SI p.Ala893=
c.2679G>A · rs751964959 · VCV1593051
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0161%, 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 -1.3 | GERP -3.3 |
| Overall | ||
| CADD | 4.506 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0161%
African / African-American · 12/74,536 alleles
Filtering AF
0.00926%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00725%
Overall
0.00267%
43/1,608,914 alleles · ultra-rare
exomes 32/1,457,804 · genomes 11/151,110 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0161% | 6,211 |
| Admixed American | 0.0101% | 9,929 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,147 |
| South Asian | 0.0022% | 45,453 |
| European (non-Finnish) | 0.0017% | 58,840 |
| Finnishnot grpmax-eligible | 0.00157% | 63,780 |
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
- SI
- Protein
- p.Ala893=
- Coding
- c.2679G>A
- MANE Select
- NM_001041
- dbSNP
- rs751964959
- Type
- single nucleotide variant
- Location
- chr3:165032579 (GRCh38)
- Gene constraint
- LOEUF 1.009 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 93.86 · 2 PDB
- Residue 893
- the 'isomaltase' region; a β-strand
Similar variants
- SI p.Ala893Val Conflicting classifications of pathogenicity ★ ⚠ same residue
- SI c.2426+1G>A Likely pathogenic ★★ same type
- SI c.2737-2A>G Likely pathogenic ★★ same type
- SI c.2893-1G>A Likely pathogenic ★★ same type
- SI c.3099+1G>C Likely pathogenic ★★ same type
- SI c.3521-1G>T Likely pathogenic ★★ same type
- SI c.373+1G>A Likely pathogenic ★★ same type
- SI c.4575+2T>C Likely 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/si-p-ala893 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown