SKI p.Cys112=
c.336C>T · rs752031916 · VCV1126478
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0198%, sas)
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 0.81 | GERP -2.8, phastCons 1 |
| Overall | ||
| CADD | 13.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0198%
South Asian · 18/91,090 alleles
Filtering AF
0.0127%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0105%
Overall
0.00124%
20/1,609,938 alleles · ultra-rare
exomes 19/1,457,780 · genomes 1/152,158 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0198% | 5,061 |
| European (non-Finnish) | 0.00017% | 589,943 |
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.Cys112=
- Coding
- c.336C>T
- MANE Select
- NM_003036
- dbSNP
- rs752031916
- Type
- single nucleotide variant
- Location
- chr1:2229102 (GRCh38)
- Gene constraint
- LOEUF 0.809 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 67.18 · 4 PDB
- Residue 112
- a β-strand
Similar variants
- 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
- SKI p.Gly34Val Pathogenic ★★ ⚠ same condition
- SKI p.Leu32Val Pathogenic ★★ ⚠ same condition
- SKI p.Pro35Ser 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-cys112 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown