ZEB2 p.Ser327=
c.981G>A · rs201579452 · VCV510410
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.06%, amr)
Conditions
2
Inborn genetic diseases
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 -0.43 | GERP -3.9, phastCons 0.1 |
| Overall | ||
| CADD | 10.79 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.06%
Admixed American · 36/60,004 alleles
Filtering AF
0.0445%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0392%
Overall
0.00266%
43/1,613,594 alleles · ultra-rare
exomes 40/1,461,422 · genomes 3/152,172 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.06% | 1,667 |
| East Asian | 0.00445% | 22,449 |
| South Asian | 0.0011% | 91,072 |
| European (non-Finnish) | 0.000339% | 295,005 |
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
- ZEB2
- Protein
- p.Ser327=
- Coding
- c.981G>A
- MANE Select
- NM_014795
- dbSNP
- rs201579452
- Type
- single nucleotide variant
- Location
- chr2:144400206 (GRCh38)
- Gene constraint
- LOEUF 0.114 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 48.91 · 1 PDB
Similar variants
- ZEB2 p.Ser327Leu Uncertain significance ★★ ⚠ same residue
- ZEB2 p.Ser327Ter Pathogenic ★★ same residue
- ZEB2 c.2886+1G>A Pathogenic ★★ same condition
- ZEB2 c.73+1G>A Pathogenic ★★ same condition
- ZEB2 c.73+2T>C Pathogenic/Likely pathogenic ★★ same condition
- ZEB2 c.808-2A>G Pathogenic ★★ same condition
- ZEB2 p.Arg1016Ter Pathogenic/Likely pathogenic ★★ same condition
- ZEB2 p.Arg302Ter Pathogenic/Likely pathogenic ★★ same condition
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/zeb2-p-ser327 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown