ALPG p.His466=
c.1398C>T · rs756069446 · VCV2652007
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00935%, 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 0.89 | GERP 0.39, phastCons 1 |
| Overall | ||
| CADD | 9.189 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00935%
African / African-American · 7/74,892 alleles
Filtering AF
0.00437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00309%
Overall
0.000807%
13/1,611,590 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00935% | 10,699 |
| Remaining individualsnot grpmax-eligible | 0.00802% | 12,470 |
| European (non-Finnish) | 8.48e-05% | 1,179,306 |
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.His466=
- Coding
- c.1398C>T
- MANE Select
- NM_031313
- dbSNP
- rs756069446
- Type
- single nucleotide variant
- Location
- chr2:232409671 (GRCh38)
- Gene constraint
- LOEUF 1.103 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.31
Similar variants
- ALPG p.His466Tyr 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.Leu8= Benign ★★ same type
- ALPG p.Pro228Arg Benign ★★ ⚠ same type
- ALPG p.Pro94Ser 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-his466 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown