ATF6B p.Leu29=
c.85C>T · rs572464548 · VCV3130816
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0495%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.64 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.4 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 13.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0495%
Middle Eastern · 3/6,056 alleles
Filtering AF
0.0141%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0112%
Overall
0.0031%
50/1,613,120 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0495% | 2,019 |
| Admixed American | 0.0233% | 4,283 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,498 |
| African / African-American | 0.004% | 24,977 |
| European (non-Finnish) | 0.00212% | 47,198 |
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
- ATF6B
- Protein
- p.Leu29=
- Coding
- c.85C>T
- MANE Select
- NM_004381
- dbSNP
- rs572464548
- Type
- single nucleotide variant
- Location
- chr6:32128123 (GRCh38)
- Gene constraint
- LOEUF 0.752 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 55.31
- Residue 29
- the 'transcription activation' region
Similar variants
- ATF6B p.His601Leu Likely benign ★★ same type
- ATF6B p.Ala11Thr Uncertain significance ★ ⚠ same type
- ATF6B p.Ala236Asp Uncertain significance ★ ⚠ same type
- ATF6B p.Ala2Thr Uncertain significance ★ ⚠ same type
- ATF6B p.Ala2Val Uncertain significance ★ ⚠ same type
- ATF6B p.Ala422Val Uncertain significance ★ ⚠ same type
- ATF6B p.Ala686Glu Uncertain significance ★ ⚠ same type
- ATF6B p.Ala686Val 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/atf6b-p-leu29 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown