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Gene

RAB3GAP2

RAB3 GTPase activating non-catalytic protein subunit 2

Summary

Cytogenetic location
1q41
Coordinates
Chromosome 1: 220,148,293–220,272,453 (GRCh38)
Exons
35 exons across 124.2 kb
Protein
1,393 amino acids
Also known as
RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69
MANE Select transcript
ENST00000358951.7NM_012414.4
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

  • Hypogonadotropic Hypogonadism

    • Abnormal ovarian or testicular function due to insufficient hormonal stimulation from the hypothalamic-pituitary axis.

      • 1 GenCC submitter rates it definitive or strong

  • 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.

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

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

How RAB3GAP2 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 1, with a bracket where RAB3GAP2 sits. RAB3GAP2 and 6 genes near it on chromosome 1, from 219,710,373 to 220,710,372.Chromosome 11q41p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q44219.8 Mb220 Mb220.2 Mb220.4 Mb220.6 MbSLC30A10: 219,685,427–219,959,018, reverse strandSLC30A10EPRS1: 219,968,598–220,046,669, reverse strandEPRS1BPNT1: 220,057,079–220,119,267, reverse strandBPNT1IARS2: 220,094,086–220,148,043, forward strandIARS2RAB3GAP2: 220,148,293–220,272,453, reverse strandRAB3GAP2MARK1: 220,528,086–220,664,461, forward strandMARK1C1orf115: 220,690,291–220,701,283, forward strandC1orf115Diagram of RAB3GAP2: 35 exons on the reverse strand of chromosome 1Exon 32: 2 known disease-causing sitesExon 31: 1 known disease-causing siteExon 30: 1 known disease-causing siteExon 28: 1 known disease-causing siteExon 25: 1 known disease-causing siteExon 22: 1 known disease-causing siteExon 21: 1 known disease-causing siteExon 20: 1 known disease-causing siteExon 14: 3 known disease-causing sitesExon 13: 1 known disease-causing siteExon 9: 1 known disease-causing siteExon 8: 1 known disease-causing siteExon 4: 3 known disease-causing sitesExon 35: 220,148,293–220,151,406, 3,114 basesExon 34: 220,151,606–220,151,764, 159 basesExon 33: 220,153,185–220,153,406, 222 basesExon 32: 220,153,968–220,154,057, 90 basesExon 31: 220,157,270–220,157,488, 219 basesExon 30: 220,157,802–220,157,876, 75 basesExon 29: 220,159,386–220,159,421, 36 basesExon 28: 220,162,198–220,162,268, 71 basesExon 27: 220,164,733–220,164,799, 67 basesExon 26: 220,167,293–220,167,399, 107 basesExon 25: 220,167,502–220,167,675, 174 basesExon 24: 220,170,892–220,171,120, 229 basesExon 23: 220,171,889–220,172,049, 161 basesExon 22: 220,172,637–220,172,742, 106 basesExon 21: 220,182,257–220,182,354, 98 basesExon 20: 220,182,718–220,182,931, 214 basesExon 19: 220,184,036–220,184,163, 128 basesExon 18: 220,185,651–220,185,741, 91 basesExon 17: 220,189,703–220,189,767, 65 basesExon 16: 220,190,064–220,190,146, 83 basesExon 15: 220,190,377–220,190,520, 144 basesExon 14: 220,191,068–220,191,284, 217 basesExon 13: 220,193,240–220,193,379, 140 basesExon 12: 220,195,078–220,195,167, 90 basesExon 11: 220,195,298–220,195,377, 80 basesExon 10: 220,196,250–220,196,398, 149 basesExon 9: 220,202,276–220,202,374, 99 basesExon 8: 220,205,907–220,206,006, 100 basesExon 7: 220,210,388–220,210,489, 102 basesExon 6: 220,210,801–220,210,876, 76 basesExon 5: 220,210,955–220,211,002, 48 basesExon 4: 220,212,887–220,212,968, 82 basesExon 3: 220,213,856–220,213,979, 124 basesExon 2: 220,232,799–220,232,863, 65 basesExon 1: 220,272,223–220,272,453, 231 bases353025201510515′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 7.3 kb of the gene's 124.2 kb; 4,182 of those bases code for the protein.

How a genome test reads RAB3GAP2

27

positions in RAB3GAP2 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 124.2 kb of RAB3GAP2, introns included, not only the 7.3 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.). RAB3GAP2 gene: RAB3 GTPase activating non-catalytic protein subunit 2. Retrieved 16 October 2026, from https://dantelabs.com/genes/rab3gap2

Vancouver

Dante Labs. RAB3GAP2 gene: RAB3 GTPase activating non-catalytic protein subunit 2 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/rab3gap2

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