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Gene

UBE3A

ubiquitin protein ligase E3A

Summary

Cytogenetic location
15q11.2
Coordinates
Chromosome 15: 25,333,728–25,439,024 (GRCh38)
Exons
13 exons across 105.3 kb
Protein
872 amino acids
Also known as
AS, ANCR, E6-AP, FLJ26981
Previous symbols
EPVE6AP, HPVE6A
MANE Select transcript
ENST00000648336.2NM_130839.5
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

  • Angelman Syndrome

    • A disorder caused by loss of maternal UBE3A function through a 15q11-q13 deletion, paternal uniparental disomy, an imprinting defect or a UBE3A variant.

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

      Seizure, sleep and developmental support; families with a maternally inherited UBE3A variant have a 50% recurrence risk, so genetic counselling is important.

How UBE3A is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
  • Variants with a page
Chromosome 15, with a bracket where UBE3A sits. UBE3A and 4 genes near it on chromosome 15, from 24,886,376 to 25,886,375.Chromosome 1515q11.2p13p12p11.2p11.1q11.1q11.2q12q13.1q13.2q13.3q14q15.1q15.2q15.3q21.1q21.2q21.3q22.1q22.2q22.31q22.32q22.33q23q24.1q24.2q24.3q25.1q25.2q25.3q26.1q26.2q26.325 Mb25.2 Mb25.4 Mb25.6 Mb25.8 MbSNRPN: 24,823,627–24,978,723, forward strandSNRPNSNURF: 24,954,920–24,977,850, forward strandSNURF: 24,955,034–25,000,276, forward strandUBE3A: 25,333,728–25,439,024, reverse strandUBE3AATP10A: 25,677,273–25,865,184, reverse strandATP10ADiagram of UBE3A: 13 exons on the reverse strand of chromosome 15Exon 13: 23 known disease-causing sitesExon 12: 16 known disease-causing sitesExon 11: 3 known disease-causing sitesExon 10: 8 known disease-causing sitesExon 9: 6 known disease-causing sitesExon 8: 12 known disease-causing sitesExon 7: 9 known disease-causing sitesExon 6: 59 known disease-causing sitesExon 5: 10 known disease-causing sitesExon 4: 1 known disease-causing siteExon 13: 25,333,728–25,339,257, 5,530 bases. 4 variants with a page in exon 13. List themExon 12: 25,340,085–25,340,228, 144 bases. 2 variants with a page in exon 12. List themExon 11: 25,354,353–25,354,426, 74 basesExon 10: 25,354,528–25,354,683, 156 basesExon 9: 25,355,892–25,356,056, 165 basesExon 8: 25,356,691–25,356,896, 206 bases. 2 variants with a page in exon 8. List themExon 7: 25,360,383–25,360,527, 145 basesExon 6: 25,370,566–25,371,812, 1,247 bases. 5 variants with a page in exon 6. List themExon 5: 25,375,465–25,375,763, 299 basesExon 4: 25,405,461–25,405,502, 42 bases. 1 variant with a page in exon 4. List themExon 3: 25,409,088–25,409,207, 120 basesExon 2: 25,411,908–25,411,971, 64 basesExon 1: 25,438,489–25,439,024, 536 bases131210864215′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 8.7 kb of the gene's 105.3 kb; 2,619 of those bases code for the protein.

How a genome test reads UBE3A

154

positions in UBE3A where ClinVar classes a change as pathogenic or likely pathogenic

59 of them (38%) fall in regions short reads find hard.

  • Low mappability (8 sites)Regions where 100 bp or 250 bp reads cannot be placed uniquely.
  • Segmental duplications (59 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 105.3 kb of UBE3A, introns included, not only the 8.7 kb of exons.

Variants with a page (15)

The UBE3A variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.

VariantHGVS c.Exon or intronPosition (GRCh38)ClinVar classificationReview status
c.2125-1G>AIntron 925,354,684Likely pathogenic3 stars out of 4 reviewed by expert panel
E403Xc.1207G>TExon 625,370,967Pathogenic3 stars out of 4 reviewed by expert panel
F474Yfs*19c.1421_1422delExon 625,370,751Pathogenic3 stars out of 4 reviewed by expert panel
G815Ec.2444G>AExon 1225,340,139Likely pathogenic3 stars out of 4 reviewed by expert panel
G870Dc.2609G>AExon 1325,339,147Likely pathogenic3 stars out of 4 reviewed by expert panel
K856Rfs*4c.2567_2570delExon 1325,339,185Pathogenic3 stars out of 4 reviewed by expert panel
L855_K856delc.2563_2568delExon 1325,339,187Pathogenic3 stars out of 4 reviewed by expert panel
L855Fc.2563C>TExon 1325,339,193Likely pathogenic3 stars out of 4 reviewed by expert panel
M21Tc.62T>CExon 425,405,461Pathogenic3 stars out of 4 reviewed by expert panel
N622Sc.1865A>GExon 825,356,785Likely pathogenic3 stars out of 4 reviewed by expert panel

See all 15 UBE3A variants →

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.). UBE3A gene: ubiquitin protein ligase E3A. Retrieved 17 October 2026, from https://dantelabs.com/genes/ube3a

Vancouver

Dante Labs. UBE3A gene: ubiquitin protein ligase E3A [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/ube3a

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