ALAD p.Ser92=
c.276C>T · rs577688753 · VCV744668
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0312%, eas)
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 -3.3 | GERP -4.2 |
| Overall | ||
| CADD | 5.709 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0312%
East Asian · 14/44,878 alleles
Filtering AF
0.0188%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0151%
Overall
0.00366%
59/1,614,106 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0312% | 3,206 |
| Middle Eastern | 0.0165% | 6,048 |
| South Asian | 0.0121% | 8,280 |
| European (non-Finnish) | 0.00263% | 38,065 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,506 |
| African / African-American | 0.00133% | 75,042 |
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
- ALAD
- Protein
- p.Ser92=
- Coding
- c.276C>T
- MANE Select
- NM_000031
- dbSNP
- rs577688753
- Type
- single nucleotide variant
- Location
- chr9:113390919 (GRCh38)
- Gene constraint
- LOEUF 0.63 · pLI 0.10 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 96.34 · 4 PDB
- Residue 92
- an α-helix
Similar variants
- ALAD p.Gly133Arg Likely pathogenic ★★ same type
- ALAD c.*127C>T Uncertain significance ★★ same type
- ALAD c.*363G>A Uncertain significance ★★ same type
- ALAD p.Ala93Thr Uncertain significance ★★ ⚠ same type
- ALAD p.Arg147Cys Uncertain significance ★★ ⚠ same type
- ALAD p.Arg174His Uncertain significance ★★ ⚠ same type
- ALAD p.Arg17Gln Uncertain significance ★★ ⚠ same type
- ALAD p.Arg222Cys 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/alad-p-ser92 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown