ALPG p.Leu8=
c.24C>T · rs61730279 · VCV778048
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.64%, afr)
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 1.2 | GERP -3.7, phastCons 1 |
| Overall | ||
| CADD | 3.516 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.64%
African / African-American · 3,474/74,916 alleles
Filtering AF
4.51%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.46%
Overall
0.253%
4,073/1,612,630 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.64% | 22 |
| Admixed American | 0.354% | 283 |
| Remaining individualsnot grpmax-eligible | 0.309% | 323 |
| Middle Eastern | 0.203% | 493 |
| European (non-Finnish) | 0.0149% | 6,703 |
| South Asian | 0.00661% | 15,137 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,548 |
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
- ALPG
- Protein
- p.Leu8=
- Coding
- c.24C>T
- MANE Select
- NM_031313
- dbSNP
- rs61730279
- Type
- single nucleotide variant
- Location
- chr2:232406918 (GRCh38)
- Gene constraint
- LOEUF 1.103 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.31
Similar variants
- ALPG p.Leu8Phe Uncertain significance ★ ⚠ same residue
- ALPG p.Arg498Pro Benign ★★ same type
- ALPG p.Gly230= Benign ★★ same type
- ALPG p.Gly500Asp Likely benign ★★ same type
- ALPG p.His172= Benign/Likely benign ★★ same type
- ALPG p.Pro228Arg Benign ★★ ⚠ same type
- ALPG p.Pro94Ser Benign ★★ ⚠ same type
- ALPG p.Ser150= Benign ★★ 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/alpg-p-leu8 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown