ALAD p.Val153=
c.459G>A · rs766413112 · VCV725318
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00653%, nfe)
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 0.28 | GERP -3.5, phastCons 0.98 |
| Overall | ||
| CADD | 5.932 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00653%
European (non-Finnish) · 77/1,180,026 alleles
Filtering AF
0.0053%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0049%
Overall
0.00551%
89/1,613,968 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00653% | 15,325 |
| South Asian | 0.00549% | 18,218 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,819 |
| African / African-American | 0.004% | 24,980 |
| Admixed American | 0.00167% | 60,012 |
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.Val153=
- Coding
- c.459G>A
- MANE Select
- NM_000031
- dbSNP
- rs766413112
- Type
- single nucleotide variant
- Location
- chr9:113390615 (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 153
- a UniProt-annotated variant site (in ahepp; about 95% octamer; about 40% residual activity); 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-val153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown