SI p.Thr317=
c.951C>T · rs144637860 · VCV2068268
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0187%, 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 0.82 | GERP -1.1, phastCons 0.024 |
| Overall | ||
| CADD | 11.34 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0187%
African / African-American · 14/74,692 alleles
Filtering AF
0.0112%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00907%
Overall
0.00274%
44/1,605,078 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0187% | 5,335 |
| Middle Eastern | 0.0167% | 5,976 |
| East Asian | 0.0134% | 7,436 |
| Admixed American | 0.00836% | 11,964 |
| Finnishnot grpmax-eligible | 0.00313% | 31,968 |
| European (non-Finnish) | 0.00136% | 73,287 |
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.Thr317=
- Coding
- c.951C>T
- MANE Select
- NM_001041
- dbSNP
- rs144637860
- Type
- single nucleotide variant
- Location
- chr3:165062440 (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 317
- the 'isomaltase' region; a β-strand
Similar variants
- 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
- SI c.4927-1G>A 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-thr317 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown