ATAD3B p.Phe459=
c.1377C>T · VCV3770406
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.708%, 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 -12 | GERP -2.8 |
| Overall | ||
| CADD | 0.075 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.708%
European (non-Finnish) · 8,351/1,179,666 alleles
Filtering AF
0.695%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.69%
Overall
0.582%
9,396/1,613,104 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.708% | 141 |
| Finnishnot grpmax-eligible | 0.509% | 196 |
| Remaining individualsnot grpmax-eligible | 0.498% | 201 |
| Admixed American | 0.232% | 432 |
| South Asian | 0.204% | 489 |
| Middle Eastern | 0.148% | 674 |
| African / African-American | 0.0986% | 1,014 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0101% | 9,869 |
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
- ATAD3B
- Protein
- p.Phe459=
- Coding
- c.1377C>T
- MANE Select
- NM_031921
- Type
- single nucleotide variant
- Location
- chr1:1490296 (GRCh38)
- Gene constraint
- LOEUF 1.152 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.69
Similar variants
- ATAD3B c.445-11C>G Benign ★★ same type
- ATAD3B p.Ala71Ser Benign ★★ same type
- ATAD3B p.Cys641= Benign ★★ same type
- ATAD3B p.Phe274Tyr Benign/Likely benign ★★ same type
- ATAD3B p.Pro639Ser Benign ★★ same type
- ATAD3B p.Val259= Likely benign ★★ same type
- ATAD3B c.1090-3C>T Uncertain significance ★ same type
- ATAD3B c.325C>T 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/atad3b-p-phe459 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown