SKI p.Pro728=
c.2184G>A · rs543584871 · VCV1981641
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00288%, afr)
Conditions
1
Shprintzen-Goldberg syndrome
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 0.23 | GERP -3.8, phastCons 0.98 |
| Overall | ||
| CADD | 3.629 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00288%
African / African-American · 2/69,376 alleles
Filtering AF
0.000478%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000219%
Overall
0.000727%
11/1,513,356 alleles · very rare
exomes 9/1,361,304 · genomes 2/152,052 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00288% | 34,688 |
| Remaining individualsnot grpmax-eligible | 0.00171% | 58,426 |
| European (non-Finnish) | 0.000705% | 141,818 |
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
- SKI
- Protein
- p.Pro728=
- Coding
- c.2184G>A
- MANE Select
- NM_003036
- dbSNP
- rs543584871
- Type
- single nucleotide variant
- Location
- chr1:2306762 (GRCh38)
- Gene constraint
- LOEUF 0.809 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 67.18 · 4 PDB
Similar variants
- SKI p.Pro728Ala Uncertain significance ★★ ⚠ same residue
- SKI p.Pro728Arg Uncertain significance ★ ⚠ same residue
- SKI p.Pro728Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- SKI p.Gly116Glu Pathogenic/Likely pathogenic ★★ same condition
- SKI p.Gly117Arg Pathogenic/Likely pathogenic ★★ same condition
- SKI p.Gly117Ser Pathogenic/Likely pathogenic ★★ same condition
- SKI p.Gly34Cys Pathogenic ★★ ⚠ same condition
- SKI p.Gly34Ser Pathogenic/Likely pathogenic ★★ ⚠ same condition
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/ski-p-pro728 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown