POPDC1 p.Pro348=
c.1044G>A · VCV4820676
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.099%, mid)
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 -11 | GERP -3.2 |
| Overall | ||
| CADD | 0.757 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.099%
Middle Eastern · 6/6,062 alleles
Filtering AF
0.043%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0294%
Overall
0.00434%
70/1,613,484 alleles · ultra-rare
exomes 66/1,461,270 · genomes 4/152,214 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.099% | 1,010 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,248 |
| East Asian | 0.00669% | 14,949 |
| South Asian | 0.0044% | 22,735 |
| European (non-Finnish) | 0.00398% | 25,102 |
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
- POPDC1
- Protein
- p.Pro348=
- Coding
- c.1044G>A
- MANE Select
- NM_001199563
- Type
- single nucleotide variant
- Location
- chr6:105101128 (GRCh38)
- Structure
- AlphaFold pLDDT 76.08
- Residue 348
- the 'disordered' region
Similar variants
- POPDC1 p.Pro348Leu Uncertain significance ★ ⚠ 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
- POP1 p.Ala44Pro 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/popdc1-p-pro348 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown