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Gene

ARHGEF9

Cdc42 guanine nucleotide exchange factor 9

Summary

Cytogenetic location
Xq11.1
Coordinates
Chromosome X: 63,634,967–63,785,214 (GRCh38)
Exons
10 exons across 150.2 kb
Protein
523 amino acids
Also known as
KIAA0424, PEM-2
MANE Select transcript
ENST00000671741.2NM_001353921.2
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 reports relevant to this gene

  • Epilepsy (Full Panel)

    • X-Linked Complex Neurodevelopmental Disorder

      A complex neurodevelopmental disorder that is transmitted via X-linked inheritance, and is characterized by intellectual disability, autism and epilepsy.

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

      One of 171 genes linked to it

      A brain disorder characterized by episodes of abnormally increased neuronal discharge resulting in transient episodes of sensory or motor neurological dysfunction, or psychic dysfunction. These episodes may or may not be associated with loss of consciousness or convulsions.

      • 4 GenCC submitters rate it definitive or strong

Broader groupings

How ARHGEF9 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome X, with a bracket where ARHGEF9 sits. ARHGEF9 and 3 genes near it on chromosome X, from 63,210,091 to 64,210,090.Chromosome XXq11.1p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q2863.4 Mb63.6 Mb63.8 Mb64 Mb64.2 MbSPIN4: 63,347,228–63,351,332, reverse strandSPIN4ARHGEF9: 63,634,967–63,785,214, reverse strandARHGEF9: 63,754,485–63,754,664, reverse strandAMER1: 64,185,117–64,205,708, reverse strandAMER1Diagram of ARHGEF9: 10 exons on the reverse strand of chromosome XExon 10: 2 known disease-causing sitesExon 9: 1 known disease-causing siteExon 8: 6 known disease-causing sitesExon 7: 4 known disease-causing sitesExon 6: 8 known disease-causing sitesExon 5: 2 known disease-causing sitesExon 4: 4 known disease-causing sitesExon 3: 4 known disease-causing sitesExon 2: 1 known disease-causing siteExon 10: 63,634,967–63,638,209, 3,243 basesExon 9: 63,643,980–63,644,048, 69 basesExon 8: 63,655,494–63,655,737, 244 basesExon 7: 63,665,886–63,666,017, 132 basesExon 6: 63,674,038–63,674,167, 130 basesExon 5: 63,678,340–63,678,572, 233 basesExon 4: 63,697,125–63,697,304, 180 basesExon 3: 63,706,258–63,706,449, 192 basesExon 2: 63,724,532–63,724,711, 180 basesExon 1: 63,785,116–63,785,214, 99 bases109876543215′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 4.7 kb of the gene's 150.2 kb; 1,572 of those bases code for the protein.

How a genome test reads ARHGEF9

36

positions in ARHGEF9 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 150.2 kb of ARHGEF9, introns included, not only the 4.7 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.). ARHGEF9 gene: Cdc42 guanine nucleotide exchange factor 9. Retrieved 16 October 2026, from https://dantelabs.com/genes/arhgef9

Vancouver

Dante Labs. ARHGEF9 gene: Cdc42 guanine nucleotide exchange factor 9 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/arhgef9

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