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Gene

SATB2

SATB homeobox 2

Summary

Cytogenetic location
2q33.1
Coordinates
Chromosome 2: 199,269,505–199,457,939 (GRCh38)
Exons
11 exons across 188.4 kb
Protein
733 amino acids
Also known as
KIAA1034, FLJ21474
MANE Select transcript
ENST00000417098.6NM_001172509.2
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

    • Intellectual Disability

      • One of 233 genes linked to it

        • ClinGen rates the link definitive
        • 5 GenCC submitters rate it definitive or strong

    How SATB2 is laid out

    • Coding sequence
    • Untranslated region
    • Intron
    • Direction of transcription
    • Known disease-causing sites
    • Stretches short reads find hard
    Chromosome 2, with a bracket where SATB2 sits. SATB2 and 1 gene near it on chromosome 2, from 198,863,722 to 199,863,721.Chromosome 22q33.1p25.3p25.2p25.1p24.3p24.2p24.1p23.3p23.2p23.1p22.3p22.2p22.1p21p16.3p16.2p16.1p15p14p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13q14.1q14.2q14.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q34q35q36.1q36.2q36.3q37.1q37.2q37.3199 Mb199.2 Mb199.4 Mb199.6 Mb199.8 MbSATB2: 199,269,505–199,457,939, reverse strandSATB2FTCDNL1: 199,758,265–199,851,214, reverse strandFTCDNL1Diagram of SATB2: 11 exons on the reverse strand of chromosome 2Exon 11: 13 known disease-causing sitesExon 10: 13 known disease-causing sitesExon 9: 5 known disease-causing sitesExon 8: 16 known disease-causing sitesExon 7: 29 known disease-causing sitesExon 6: 6 known disease-causing sitesExon 5: 8 known disease-causing sitesExon 4: 2 known disease-causing sitesExon 3: 10 known disease-causing sitesExon 2: 5 known disease-causing sitesExon 11: 199,269,505–199,272,672, 3,168 basesExon 10: 199,308,760–199,308,957, 198 basesExon 9: 199,323,803–199,323,958, 156 basesExon 8: 199,328,698–199,328,910, 213 basesExon 7: 199,348,701–199,349,173, 473 basesExon 6: 199,368,605–199,368,707, 103 basesExon 5: 199,380,364–199,380,487, 124 basesExon 4: 199,381,694–199,381,820, 127 basesExon 3: 199,433,338–199,433,514, 177 basesExon 2: 199,455,869–199,456,096, 228 basesExon 1: 199,457,339–199,457,939, 601 bases1110515′3′

    Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

    Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

    Nearby genes from Ensembl release 116, on GRCh38.

    Exons make up 5.6 kb of the gene's 188.4 kb; 2,202 of those bases code for the protein.

    How a genome test reads SATB2

    120

    positions in SATB2 where ClinVar classes a change as pathogenic or likely pathogenic

    None of them falls in a region short reads find hard.

    A whole genome covers all 188.4 kb of SATB2, introns included, not only the 5.6 kb of exons.

    Where this comes from

    • HGNC: the gene's symbol, name, other symbols and location.
    • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
    • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
    • The ACMG secondary findings list, SF v3.2.
    • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
    • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
    • Data release 2026.10.16-c6eea6bf.

    Cite this page

    APA

    Dante Labs. (n.d.). SATB2 gene: SATB homeobox 2. Retrieved 17 October 2026, from https://dantelabs.com/genes/satb2

    Vancouver

    Dante Labs. SATB2 gene: SATB homeobox 2 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/satb2

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