Is SATB2 p.Ser7fs (c.19dup) pathogenic?

SATB2 p.Ser7fs (c.19dup) is classified Pathogenic in SATB2 (ClinVar, Single submitter, 2 submitters; last evaluated 2017-09-13). No gnomAD frequency available for this variant.

How common is SATB2 p.Ser7fs (c.19dup) in the general population?

SATB2 p.Ser7fs (c.19dup) is no gnomAD frequency available for this variant (gnomAD).

SATB2 p.Ser7fs

c.19dup · rs1553507389 · VCV451780

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

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 2 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.5	GERP 1.6, 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.Ser7fs
Coding: c.19dup
MANE Select: NM_001172509
dbSNP: rs1553507389
Type: Duplication
Location: chr2:199456018 (GRCh38)
Gene constraint: LOEUF 0.077 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 66.87 · 3 PDB
Residue 7: the 'disordered' region

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

Similar variants

SATB2 p.Ser7Asn Uncertain significance ★ ⚠ same residue
SATB2 c.598-13dup Benign ★★ same type
SATB2 c.344_346+1dup Pathogenic ★ same type
SATB2 p.Arg439fs Pathogenic ★ same type
SATB2 p.Arg542fs Likely pathogenic ★ same type
SATB2 p.Asn241fs Likely pathogenic ★ same type
SATB2 p.Asn531fs Pathogenic ★ same type
SATB2 p.Gln409fs 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-ser7fs (accessed [today's date]).

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