Is SATB2 p.Val31= (c.93G>C) pathogenic?

SATB2 p.Val31= (c.93G>C) is classified Likely benign in SATB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-22). Very rare (popmax 0.00195%, amr); Associated with chromosome 2q32-q33 deletion syndrome.

What condition is associated with SATB2 p.Val31= (c.93G>C)?

SATB2 p.Val31= (c.93G>C) is associated with chromosome 2q32-q33 deletion syndrome (ClinVar).

How common is SATB2 p.Val31= (c.93G>C) in the general population?

SATB2 p.Val31= (c.93G>C) is very rare (popmax 0.00195%, amr) (gnomAD).

SATB2 p.Val31=

c.93G>C · VCV3718328

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00195%, amr)

Conditions

chromosome 2q32-q33 deletion syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>T here scores Δ0.43 · evaluated, not missing
Constraint at this position
Conservation	phyloP 3.9	GERP 1.6, phastCons 1
Overall
CADD	14.14	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00195% Admixed American · 1/51,254 alleles

Filtering AF 2.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.00026% 4/1,538,026 alleles · very rare exomes 3/1,385,808 · genomes 1/152,218 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00195%	51,254
Remaining individualsnot grpmax-eligible	0.00167%	59,966
European (non-Finnish)	0.000174%	573,714

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: SATB2
Protein: p.Val31=
Coding: c.93G>C
MANE Select: NM_001172509
Type: single nucleotide variant
Location: chr2:199455945 (GRCh38)
Gene constraint: LOEUF 0.077 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 66.87 · 3 PDB
Residue 31: the 'disordered' region

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.Val31Met Benign ★ same residue
SATB2 c.1174-2A>G Pathogenic ★★ same condition
SATB2 c.474-2A>G Pathogenic ★★ same condition
SATB2 c.597+1G>A Pathogenic/Likely pathogenic ★★ same condition
SATB2 c.700+1G>A Likely pathogenic ★★ same condition
SATB2 p.Arg239Ter Pathogenic ★★ same condition
SATB2 p.Arg283Ter Pathogenic ★★ same condition
SATB2 p.Arg389Cys 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/satb2-p-val31 (accessed [today's date]).

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