PCGF2 p.Ala100=
c.300G>A · rs758029170 · VCV1913272
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
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 -20 | GERP -3.9 |
| Overall | ||
| CADD | 0.135 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,868 alleles
Filtering AF
0.00157%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00134%
Overall
0.00205%
33/1,613,202 alleles · very rare
exomes 29/1,461,108 · genomes 4/152,094 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00267% | 37,434 |
| European (non-Finnish) | 0.00229% | 43,703 |
| South Asian | 0.0022% | 45,515 |
| Admixed American | 0.00167% | 59,992 |
| Finnishnot grpmax-eligible | 0.00156% | 64,018 |
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.Ala100=
- Coding
- c.300G>A
- MANE Select
- NM_007144
- dbSNP
- rs758029170
- Type
- single nucleotide variant
- Location
- chr17:38739084 (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-ala100 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown