SKIC2 p.Pro301=
c.903C>T · rs763616683 · VCV2755787
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
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 0.12 | GERP -3.5, phastCons 0.94 |
| Overall | ||
| CADD | 9.253 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,036 alleles
Overall
6.2e-05%
1/1,612,510 alleles · very rare
exomes 1/1,460,174 · genomes 0/152,336 · joint denominator
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
- SKIC2
- Protein
- p.Pro301=
- Coding
- c.903C>T
- MANE Select
- NM_006929
- dbSNP
- rs763616683
- Type
- single nucleotide variant
- Location
- chr6:31961660 (GRCh38)
- Structure
- AlphaFold pLDDT 81.32 · 11 PDB
Similar variants
- SKIC2 p.Pro301Ser Uncertain significance ★ ⚠ same residue
- SKIC2 c.1404-2A>G Pathogenic/Likely pathogenic ★★ same type
- SKIC2 c.2203-1G>A Pathogenic/Likely pathogenic ★★ same type
- SKIC2 c.2341-1G>T Pathogenic/Likely pathogenic ★★ same type
- SKIC2 c.2341-2A>G Pathogenic/Likely pathogenic ★★ same type
- SKIC2 c.470-1G>A Likely pathogenic ★★ same type
- SKIC2 p.Arg1063Ter Pathogenic ★★ same type
- SKIC2 p.Arg253Ter Pathogenic/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/skic2-p-pro301 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown