Is SATB2 p.Ser299fs (c.895del) pathogenic?

SATB2 p.Ser299fs (c.895del) is classified Pathogenic in SATB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2017-10-02). No gnomAD frequency available for this variant.

How common is SATB2 p.Ser299fs (c.895del) in the general population?

SATB2 p.Ser299fs (c.895del) is no gnomAD frequency available for this variant (gnomAD).

SATB2 p.Ser299fs

c.895del · rs1553551647 · VCV452556

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

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 12	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.Ser299fs
Coding: c.895del
MANE Select: NM_001172509
dbSNP: rs1553551647
Type: Deletion
Location: chr2:199348979 (GRCh38)
Gene constraint: LOEUF 0.077 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 66.87 · 3 PDB

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

Similar variants

SATB2 p.Gln270fs Pathogenic ★★ same type
SATB2 c.1174-16del Benign/Likely benign ★★ same type
SATB2 c.1740+20_1740+29del Likely benign ★★ same type
SATB2 c.598-4del Likely benign ★★ same type
SATB2 c.473+1del Likely pathogenic ★ same type
SATB2 c.474-2_474-1del Likely pathogenic ★ same type
SATB2 p.Ala383fs Pathogenic ★ same type
SATB2 p.Ala407fs Likely pathogenic ★ same type

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-ser299fs (accessed [today's date]).

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