AP1G1 p.His211=
c.633T>C · VCV4681344
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.23%, sas)
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 8.1 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 9.299 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.23%
South Asian · 209/91,040 alleles
Filtering AF
0.204%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.194%
Overall
0.0174%
280/1,613,352 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.23% | 436 |
| Middle Eastern | 0.0992% | 1,008 |
| Remaining individualsnot grpmax-eligible | 0.0272% | 3,675 |
| European (non-Finnish) | 0.00399% | 25,094 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,580 |
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
- AP1G1
- Protein
- p.His211=
- Coding
- c.633T>C
- MANE Select
- NM_001128
- Type
- single nucleotide variant
- Location
- chr16:71769632 (GRCh38)
- Gene constraint
- LOEUF 0.113 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.56 · 1 PDB
Similar variants
- AP1G1 p.Arg15Trp Likely pathogenic ★★ same type
- AP1G1 p.Arg416Ter Pathogenic ★★ same type
- AP1G1 p.Arg46Ter Uncertain significance ★★ same type
- AP1G1 p.Gly120Val Uncertain significance ★★ ⚠ same type
- AP1G1 p.His575Asp Uncertain significance ★★ ⚠ same type
- AP1G1 p.Ile769Val Uncertain significance ★★ ⚠ same type
- AP1G1 c.2367+12A>G Benign ★★ same type
- AP1G1 p.Thr179Ser Likely 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/ap1g1-p-his211 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown