Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

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Variant: NM_130839.5(UBE3A):c.2096A>C (p.Lys699Thr)

CA206151

156144 (ClinVar)

Gene: UBE3A

Condition: Angelman syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: d19ee94f-a011-463d-bbf0-0fa8dc6e5da9

Approved on: 2023-12-06

Published on: 2023-12-11

HGVS expressions

NM_130839.5:c.2096A>C

NM_130839.5(UBE3A):c.2096A>C (p.Lys699Thr)

NC_000015.10:g.25355920T>G

CM000677.2:g.25355920T>G

NC_000015.9:g.25601067T>G

CM000677.1:g.25601067T>G

NC_000015.8:g.23152160T>G

NG_009268.1:g.88062A>C

ENST00000438097.6:c.2036A>C

ENST00000625778.3:c.2036A>C

ENST00000635914.1:c.2036A>C

ENST00000637886.1:c.2096A>C

ENST00000638011.1:c.2036A>C

ENST00000638155.1:c.2036A>C

ENST00000648336.2:c.2096A>C

ENST00000649550.1:c.2036A>C

ENST00000650110.1:c.2105A>C

ENST00000675177.1:c.1919A>C

ENST00000675593.1:n.4792A>C

ENST00000232165.7:c.2036A>C

ENST00000397954.6:c.2105A>C

ENST00000428984.6:c.2036A>C

ENST00000438097.5:c.2036A>C

ENST00000566215.5:c.2036A>C

ENST00000604860.3:c.75+771A>C

ENST00000614096.4:c.2096A>C

ENST00000625778.2:c.2036A>C

ENST00000626176.2:c.63A>C

ENST00000630424.2:c.2036A>C

ENST00000631247.1:n.585A>C

NM_000462.3:c.2105A>C

NM_130838.1:c.2036A>C

NM_130839.2:c.2096A>C

NM_000462.5:c.2105A>C

NM_001354505.1:c.2096A>C

NM_001354506.1:c.2036A>C

NM_001354507.1:c.2036A>C

NM_001354508.1:c.2036A>C

NM_001354509.1:c.2036A>C

NM_001354511.1:c.2036A>C

NM_001354512.1:c.2036A>C

NM_001354513.1:c.2036A>C

NM_001354523.1:c.2036A>C

NM_001354526.1:c.2036A>C

NM_001354538.1:c.2096A>C

NM_001354539.1:c.2036A>C

NM_001354540.1:c.2036A>C

NM_001354541.1:c.2036A>C

NM_001354542.1:c.2036A>C

NM_001354543.1:c.2036A>C

NM_001354544.1:c.2036A>C

NM_001354545.1:c.2096A>C

NM_001354546.1:c.1919A>C

NM_001354547.1:c.2036A>C

NM_001354548.1:c.2036A>C

NM_001354549.1:c.1899+771A>C

NM_001354550.1:c.845A>C

NM_001354551.1:c.785A>C

NM_130838.3:c.2036A>C

NM_130839.4:c.2096A>C

NR_146177.1:n.18393-35676T>G

NR_148916.1:n.2640A>C

NM_001354506.2:c.2036A>C

NM_001354507.2:c.2036A>C

NM_001354508.2:c.2036A>C

NM_001354509.2:c.2036A>C

NM_001354511.2:c.2036A>C

NM_001354512.2:c.2036A>C

NM_001354513.2:c.2036A>C

NM_001354523.2:c.2036A>C

NM_001354538.2:c.2096A>C

NM_001354539.2:c.2036A>C

NM_001354540.2:c.2036A>C

NM_001354541.2:c.2036A>C

NM_001354542.2:c.2036A>C

NM_001354543.2:c.2036A>C

NM_001354544.2:c.2036A>C

NM_001354545.2:c.2096A>C

NM_001354546.2:c.1919A>C

NM_001354547.2:c.2036A>C

NM_001354548.2:c.2036A>C

NM_001354549.2:c.1899+771A>C

NM_001354550.2:c.845A>C

NM_001354551.2:c.785A>C

NM_001374461.1:c.2036A>C

NM_130838.4:c.2036A>C

NR_148916.2:n.2608A>C

Benign

BA1 BP5

BS2

Evidence Links 0

Expert Panel

Rett and Angelman-like Disorders VCEP

Criteria Specification Information

Criteria Specification: ClinGen Rett and Angelman-like Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for UBE3A Version 4.0.0

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Rett and Angelman-like Disorders VCEP

The allele frequency of The p.Lys679Thr variant in UBE3A (NM_130838.2) is 0.03187% in European (non-Finnish) sub population in gnomAD v4, which is high enough to be classified as benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BA1). The p.Lys679Thr variant is found in a patient with an alternate molecular basis of disease (internal database - Baylor) (BP5). In summary, the p.Lys679Thr variant in UBE3A (NM_130838.2) is classified as benign based on the ACMG/AMP criteria (BA1, BP5).

BA1

The allele frequency of The p.Lys679Thr variant in UBE3A (NM_130838.2) is 0.03187% in European (non-Finnish) sub population in gnomAD, which is high enough to meet the BS1 criteria based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions.

BP5

The p.Lys679Thr variant in UBE3A (NM_130838.2) is found in a patient with an alternate molecular basis of disease (internal database) (BP5).

BS2

The p.Lys679Thr variant in UBE3A (NM_130838.2) is observed in at least 4 unaffected individuals (gnomAD) (BS2).

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