ABHD12 p.Arg2=
c.6G>A · VCV3716777
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00302%, afr)
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 3.5 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 16.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00302%
African / African-American · 2/66,240 alleles
Filtering AF
0.000501%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000188%
Overall
0.000287%
4/1,391,668 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00302% | 33,120 |
| European (non-Finnish) | 0.000187% | 535,409 |
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.Arg2=
- Coding
- c.6G>A
- MANE Select
- NM_001042472
- Type
- single nucleotide variant
- Location
- chr20:25390698 (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.Arg2Lys 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
- ABHD12 c.620-3C>T Uncertain significance ★★ same type
- ABHD12 c.867+2C>T Uncertain significance ★★ 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-arg2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown