Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_130839.5(UBE3A):c.1620C>T (p.Ile540=)

CA16606897

390176 (ClinVar)

Gene: UBE3A
Condition: Angelman syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 7b007461-92df-4c83-a245-e27e7b08a5ce
Approved on: 2025-05-07
Published on: 2025-06-30

HGVS expressions

NM_130839.5:c.1620C>T
NM_130839.5(UBE3A):c.1620C>T (p.Ile540=)
NC_000015.10:g.25360516G>A
CM000677.2:g.25360516G>A
NC_000015.9:g.25605663G>A
CM000677.1:g.25605663G>A
NC_000015.8:g.23156756G>A
NG_009268.1:g.83466C>T
ENST00000438097.6:c.1560C>T
ENST00000625778.3:c.1560C>T
ENST00000635914.1:c.1560C>T
ENST00000637886.1:c.1620C>T
ENST00000638011.1:c.1560C>T
ENST00000638155.1:c.1560C>T
ENST00000648336.2:c.1620C>T
ENST00000649550.1:c.1560C>T
ENST00000650110.1:c.1629C>T
ENST00000675177.1:c.1443C>T
ENST00000675593.1:n.4316C>T
ENST00000232165.7:c.1560C>T
ENST00000397954.6:c.1629C>T
ENST00000428984.6:c.1560C>T
ENST00000438097.5:c.1560C>T
ENST00000566215.5:c.1560C>T
ENST00000614096.4:c.1620C>T
ENST00000625778.2:c.1560C>T
ENST00000630424.2:c.1560C>T
NM_000462.3:c.1629C>T
NM_130838.1:c.1560C>T
NM_130839.2:c.1620C>T
NM_000462.5:c.1629C>T
NM_001354505.1:c.1620C>T
NM_001354506.1:c.1560C>T
NM_001354507.1:c.1560C>T
NM_001354508.1:c.1560C>T
NM_001354509.1:c.1560C>T
NM_001354511.1:c.1560C>T
NM_001354512.1:c.1560C>T
NM_001354513.1:c.1560C>T
NM_001354523.1:c.1560C>T
NM_001354526.1:c.1560C>T
NM_001354538.1:c.1620C>T
NM_001354539.1:c.1560C>T
NM_001354540.1:c.1560C>T
NM_001354541.1:c.1560C>T
NM_001354542.1:c.1560C>T
NM_001354543.1:c.1560C>T
NM_001354544.1:c.1560C>T
NM_001354545.1:c.1620C>T
NM_001354546.1:c.1443C>T
NM_001354547.1:c.1560C>T
NM_001354548.1:c.1560C>T
NM_001354549.1:c.1560C>T
NM_001354550.1:c.369C>T
NM_001354551.1:c.309C>T
NM_130838.3:c.1560C>T
NM_130839.4:c.1620C>T
NR_146177.1:n.18393-31080G>A
NR_148916.1:n.2164C>T
NM_001354506.2:c.1560C>T
NM_001354507.2:c.1560C>T
NM_001354508.2:c.1560C>T
NM_001354509.2:c.1560C>T
NM_001354511.2:c.1560C>T
NM_001354512.2:c.1560C>T
NM_001354513.2:c.1560C>T
NM_001354523.2:c.1560C>T
NM_001354538.2:c.1620C>T
NM_001354539.2:c.1560C>T
NM_001354540.2:c.1560C>T
NM_001354541.2:c.1560C>T
NM_001354542.2:c.1560C>T
NM_001354543.2:c.1560C>T
NM_001354544.2:c.1560C>T
NM_001354545.2:c.1620C>T
NM_001354546.2:c.1443C>T
NM_001354547.2:c.1560C>T
NM_001354548.2:c.1560C>T
NM_001354549.2:c.1560C>T
NM_001354550.2:c.369C>T
NM_001354551.2:c.309C>T
NM_001374461.1:c.1560C>T
NM_130838.4:c.1560C>T
NR_148916.2:n.2132C>T
More

Likely Benign

Met criteria codes 4
PM2_Supporting BS2 BP7 BP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Rett and Angelman-like Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for UBE3A Version 5.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Rett and Angelman-like Disorders VCEP
The c.1560C>T p.Ile520= variant in UBE3A (NM_130838.2) is absent from gnomAD v4.1 (PM2_Supporting). However, the p.Ile520= variant is observed in at least 4 unaffected individuals (GeneDx internal database) (BS2). The silent p.Ile520= variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide (BP4, BP7). In summary, this variant meets the criteria to be classified as likely benign. Although there are both pathogenic and benign types of evidence for this variant, the pathogenic evidence is not considered inconsistent with the final classification. ACMG/AMP criteria applied, as specified by the ClinGen Rett/Angelman-like expert panel: BS2, BP4, BP7. (UBE3A Specification v5.0; curation approved on [5/7/2025])
Met criteria codes
PM2_Supporting
The c.1560C>T p.(Ile520=) variant in UBE3A (NM_130838.2) is absent from gnomAD v4.1.
BS2
The p.(Ile520=) variant is observed in at least 4 unaffected individuals (GeneDx internal database) (BS2).
BP7
The silent p.(Ile520=) variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide.
BP4
The silent p.(Ile520=) variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide.
Curation History
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