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Gene

SOX2

SRY-box transcription factor 2

Summary

Cytogenetic location
3q26.33
Coordinates
Chromosome 3: 181,711,925–181,714,436 (GRCh38)
Exons
1 exon across 2.5 kb
Protein
317 amino acids
MANE Select transcript
ENST00000325404.3NM_003106.4
Locus type
Protein-coding
  • Very high
  • Confident
  • Low
  • Very low

Curated report relevant to this gene

  • Microphthalmia, Anophthalmia & Coloboma

    • Syndromic Microphthalmia

      Microphthalmia occurring with features outside the eye, caused by changes in genes such as SOX2, OTX2, BCOR, STRA6 and BMP4.

      • 4 GenCC submitters rate it definitive or strong
      Actionability

      A genetic diagnosis guides checks for associated features, such as pituitary hormone problems with SOX2 or OTX2, and informs recurrence risk.

How SOX2 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 3, with a bracket where SOX2 sits. SOX2 and 0 genes near it on chromosome 3, from 181,213,181 to 182,213,180.Chromosome 33q26.33p26.3p26.2p26.1p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13.11q13.12q13.13q13.2q13.31q13.32q13.33q21.1q21.2q21.3q22.1q22.2q22.3q23q24q25.1q25.2q25.31q25.32q25.33q26.1q26.2q26.31q26.32q26.33q27.1q27.2q27.3q28q29181.4 Mb181.6 Mb181.8 Mb182 Mb182.2 MbSOX2: 181,711,925–181,714,436, forward strandSOX2Diagram of SOX2: one exon on the forward strand of chromosome 3Exon 1: 45 known disease-causing sitesExon 1: 181,711,925–181,714,436, 2,512 bases15′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 2.5 kb of the gene's 2.5 kb; 954 of those bases code for the protein.

Sequencing SOX2

45

positions in SOX2 where ClinVar classes a change as pathogenic or likely pathogenic

19 of them (42%) fall in regions short reads find hard.

  • Low mappability (1 site)Regions where 100 bp or 250 bp reads cannot be placed uniquely.
  • Segmental duplications (18 sites)Copies of at least 1 kb sharing at least 90% identity with another part of the genome (paralogues, pseudogenes); reads may align to the wrong copy.

A whole genome covers all 2.5 kb of SOX2, introns included, not only the 2.5 kb of exons.

Genes linked to the same conditions

Traits linked to SOX2

The Human Phenotype Ontology lists these as features of the rare conditions SOX2 can cause. Each trait's page lists the other genes linked to it.

External links

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 2026-10-17: 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 2026.10.17-8666dff2.

Cite this page

APA

Dante Labs. (n.d.). SOX2 gene: SRY-box transcription factor 2. Retrieved 17 October 2026, from https://dantelabs.com/genes/sox2

Vancouver

Dante Labs. SOX2 gene: SRY-box transcription factor 2 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/sox2

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