ACER3 p.Thr124=
c.372C>T · rs370822453 · VCV2718738
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.068%, mid)
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 -0.45 | GERP -3.4 |
| Overall | ||
| CADD | 4.925 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.068%
Middle Eastern · 4/5,882 alleles
Filtering AF
0.0324%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0282%
Overall
0.00249%
39/1,567,462 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.068% | 1,470 |
| African / African-American | 0.0445% | 2,246 |
| Remaining individualsnot grpmax-eligible | 0.0033% | 30,299 |
| European (non-Finnish) | 8.59e-05% | 1,164,702 |
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.Thr124=
- Coding
- c.372C>T
- MANE Select
- NM_018367
- dbSNP
- rs370822453
- Type
- single nucleotide variant
- Location
- chr11:76985694 (GRCh38)
- Gene constraint
- LOEUF 0.815 · pLI 0.30 (gnomAD)
- Structure
- AlphaFold pLDDT 93.23 · 2 PDB
- Residue 124
- an α-helix
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-thr124 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown