Is ZEB2 p.Ser360fs (c.1077_1081del) pathogenic?

ZEB2 p.Ser360fs (c.10771081del) is classified Pathogenic in ZEB2 (ClinVar, Single submitter, 2 submitters; last evaluated 2019-04-19). No gnomAD frequency available for this variant; Associated with Mowat-Wilson syndrome.

What condition is associated with ZEB2 p.Ser360fs (c.1077_1081del)?

ZEB2 p.Ser360fs (c.1077_1081del) is associated with Mowat-Wilson syndrome (ClinVar).

How common is ZEB2 p.Ser360fs (c.1077_1081del) in the general population?

ZEB2 p.Ser360fs (c.1077_1081del) is no gnomAD frequency available for this variant (gnomAD).

ZEB2 p.Ser360fs

c.1077_1081del · rs1703290664 · VCV947462

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Mowat-Wilson syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 8 of 10
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 1.1, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ZEB2
Protein: p.Ser360fs
Coding: c.1077_1081del
MANE Select: NM_014795
dbSNP: rs1703290664
Type: Deletion
Location: chr2:144400106 (GRCh38)
Gene constraint: LOEUF 0.114 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 48.91 · 1 PDB
Residue 360: a modified residue (phosphoserine)

Full ZEB2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Mowat-Wilson syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ZEB2 p.Ser360Cys Likely benign ★ same residue
ZEB2 p.Ala907fs Pathogenic ★★ same condition
ZEB2 p.Arg953fs Pathogenic ★★ same condition
ZEB2 p.Gly351fs Pathogenic ★★ same condition
ZEB2 p.Lys834fs Pathogenic ★★ same condition
ZEB2 p.Pro906fs Pathogenic ★★ same condition
ZEB2 p.Ser1011fs Pathogenic ★★ same condition
ZEB2 p.Ser726fs 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-ser360fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown