Is SATB2 p.Val368fs (c.1103_1106del) pathogenic?

SATB2 p.Val368fs (c.11031106del) is classified Pathogenic in SATB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-04-09). Absent from gnomAD; Associated with chromosome 2q32-q33 deletion syndrome.

What condition is associated with SATB2 p.Val368fs (c.1103_1106del)?

SATB2 p.Val368fs (c.1103_1106del) is associated with chromosome 2q32-q33 deletion syndrome (ClinVar).

How common is SATB2 p.Val368fs (c.1103_1106del) in the general population?

SATB2 p.Val368fs (c.1103_1106del) is absent from gnomAD (gnomAD).

SATB2 p.Val368fs

c.1103_1106del · rs1574532220 · VCV807482

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

chromosome 2q32-q33 deletion 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 7 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.9	GERP 2.2, 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: SATB2
Protein: p.Val368fs
Coding: c.1103_1106del
MANE Select: NM_001172509
dbSNP: rs1574532220
Type: Deletion
Location: chr2:199348768 (GRCh38)
Gene constraint: LOEUF 0.077 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 66.87 · 3 PDB
Residue 368: a DNA-binding region; an α-helix

Full SATB2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

chromosome 2q32-q33 deletion syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SATB2 p.Gln270fs Pathogenic ★★ same condition
SATB2 c.1174-16del Benign/Likely benign ★★ same condition
SATB2 c.1740+20_1740+29del Likely benign ★★ same condition
SATB2 c.598-4del Likely benign ★★ same condition
SATB2 c.474-2_474-1del Likely pathogenic ★ same condition
SATB2 p.Ala407fs Likely pathogenic ★ same condition
SATB2 p.Ala417fs Pathogenic ★ same condition
SATB2 p.Arg46fs 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/satb2-p-val368fs (accessed [today's date]).

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