ABHD5 p.Glu15=
c.45G>A · VCV3665333
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0268%, 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 -2.6, phastCons 1 |
| Overall | ||
| CADD | 4.817 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0268%
South Asian · 23/85,862 alleles
Filtering AF
0.0183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0155%
Overall
0.00173%
27/1,558,910 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0268% | 3,733 |
| East Asian | 0.0026% | 38,430 |
| Remaining individualsnot grpmax-eligible | 0.00167% | 59,924 |
| African / African-American | 0.00142% | 70,530 |
| European (non-Finnish) | 8.66e-05% | 1,154,698 |
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
- ABHD5
- Protein
- p.Glu15=
- Coding
- c.45G>A
- MANE Select
- NM_016006
- Type
- single nucleotide variant
- Location
- chr3:43691037 (GRCh38)
- Gene constraint
- LOEUF 0.922 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.62
Similar variants
- ABHD5 p.Glu15Lys Uncertain significance ★★ ⚠ same residue
- ABHD5 p.Glu15Gly Uncertain significance ★ ⚠ same residue
- ABHD5 c.133+1G>A Likely pathogenic ★★ same type
- ABHD5 c.507-1G>A Pathogenic ★★ same type
- ABHD5 p.Arg184Ter Pathogenic ★★ same type
- ABHD5 p.Arg234Ter Pathogenic ★★ same type
- ABHD5 p.Arg280Ter Pathogenic/Likely pathogenic ★★ same type
- ABHD5 p.Glu336Ter Pathogenic/Likely 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/abhd5-p-glu15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown