ABHD12 p.Thr43=
c.129G>A · rs757700898 · VCV1016835
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0278%, sas)
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 -1.8 | GERP -0.68 |
| Overall | ||
| CADD | 7.406 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0278%
South Asian · 22/79,216 alleles
Filtering AF
0.0187%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0159%
Overall
0.00872%
129/1,479,512 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0278% | 3,601 |
| European (non-Finnish) | 0.00891% | 11,222 |
| Remaining individualsnot grpmax-eligible | 0.00703% | 14,233 |
| African / African-American | 0.00293% | 34,084 |
| Admixed American | 0.00226% | 44,232 |
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.Thr43=
- Coding
- c.129G>A
- MANE Select
- NM_001042472
- dbSNP
- rs757700898
- Type
- single nucleotide variant
- Location
- chr20:25390575 (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.Thr43Arg Uncertain significance ★★ ⚠ same residue
- ABHD12 p.Thr43Met Uncertain significance ★★ ⚠ same residue
- ABHD12 p.Thr43fs Pathogenic/Likely pathogenic ★★ 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-thr43 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown