PACS2 p.Ser487=
c.1461C>T · rs113443045 · VCV1634891
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.117%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.33 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -15 | GERP -3.8 |
| Overall | ||
| CADD | 0.29 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.117%
African / African-American · 88/74,896 alleles
Filtering AF
0.0977%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0903%
Overall
0.00719%
116/1,613,188 alleles · rare
exomes 68/1,460,978 · genomes 48/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.117% | 851 |
| Remaining individualsnot grpmax-eligible | 0.0256% | 3,902 |
| Admixed American | 0.005% | 20,001 |
| Finnishnot grpmax-eligible | 0.00156% | 64,006 |
| European (non-Finnish) | 0.000678% | 147,410 |
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
- PACS2
- Protein
- p.Ser487=
- Coding
- c.1461C>T
- MANE Select
- NM_001100913
- dbSNP
- rs113443045
- Type
- single nucleotide variant
- Location
- chr14:105382524 (GRCh38)
- Gene constraint
- LOEUF 0.561 · pLI 0.33 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 67.10
Similar variants
- PACS2 p.Glu209Lys Pathogenic/Likely pathogenic ★★ ⚠ same type
- PACS2 c.1413+2T>C Uncertain significance ★★ same type
- PACS2 p.Ala526Val Uncertain significance ★★ ⚠ same type
- PACS2 p.Ala704Thr Uncertain significance ★★ ⚠ same type
- PACS2 p.Ala883Thr Uncertain significance ★★ ⚠ same type
- PACS2 p.Arg431Gln Uncertain significance ★★ ⚠ same type
- PACS2 p.Arg445Trp Uncertain significance ★★ ⚠ same type
- PACS2 p.Arg514Lys 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/pacs2-p-ser487 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown