SI p.Pro1151=
c.3453C>T · rs151179622 · VCV1600117
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0534%, 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 -0.35 | GERP 0.41, phastCons 0.009 |
| Overall | ||
| CADD | 5.274 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0534%
African / African-American · 40/74,876 alleles
Filtering AF
0.0402%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0357%
Overall
0.00329%
53/1,609,774 alleles · ultra-rare
exomes 22/1,457,834 · genomes 31/151,940 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0534% | 1,872 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,184 |
| South Asian | 0.0022% | 45,506 |
| Admixed American | 0.00167% | 59,914 |
| European (non-Finnish) | 0.00068% | 147,046 |
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.Pro1151=
- Coding
- c.3453C>T
- MANE Select
- NM_001041
- dbSNP
- rs151179622
- Type
- single nucleotide variant
- Location
- chr3:165018037 (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 1151
- the 'sucrase' region
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-pro1151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown