Is SATB1 p.Pro352fs (c.1055_1056del) pathogenic?

SATB1 p.Pro352fs (c.10551056del) is classified Pathogenic/Likely pathogenic in SATB1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-08-19). No gnomAD frequency available for this variant; Associated with developmental delay with dysmorphic facies and dental anomalies.

What condition is associated with SATB1 p.Pro352fs (c.1055_1056del)?

SATB1 p.Pro352fs (c.1055_1056del) is associated with developmental delay with dysmorphic facies and dental anomalies (ClinVar).

How common is SATB1 p.Pro352fs (c.1055_1056del) in the general population?

SATB1 p.Pro352fs (c.1055_1056del) is no gnomAD frequency available for this variant (gnomAD).

SATB1 p.Pro352fs

c.1055_1056del · rs2125115880 · VCV1699824

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

developmental delay with dysmorphic facies and dental anomalies

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 LoF-intolerant gene
NMD	predicted	premature termination codon in exon 7 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 0.89, 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: SATB1
Protein: p.Pro352fs
Coding: c.1055_1056del
MANE Select: NM_002971
dbSNP: rs2125115880
Type: Deletion
Location: chr3:18394612 (GRCh38)
Gene constraint: LOEUF 0.209 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 65.88 · 8 PDB

Full SATB1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

developmental delay with dysmorphic facies and dental anomalies — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SATB1 p.Arg335fs Pathogenic ★ same condition
SATB1 p.Gly46fs Pathogenic ★ same condition
SATB1 p.Leu321fs Pathogenic ★ same condition
SATB1 p.Leu545fs Pathogenic ★ same condition
SATB1 p.Pro610fs Likely pathogenic ★ same condition
SATB1 p.Pro352Thr Uncertain significance ★ ⚠ same residue
SATB1 p.Asp150fs Likely pathogenic same condition
SATB1 p.Arg553Ter 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/satb1-p-pro352fs (accessed [today's date]).

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