ATAD3A p.Ser162=
c.486C>T · rs138279686 · VCV733718
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.271%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.041 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -8.7 | GERP -2.4 |
| Overall | ||
| CADD | 1.327 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.271%
African / African-American · 203/75,044 alleles
Filtering AF
0.24%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.228%
Overall
0.0155%
250/1,614,116 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.271% | 370 |
| Admixed American | 0.0516% | 1,936 |
| East Asian | 0.0111% | 8,976 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,502 |
| European (non-Finnish) | 0.000508% | 196,663 |
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.Ser162=
- Coding
- c.486C>T
- MANE Select
- NM_001170535
- dbSNP
- rs138279686
- Type
- single nucleotide variant
- Location
- chr1:1518962 (GRCh38)
- Gene constraint
- LOEUF 0.861 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.35
Similar variants
- 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
- ATAD3A p.Ala462Thr 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-ser162 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown