ZEB1 p.Ser46=
c.138T>C · rs2542042868 · VCV2031411
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 | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.15 | GERP -0.86, phastCons 0.94 |
| Overall | ||
| CADD | 9.035 | 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
- ZEB1
- Protein
- p.Ser46=
- Coding
- c.138T>C
- MANE Select
- NM_001174096
- dbSNP
- rs2542042868
- Type
- single nucleotide variant
- Location
- chr10:31461116 (GRCh38)
- Gene constraint
- LOEUF 0.339 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 48.64 · 1 PDB
- Residue 46
- the 'disordered' region
Similar variants
- ZEB1 p.Arg326Ter Pathogenic ★★ same type
- ZEB1 p.Glu120Lys Uncertain significance ★★ ⚠ same type
- ZEB1 p.Glu481Gln Uncertain significance ★★ ⚠ same type
- ZEB1 p.Glu74Lys Uncertain significance ★★ ⚠ same type
- ZEB1 p.Ile333Thr Uncertain significance ★★ ⚠ same type
- ZEB1 c.688-15G>A Benign ★★ same type
- ZEB1 p.Ala420= Benign ★★ same type
- ZEB1 p.Asn659Lys Likely benign ★★ 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/zeb1-p-ser46 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown