PCGF2 p.Val193=
c.579G>A · rs2508670807 · VCV1972647
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000346%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.48 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.22 | gain · loss 0.02 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP -0.68, phastCons 1 |
| Overall | ||
| CADD | 17.33 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000346%
European (non-Finnish) · 4/1,156,116 alleles
Filtering AF
8.1e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.5e-05%
Overall
0.000255%
4/1,568,736 alleles · very rare
exomes 4/1,416,412 · genomes 0/152,324 · 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
- PCGF2
- Protein
- p.Val193=
- Coding
- c.579G>A
- MANE Select
- NM_007144
- dbSNP
- rs2508670807
- Type
- single nucleotide variant
- Location
- chr17:38736168 (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-val193 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown