POP1 p.Ser129=
c.387A>G · rs1586230617 · VCV1536783
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 · A>T here scores Δ0.46 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.3 | GERP -4.1 |
| Overall | ||
| CADD | 1.753 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,884 alleles
Overall
6.2e-05%
1/1,614,100 alleles · very rare
exomes 1/1,461,810 · genomes 0/152,290 · joint denominator
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
- POP1
- Protein
- p.Ser129=
- Coding
- c.387A>G
- MANE Select
- NM_001145860
- dbSNP
- rs1586230617
- Type
- single nucleotide variant
- Location
- chr8:98128441 (GRCh38)
- Structure
- AlphaFold pLDDT 76.08
- Residue 129
- a UniProt-annotated variant site (in)
Similar variants
- POPDC1 p.Arg129Gln Uncertain significance ★★ ⚠ same residue
- POPDC1 p.Arg129Trp Benign/Likely benign ★★ ⚠ same residue
- POP1 p.Gln778Ter Pathogenic/Likely pathogenic ★★ same type
- POP1 p.Val696Asp Likely pathogenic ★★ ⚠ same type
- POPDC1 p.Arg88Ter Pathogenic/Likely pathogenic ★★ same type
- POPDC1 p.Ser201Phe Likely pathogenic ★★ same type
- POP1 p.Ala1011Thr Uncertain significance ★★ ⚠ same type
- POP1 p.Ala166Pro 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/pop1-p-ser129 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown