PAPPA2 p.Ser879=
c.2637C>T · rs138677844 · VCV789155
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.825%, nfe)
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 -3 | GERP -5.9 |
| Overall | ||
| CADD | 1.306 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.825%
European (non-Finnish) · 9,731/1,179,944 alleles
Filtering AF
0.811%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.805%
Overall
0.676%
10,915/1,614,020 alleles · rare
exomes 10,145/1,461,780 · genomes 770/152,240 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.825% | 121 |
| Ashkenazi Jewishnot grpmax-eligible | 0.811% | 123 |
| Remaining individualsnot grpmax-eligible | 0.613% | 163 |
| Middle Eastern | 0.479% | 209 |
| Admixed American | 0.343% | 291 |
| Finnishnot grpmax-eligible | 0.212% | 471 |
| African / African-American | 0.139% | 721 |
| South Asian | 0.0944% | 1,059 |
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
- PAPPA2
- Protein
- p.Ser879=
- Coding
- c.2637C>T
- MANE Select
- NM_020318
- dbSNP
- rs138677844
- Type
- single nucleotide variant
- Location
- chr1:176695750 (GRCh38)
- Gene constraint
- LOEUF 0.549 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.65 · 1 PDB
Similar variants
- PAPPA2 p.Glu1126Ter Pathogenic ★★ same type
- PAPPA2 p.Arg326His Uncertain significance ★★ ⚠ same type
- PAPPA2 p.Arg617His Uncertain significance ★★ ⚠ same type
- PAPPA2 p.Leu782Arg Uncertain significance ★★ ⚠ same type
- PAPPA2 p.Phe1025Leu Uncertain significance ★★ ⚠ same type
- PAPPA2 p.Pro1397Leu Uncertain significance ★★ ⚠ same type
- PAPPA2 c.3366-16A>G Benign/Likely benign ★★ same type
- PAPPA2 p.Ala1527Ser Benign/Likely benign ★★ 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/pappa2-p-ser879 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown