ATAD1 p.Ser160=
c.480G>A · rs751265064 · VCV1651850
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00729%, nfe)
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 -1.7 | GERP -3.8 |
| Overall | ||
| CADD | 6.405 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00729%
European (non-Finnish) · 86/1,179,916 alleles
Filtering AF
0.00604%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00557%
Overall
0.0057%
92/1,613,492 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00729% | 13,720 |
| South Asian | 0.0033% | 30,345 |
| East Asian | 0.00223% | 44,874 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,432 |
| African / African-American | 0.00134% | 74,888 |
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.Ser160=
- Coding
- c.480G>A
- MANE Select
- NM_001321967
- dbSNP
- rs751265064
- Type
- single nucleotide variant
- Location
- chr10:87784573 (GRCh38)
- Gene constraint
- LOEUF 0.505 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 84.05 · 2 PDB
- Residue 160
- a turn
Similar variants
- 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
- ATAD1 p.Gln352Pro 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-ser160 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown