• 3
    Haplo
    Score
  • 0
    Triplo
    Score

Gene Facts External Data Attribution

HGNC Symbol
SATB2 (HGNC:21637) HGNC Entrez Ensembl OMIM UCSC Uniprot GeneReviews LOVD LSDB ClinVar
HGNC Name
SATB homeobox 2
Gene type
protein-coding gene
Locus type
gene with protein product
Previous symbols
No previous names found
Alias symbols
KIAA1034, FLJ21474
%HI
1.6(Read more about the DECIPHER Haploinsufficiency Index)
pLI
1(Read more about gnomAD pLI score)
LOEUF
0.09(Read more about gnomAD LOEUF score)
Cytoband
2q33.1
Genomic Coordinates
GRCh37/hg19: chr2:200134223-200335989 NCBI Ensembl UCSC
GRCh38/hg38: chr2:199269500-199471266 NCBI Ensembl UCSC
MANE Select Transcript
NM_001172509.2 ENST00000417098.6 (Read more about MANE Select)
Function
Binds to DNA, at nuclear matrix- or scaffold-associated regions. Thought to recognize the sugar-phosphate structure of double- stranded DNA. Transcription factor controlling nuclear gene expression, by binding to matrix attachment regions (MARs) of DNA and inducing a local chromatin-loop remodeling. Acts as a docking site for several chromatin remodeling enzymes and also by recruiting corepressors (HDACs) or coactivators (HATs) directly to promoters and enhancers. Required for the initiation of ... (Source: Uniprot)

Dosage Sensitivity Summary (Gene)

Dosage ID:
ISCA-31904
Curation Status:
Complete
Issue Type:
Dosage Curation - Gene
Haploinsufficiency:
Sufficient Evidence for Haploinsufficiency (3)
Triplosensitivity:
No Evidence for Triplosensitivity (0)
Last Evaluated:
07/15/2020

Haploinsufficiency (HI) Score Details

HI Score:
3
HI Evidence Strength:
Sufficient Evidence for Haploinsufficiency (Disclaimer)
HI Disease:
HI Evidence:
  • PUBMED: 28139846
    In 2017, Zarate et al. used whole exome sequencing (WES) on 11 individuals with SATB2-associated syndrome. The authors identified pathogenic variants in SATB2 in these individuals, all of which were confirmed de novo. Of these variants, 1 was a splice site, 5 were frameshifts, and 3 were nonsense variants.
  • PUBMED: 28151491
    In 2017, Bengani et al. described 20 individuals with SATB2 variants identified through whole exome sequencing. Analysis identified 19 different variants in SATB2, with the same variant existing in a pair of siblings. The majority of these individuals were identified from the DDD study. 11 of these variants were de novo loss of function variants, with 4 variants being nonsense variants, 5 being frameshift variants, and 2 being splice site variants. In addition to ID, many of the individuals in this study also had severe speech impairment, drooling, and craniofacial abnormalities including cleft palate and mild dental differences. Per the authors, “The behavioral phenotype appeared to show the most marked discrepancy within the cohort, with both severe autistic features and friendly/happy personalities being recurrently reported.”
HI Evidence Comments:
Loss of function variants result in intellectual disability, cleft palate (reduced penetrance), and tooth abnormalities (variable expressivity). Of note: FitzPatrick et al. (2003) used high-resolution Fluorescence in situ hybridization studies to map two de novo translocation breakpoints in individuals with isolated cleft palate. In one individual the translocation break point disrupted the coding region of the SATB2 gene. In the second individual, the translocation break point mapped 130 kb 3' to SATB2 in a highly conserved region of noncoding DNA (PMID: 12915443)

Triplosensitivity (TS) Score Details

TS Score:
0
TS Evidence Strength:
No Evidence for Triplosensitivity (Disclaimer)

Genomic View

Select assembly: (NC_000002.11) (NC_000002.12)