016 alleles
Filtering AF
0.339%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.325%
Overall
0.02%
322/1,612,352 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.375% | 267 |
| Middle Eastern | 0.0496% | 2,017 |
| Remaining individualsnot grpmax-eligible | 0.0288% | 3,466 |
| Admixed American | 0.025% | 3,998 |
| European (non-Finnish) | 0.000424% | 235,746 |
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
- ATAD1
- Protein
- p.Pro260=
- Coding
- c.780T>A
- MANE Select
- NM_001321967
- dbSNP
- rs114428714
- Type
- single nucleotide variant
- Location
- chr10:87770952 (GRCh38)
- Gene constraint
- LOEUF 0.505 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 84.05 · 2 PDB
Similar variants
- ATAD1 p.Pro260Ala Uncertain significance ★ ⚠ same residue
- ATAD1 p.Glu276Ter Pathogenic/Likely pathogenic ★★ same type
- ATAD1 p.Ala339Val Uncertain significance ★★ ⚠ same type
- ATAD1 p.Ala55Thr Uncertain significance ★★ ⚠ same type
- ATAD1 p.Arg338Gln Uncertain significance ★★ ⚠ same type
- ATAD1 p.Arg338Trp Uncertain significance ★★ ⚠ same type
- ATAD1 p.Asp164Asn Uncertain significance ★★ ⚠ same type
- ATAD1 p.Gln185Glu 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/atad1-p-pro260 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown