POGZ p.Pro232=
c.696G>A · VCV3770790
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00619%, 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 -1.1 | GERP -5.7, phastCons 0.002 |
| Overall | ||
| CADD | 9.468 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00619%
European (non-Finnish) · 73/1,179,978 alleles
Filtering AF
0.00503%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00462%
Overall
0.00502%
81/1,613,812 alleles · very rare
exomes 72/1,461,872 · genomes 9/151,940 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00619% | 16,164 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,826 |
| African / African-American | 0.00401% | 24,941 |
| East Asian | 0.00223% | 44,890 |
| South Asian | 0.0011% | 91,072 |
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
- POGZ
- Protein
- p.Pro232=
- Coding
- c.696G>A
- MANE Select
- NM_015100
- Type
- single nucleotide variant
- Location
- chr1:151428286 (GRCh38)
- Gene constraint
- LOEUF 0.198 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.48 · 3 PDB
Similar variants
- POGZ c.1679-1G>A Pathogenic/Likely pathogenic ★★ same type
- POGZ c.1679-2A>G Pathogenic/Likely pathogenic ★★ same type
- POGZ p.Arg1001Ter Pathogenic ★★ same type
- POGZ p.Arg1008Ter Pathogenic ★★ same type
- POGZ p.Arg1087Ter Pathogenic/Likely pathogenic ★★ same type
- POGZ p.Arg1142Ter Pathogenic/Likely pathogenic ★★ same type
- POGZ p.Arg1211Ter Pathogenic/Likely pathogenic ★★ same type
- POGZ p.Arg238Ter Pathogenic ★★ 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/pogz-p-pro232 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown