ATF6 p.Ile534=
c.1602C>T · rs201527618 · VCV713560
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0237%, 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 4.6 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 18.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0237%
European (non-Finnish) · 275/1,159,242 alleles
Filtering AF
0.0214%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0205%
Overall
0.0191%
300/1,569,638 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0237% | 4,215 |
| Remaining individualsnot grpmax-eligible | 0.0182% | 5,488 |
| Admixed American | 0.0169% | 5,908 |
| African / African-American | 0.00412% | 24,291 |
| Finnishnot grpmax-eligible | 0.0032% | 31,282 |
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
- ATF6
- Protein
- p.Ile534=
- Coding
- c.1602C>T
- MANE Select
- NM_007348
- dbSNP
- rs201527618
- Type
- single nucleotide variant
- Location
- chr1:161860275 (GRCh38)
- Gene constraint
- LOEUF 0.882 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 56.09
- Residue 534
- the 'interaction with thbs4' region
Similar variants
- ATF6 p.Ile534Val Uncertain significance ★ ⚠ same residue
- ATF6 p.Ile534fs Likely pathogenic ★ same residue
- ATF6 c.1533+1G>C Pathogenic ★★ same type
- ATF6 c.160-1G>A Likely pathogenic ★★ same type
- ATF6 c.484+1G>A Likely pathogenic ★★ same type
- ATF6 c.484+1G>T Likely pathogenic ★★ same type
- ATF6 c.82+5G>T Pathogenic ★★ same type
- ATF6 p.Arg324Cys Pathogenic ★★ 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/atf6-p-ile534 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown