ABHD12 p.Ser23=
c.69C>T · rs1054346768 · VCV2164200
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0454%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Overall | ||
| CADD | 12.09 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0454%
Middle Eastern · 2/4,404 alleles
Filtering AF
0.00804%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00337%
Overall
0.00165%
24/1,453,100 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0454% | 2,202 |
| Admixed American | 0.00754% | 13,256 |
| African / African-American | 0.00445% | 22,481 |
| European (non-Finnish) | 0.00144% | 69,228 |
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
- ABHD12
- Protein
- p.Ser23=
- Coding
- c.69C>T
- MANE Select
- NM_001042472
- dbSNP
- rs1054346768
- Type
- single nucleotide variant
- Location
- chr20:25390635 (GRCh38)
- Gene constraint
- LOEUF 0.967 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 85.60
Similar variants
- ABHD12 p.Ser23Cys Uncertain significance ★ ⚠ same residue
- ABHD12 p.Ser23Phe Uncertain significance ★ same residue
- ABHD12 p.Ser23del Uncertain significance ★★ same residue
- ABHD12 c.1029+1G>T Likely pathogenic ★★ same type
- ABHD12 p.Arg262Ter Pathogenic ★★ same type
- ABHD12 p.Arg292Ter Pathogenic/Likely pathogenic ★★ same type
- ABHD12 p.Arg352Ter Pathogenic ★★ same type
- ABHD12 p.Arg355Ter 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/abhd12-p-ser23 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown