ACER3 p.Glu262=
c.786G>A · rs201953460 · VCV1576430
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0137%, 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 3.3 | GERP -0.13, phastCons 1 |
| Overall | ||
| CADD | 7.252 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0137%
European (non-Finnish) · 162/1,179,938 alleles
Filtering AF
0.012%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0113%
Overall
0.0105%
170/1,613,526 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0137% | 7,284 |
| African / African-American | 0.00534% | 18,727 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,827 |
| Finnishnot grpmax-eligible | 0.00157% | 63,672 |
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
- ACER3
- Protein
- p.Glu262=
- Coding
- c.786G>A
- MANE Select
- NM_018367
- dbSNP
- rs201953460
- Type
- single nucleotide variant
- Location
- chr11:77020309 (GRCh38)
- Gene constraint
- LOEUF 0.815 · pLI 0.30 (gnomAD)
- Structure
- AlphaFold pLDDT 93.23 · 2 PDB
Similar variants
- ACER3 p.Ala2Pro Uncertain significance ★★ ⚠ same type
- ACER3 p.Ala4Thr Uncertain significance ★★ ⚠ same type
- ACER3 p.Arg62Gln Uncertain significance ★★ ⚠ same type
- ACER3 p.Gly12Asp Uncertain significance ★★ ⚠ same type
- ACER3 p.Ile97Leu Uncertain significance ★★ ⚠ same type
- ACER3 p.Val206Ile Uncertain significance ★★ ⚠ same type
- ACER3 c.214+19C>G Benign ★★ same type
- ACER3 c.320+14A>C Benign ★★ 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/acer3-p-glu262 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown