Is SATB2 p.Val65= (c.195C>T) pathogenic?

SATB2 p.Val65= (c.195C>T) is classified Benign/Likely benign in SATB2 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-01-12). Rare (popmax 0.175%, afr); Associated with chromosome 2q32-q33 deletion syndrome.

What condition is associated with SATB2 p.Val65= (c.195C>T)?

SATB2 p.Val65= (c.195C>T) is associated with chromosome 2q32-q33 deletion syndrome (ClinVar).

How common is SATB2 p.Val65= (c.195C>T) in the general population?

SATB2 p.Val65= (c.195C>T) is rare (popmax 0.175%, afr) (gnomAD).

SATB2 p.Val65=

c.195C>T · rs147613731 · VCV469547

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

rare (popmax 0.175%, afr)

Conditions

chromosome 2q32-q33 deletion syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.29	acceptor gain · deltas
Constraint at this position
Conservation	phyloP 5	GERP -0.15, phastCons 1
Overall
CADD	20.5	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.175% African / African-American · 131/75,004 alleles

Filtering AF 0.15% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.141%

Overall 0.0193% 311/1,614,012 alleles · rare exomes 222/1,461,814 · genomes 89/152,198 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.175%	573
Middle Eastern	0.165%	606
Admixed American	0.0483%	2,069
Remaining individualsnot grpmax-eligible	0.04%	2,500
European (non-Finnish)	0.00958%	10,442
South Asian	0.00329%	30,356

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.Val65=
Coding: c.195C>T
MANE Select: NM_001172509
dbSNP: rs147613731
Type: single nucleotide variant
Location: chr2:199433489 (GRCh38)
Gene constraint: LOEUF 0.077 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 66.87 · 3 PDB
Residue 65: the cmp domain

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 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-val65 (accessed [today's date]).

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