ATF6 p.Ser196=
c.588C>T · rs1477922028 · VCV1568980
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0039%, 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 -0.1 | GERP 0.11, phastCons 0.053 |
| Overall | ||
| CADD | 9.405 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0039%
European (non-Finnish) · 46/1,180,002 alleles
Filtering AF
0.00299%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00267%
Overall
0.00285%
46/1,614,010 alleles · very rare
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.Ser196=
- Coding
- c.588C>T
- MANE Select
- NM_007348
- dbSNP
- rs1477922028
- Type
- single nucleotide variant
- Location
- chr1:161792227 (GRCh38)
- Gene constraint
- LOEUF 0.882 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 56.09
Similar variants
- 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
- ATF6 p.Arg376Ter Pathogenic ★★ same type
- ATF6 p.Gln237Ter 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-ser196 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown