POGZ p.Pro399=
c.1197A>G · rs745677294 · VCV722086
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00335%, 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 0.096 | GERP -4, phastCons 0.97 |
| Overall | ||
| CADD | 9.069 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00335%
European (non-Finnish) · 39/1,165,068 alleles
Filtering AF
0.00251%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0022%
Overall
0.00252%
40/1,588,310 alleles · very rare
exomes 40/1,435,976 · genomes 0/152,334 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00335% | 29,874 |
| Remaining individualsnot grpmax-eligible | 0.00163% | 61,410 |
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
- POGZ
- Protein
- p.Pro399=
- Coding
- c.1197A>G
- MANE Select
- NM_015100
- dbSNP
- rs745677294
- Type
- single nucleotide variant
- Location
- chr1:151424275 (GRCh38)
- Gene constraint
- LOEUF 0.198 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.48 · 3 PDB
- Residue 399
- a turn
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-pro399 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown