Is SATB2 p.Asp70= (c.210C>T) pathogenic?

SATB2 p.Asp70= (c.210C>T) is classified Benign/Likely benign in SATB2 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-01-28). Rare (popmax 0.157%, afr); Associated with Inborn genetic diseases.

What condition is associated with SATB2 p.Asp70= (c.210C>T)?

SATB2 p.Asp70= (c.210C>T) is associated with Inborn genetic diseases, chromosome 2q32-q33 deletion syndrome (ClinVar).

How common is SATB2 p.Asp70= (c.210C>T) in the general population?

SATB2 p.Asp70= (c.210C>T) is rare (popmax 0.157%, afr) (gnomAD).

SATB2 p.Asp70=

c.210C>T · rs34311963 · VCV469551

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

rare (popmax 0.157%, afr)

Conditions

Inborn genetic diseases

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 -1.7	GERP -3.7
Overall
CADD	10.22	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.157% African / African-American · 118/75,018 alleles

Filtering AF 0.134% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.126%

Overall 0.0221% 357/1,614,090 alleles · rare exomes 257/1,461,862 · genomes 100/152,228 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.157%	636
Admixed American	0.0866%	1,154
Middle Eastern	0.0825%	1,212
Remaining individualsnot grpmax-eligible	0.0432%	2,315
European (non-Finnish)	0.0127%	7,867
East Asian	0.00446%	22,439
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,608
South Asian	0.0022%	45,537

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.Asp70=
Coding: c.210C>T
MANE Select: NM_001172509
dbSNP: rs34311963
Type: single nucleotide variant
Location: chr2:199433474 (GRCh38)
Gene constraint: LOEUF 0.077 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 66.87 · 3 PDB
Residue 70: the cmp domain

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: chromosome 2q32-q33 deletion syndrome

Similar variants

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
SATB2 p.Arg389Leu 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-asp70 (accessed [today's date]).

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