PCGF2 p.Ile211=
c.633C>T · rs947817635 · VCV1984837
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00361%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.2 | GERP -3.8 |
| Overall | ||
| CADD | 2.815 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00361%
Admixed American · 2/55,338 alleles
Filtering AF
0.000599%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000224%
Overall
0.000505%
8/1,584,484 alleles · very rare
exomes 6/1,432,274 · genomes 2/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00361% | 27,669 |
| Remaining individualsnot grpmax-eligible | 0.00163% | 61,378 |
| African / African-American | 0.00134% | 74,522 |
| European (non-Finnish) | 0.000343% | 291,262 |
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
- PCGF2
- Protein
- p.Ile211=
- Coding
- c.633C>T
- MANE Select
- NM_007144
- dbSNP
- rs947817635
- Type
- single nucleotide variant
- Location
- chr17:38736114 (GRCh38)
- Gene constraint
- LOEUF 0.443 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 75.30
Similar variants
- PCGF2 p.Pro65Leu Pathogenic/Likely pathogenic ★★ ⚠ same type
- PCGF2 p.Pro65Ser Likely pathogenic ★★ same type
- PCGF2 p.Ala212Thr Uncertain significance ★★ ⚠ same type
- PCGF2 p.Arg45Cys Uncertain significance ★★ ⚠ same type
- PCGF2 p.Glu136Asp Uncertain significance ★★ ⚠ same type
- PCGF2 p.Glu198Lys Uncertain significance ★★ ⚠ same type
- PCGF2 p.Gly115Ser Uncertain significance ★★ ⚠ same type
- PCGF2 p.Gly221Arg Uncertain significance ★★ ⚠ 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/pcgf2-p-ile211 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown