ABHD5 p.Glu7=
c.21G>A · rs780461803 · VCV2176389
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0168%, 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 2.7 | GERP 0.27, phastCons 1 |
| Overall | ||
| CADD | 10.54 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0168%
Middle Eastern · 1/5,936 alleles
Filtering AF
0.00471%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00317%
Overall
0.00153%
24/1,568,190 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0168% | 5,936 |
| Admixed American | 0.0109% | 9,163 |
| Remaining individualsnot grpmax-eligible | 0.00166% | 60,392 |
| African / African-American | 0.00141% | 70,690 |
| European (non-Finnish) | 0.00129% | 77,337 |
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.Glu7=
- Coding
- c.21G>A
- MANE Select
- NM_016006
- dbSNP
- rs780461803
- Type
- single nucleotide variant
- Location
- chr3:43691013 (GRCh38)
- Gene constraint
- LOEUF 0.922 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.62
- Residue 7
- a UniProt-annotated variant site (in cds)
Similar variants
- ABHD5 p.Glu7Lys Likely benign ★ ⚠ 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
- ABHD5 p.Arg56His 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/abhd5-p-glu7 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown