ATAD1 p.Ser245=
c.735G>A · rs770242821 · VCV1629009
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -12 | GERP -3 |
| Overall | ||
| CADD | 1.519 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,078 alleles
Filtering AF
0.00215%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00191%
Overall
0.00254%
41/1,613,274 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,078 |
| European (non-Finnish) | 0.00297% | 33,704 |
| South Asian | 0.0022% | 45,510 |
| Admixed American | 0.00167% | 59,948 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,442 |
| African / African-American | 0.00134% | 74,846 |
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.Ser245=
- Coding
- c.735G>A
- MANE Select
- NM_001321967
- dbSNP
- rs770242821
- Type
- single nucleotide variant
- Location
- chr10:87770997 (GRCh38)
- Gene constraint
- LOEUF 0.505 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 84.05 · 2 PDB
Similar variants
- ATAD1 p.Ser245Leu 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-ser245 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown