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.936G>A (p.Lys312=)

CA267785638

437192 (ClinVar)

Gene: UBE3A
Condition: Angelman syndrome
Inheritance Mode: Autosomal dominant inheritance (with paternal imprinting (HP:0012274))
Link to MONDO
UUID: 7be1b922-205f-47f4-9346-b5504cf92ce9
Approved on: 2025-06-25
Published on: 2025-06-30

HGVS expressions

NM_130839.5:c.936G>A
NM_130839.5(UBE3A):c.936G>A (p.Lys312=)
NC_000015.10:g.25371238C>T
CM000677.2:g.25371238C>T
NC_000015.9:g.25616385C>T
CM000677.1:g.25616385C>T
NC_000015.8:g.23167478C>T
NG_009268.1:g.72744G>A
ENST00000438097.6:c.876G>A
ENST00000625778.3:c.876G>A
ENST00000635914.1:c.876G>A
ENST00000637886.1:c.936G>A
ENST00000638011.1:c.876G>A
ENST00000638155.1:c.876G>A
ENST00000648336.2:c.936G>A
ENST00000649550.1:c.876G>A
ENST00000650110.1:c.945G>A
ENST00000675000.1:n.1611G>A
ENST00000675177.1:c.759G>A
ENST00000675593.1:n.3632G>A
ENST00000232165.7:c.876G>A
ENST00000397954.6:c.945G>A
ENST00000428984.6:c.876G>A
ENST00000438097.5:c.876G>A
ENST00000566215.5:c.876G>A
ENST00000614096.4:c.936G>A
ENST00000625778.2:c.876G>A
ENST00000630424.2:c.876G>A
NM_000462.3:c.945G>A
NM_130838.1:c.876G>A
NM_130839.2:c.936G>A
NM_000462.5:c.945G>A
NM_001354505.1:c.936G>A
NM_001354506.1:c.876G>A
NM_001354507.1:c.876G>A
NM_001354508.1:c.876G>A
NM_001354509.1:c.876G>A
NM_001354511.1:c.876G>A
NM_001354512.1:c.876G>A
NM_001354513.1:c.876G>A
NM_001354523.1:c.876G>A
NM_001354526.1:c.876G>A
NM_001354538.1:c.936G>A
NM_001354539.1:c.876G>A
NM_001354540.1:c.876G>A
NM_001354541.1:c.876G>A
NM_001354542.1:c.876G>A
NM_001354543.1:c.876G>A
NM_001354544.1:c.876G>A
NM_001354545.1:c.936G>A
NM_001354546.1:c.759G>A
NM_001354547.1:c.876G>A
NM_001354548.1:c.876G>A
NM_001354549.1:c.876G>A
NM_001354550.1:c.361+4227G>A
NM_001354551.1:c.301+4227G>A
NM_130838.3:c.876G>A
NM_130839.4:c.936G>A
NR_146177.1:n.18393-20358C>T
NR_148916.1:n.1484G>A
NM_001354506.2:c.876G>A
NM_001354507.2:c.876G>A
NM_001354508.2:c.876G>A
NM_001354509.2:c.876G>A
NM_001354511.2:c.876G>A
NM_001354512.2:c.876G>A
NM_001354513.2:c.876G>A
NM_001354523.2:c.876G>A
NM_001354538.2:c.936G>A
NM_001354539.2:c.876G>A
NM_001354540.2:c.876G>A
NM_001354541.2:c.876G>A
NM_001354542.2:c.876G>A
NM_001354543.2:c.876G>A
NM_001354544.2:c.876G>A
NM_001354545.2:c.936G>A
NM_001354546.2:c.759G>A
NM_001354547.2:c.876G>A
NM_001354548.2:c.876G>A
NM_001354549.2:c.876G>A
NM_001354550.2:c.361+4227G>A
NM_001354551.2:c.301+4227G>A
NM_001374461.1:c.876G>A
NM_130838.4:c.876G>A
NR_148916.2:n.1452G>A
More

Benign

Met criteria codes 2
BP7 BA1
Not Met criteria codes 1
PM2

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 highest population minor allele frequency of the p.Lys312= variant in UBE3A in gnomAD v4.1 is 0.0003300 in the Middle Eastern population, which is higher than the ClinGen Rett and Angelman-like Disorders VCEP threshold (≥0.0003) for BA1, and therefore meets this criterion (BA1). The silent c.876G>A (p.Lys292=) variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide (BP7). In summary, the p.Lys312= variant in UBE3A is classified as benign based on the ACMG/AMP criteria (BA1, BP7). (UBE3A Specifications v.5.0; curation approved on [06/25/2025])
Met criteria codes
BP7
The silent c.876G>A (p.Lys292=) variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide (BP7).
BA1
The highest population minor allele frequency of the p.Lys312= variant in UBE3A in gnomAD v4.1 is 0.0003300 in the Middle Eastern population, which is higher than the ClinGen Rett and Angelman-like Disorders VCEP threshold (≥0.0003) for BA1, and therefore meets this criterion (BA1).
Not Met criteria codes
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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