ATAD1 p.Phe26=
c.78T>C · rs780106325 · VCV1635371
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00153%, 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 4.7 | GERP -0.57, phastCons 1 |
| Overall | ||
| CADD | 13.43 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00153%
European (non-Finnish) · 18/1,179,186 alleles
Filtering AF
0.000954%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000787%
Overall
0.00118%
19/1,612,224 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00153% | 65,510 |
| African / African-American | 0.00134% | 74,870 |
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.Phe26=
- Coding
- c.78T>C
- MANE Select
- NM_001321967
- dbSNP
- rs780106325
- Type
- single nucleotide variant
- Location
- chr10:87814522 (GRCh38)
- Gene constraint
- LOEUF 0.505 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 84.05 · 2 PDB
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-phe26 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown