PCGF2 p.Ser251=
c.753C>T · VCV4750257
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00228%, 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 -0.56 | GERP -4.2, phastCons 0.001 |
| Overall | ||
| CADD | 6.394 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00228%
South Asian · 2/87,886 alleles
Filtering AF
0.000378%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000141%
Overall
0.000251%
4/1,592,332 alleles · very rare
exomes 3/1,440,360 · genomes 1/151,972 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00228% | 43,943 |
| European (non-Finnish) | 0.000171% | 584,888 |
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.Ser251=
- Coding
- c.753C>T
- MANE Select
- NM_007144
- Type
- single nucleotide variant
- Location
- chr17:38735505 (GRCh38)
- Gene constraint
- LOEUF 0.443 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 75.30
- Residue 251
- the 'disordered' region
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-ser251 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown