POGZ p.Leu725=
c.2175G>T · rs2102166900 · VCV1202061
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 0.078 | GERP 0.53, phastCons 0.87 |
| Overall | ||
| CADD | 8.195 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- POGZ
- Protein
- p.Leu725=
- Coding
- c.2175G>T
- MANE Select
- NM_015100
- dbSNP
- rs2102166900
- Type
- single nucleotide variant
- Location
- chr1:151408468 (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-leu725 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown