PCGF2 p.Asp89=
c.267T>C · rs780159639 · VCV2716063
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00781%, nfe)
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 5.4 | GERP 0.96, phastCons 1 |
| Overall | ||
| CADD | 16.05 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00781%
European (non-Finnish) · 92/1,177,594 alleles
Filtering AF
0.00649%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00601%
Overall
0.00608%
98/1,611,214 alleles · very rare
exomes 90/1,459,108 · genomes 8/152,106 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00781% | 12,800 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,791 |
| African / African-American | 0.00267% | 37,409 |
| Admixed American | 0.00167% | 59,986 |
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.Asp89=
- Coding
- c.267T>C
- MANE Select
- NM_007144
- dbSNP
- rs780159639
- Type
- single nucleotide variant
- Location
- chr17:38739117 (GRCh38)
- Gene constraint
- LOEUF 0.443 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 75.30
Similar variants
- PCGF2 p.Asp89Glu Uncertain significance ★ ⚠ same residue
- PCGF2 p.Asp89Gly Uncertain significance ★ ⚠ same residue
- 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
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-asp89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown