Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.1%, eas)
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 2.5 | GERP -1.1, phastCons 1 |
| Overall | ||
| CADD | 12.79 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.1%
East Asian · 1,838/44,866 alleles
Filtering AF
3.94%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.88%
Overall
0.139%
2,244/1,614,114 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 4.1% | 24 |
| Remaining individualsnot grpmax-eligible | 0.19% | 525 |
| South Asian | 0.178% | 562 |
| Middle Eastern | 0.0165% | 6,062 |
| African / African-American | 0.012% | 8,337 |
| Admixed American | 0.0117% | 8,574 |
| European (non-Finnish) | 0.00907% | 11,028 |
| Finnishnot grpmax-eligible | 0.00156% | 64,026 |
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
- AUTS2
- Protein
- p.Pro862=
- Coding
- c.2586G>A
- MANE Select
- NM_015570
- dbSNP
- rs3750174
- Type
- single nucleotide variant
- Location
- chr7:70789802 (GRCh38)
- Gene constraint
- LOEUF 0.232 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 41.89
- Residue 862
- the 'disordered' region
Similar variants
- AUTS2 p.Pro862Leu Uncertain significance ★ same residue
- AUTS2 c.2005-1G>C Likely pathogenic ★★ same type
- AUTS2 c.742+1G>A Pathogenic ★★ same type
- AUTS2 p.Arg126Ter Pathogenic/Likely pathogenic ★★ same type
- AUTS2 p.Arg152Ter Pathogenic/Likely pathogenic ★★ same type
- AUTS2 p.Arg316Ter Pathogenic/Likely pathogenic ★★ same type
- AUTS2 p.Arg495Ter Pathogenic ★★ same type
- AUTS2 p.Arg798Ter Pathogenic ★★ 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/auts2-p-pro862 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown