ALPG p.Ala51=
c.153C>T · rs61730280 · VCV712452
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.48%, 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 -20 | GERP -3.7 |
| Overall | ||
| CADD | 0.127 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.48%
African / African-American · 2,607/75,008 alleles
Filtering AF
3.36%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.32%
Overall
0.177%
2,857/1,613,936 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.48% | 29 |
| Admixed American | 0.172% | 582 |
| Remaining individualsnot grpmax-eligible | 0.171% | 584 |
| Middle Eastern | 0.033% | 3,029 |
| South Asian | 0.00989% | 10,108 |
| European (non-Finnish) | 0.00237% | 42,143 |
| Finnishnot grpmax-eligible | 0.00156% | 63,992 |
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.Ala51=
- Coding
- c.153C>T
- MANE Select
- NM_031313
- dbSNP
- rs61730280
- Type
- single nucleotide variant
- Location
- chr2:232407142 (GRCh38)
- Gene constraint
- LOEUF 1.103 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.31
Similar variants
- 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.Leu8= 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-ala51 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown