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]

Link to SEPIO compliant JSON-LD document

Variant: NM_130839.5(UBE3A):c.373T>C (p.Leu125=)

CA149410

96263 (ClinVar)

Gene: UBE3A

Condition: Angelman syndrome

Inheritance Mode: Autosomal dominant inheritance (with paternal imprinting (HP:0012274))

Link to MONDO

UUID: bdcbe3b1-3716-4af6-a36e-6baf3bea90ab

Approved on: 2022-06-30

Published on: 2022-06-30

HGVS expressions

NM_130839.5:c.373T>C

NM_130839.5(UBE3A):c.373T>C (p.Leu125=)

NC_000015.10:g.25371801A>G

CM000677.2:g.25371801A>G

NC_000015.9:g.25616948A>G

CM000677.1:g.25616948A>G

NC_000015.8:g.23168041A>G

NG_009268.1:g.72181T>C

ENST00000438097.6:c.313T>C

ENST00000625778.3:c.313T>C

ENST00000635914.1:c.313T>C

ENST00000637886.1:c.373T>C

ENST00000638011.1:c.313T>C

ENST00000638155.1:c.313T>C

ENST00000648336.2:c.373T>C

ENST00000649550.1:c.313T>C

ENST00000650110.1:c.382T>C

ENST00000675000.1:n.1048T>C

ENST00000675177.1:c.196T>C

ENST00000675593.1:n.3069T>C

ENST00000232165.7:c.313T>C

ENST00000397954.6:c.382T>C

ENST00000428984.6:c.313T>C

ENST00000438097.5:c.313T>C

ENST00000566215.5:c.313T>C

ENST00000614096.4:c.373T>C

ENST00000625778.2:c.313T>C

ENST00000626068.2:c.394T>C

ENST00000626793.2:n.424T>C

ENST00000628733.2:c.373T>C

ENST00000630424.2:c.313T>C

ENST00000630907.2:c.373T>C

NM_000462.3:c.382T>C

NM_130838.1:c.313T>C

NM_130839.2:c.373T>C

NM_000462.5:c.382T>C

NM_001354505.1:c.373T>C

NM_001354506.1:c.313T>C

NM_001354507.1:c.313T>C

NM_001354508.1:c.313T>C

NM_001354509.1:c.313T>C

NM_001354511.1:c.313T>C

NM_001354512.1:c.313T>C

NM_001354513.1:c.313T>C

NM_001354523.1:c.313T>C

NM_001354526.1:c.313T>C

NM_001354538.1:c.373T>C

NM_001354539.1:c.313T>C

NM_001354540.1:c.313T>C

NM_001354541.1:c.313T>C

NM_001354542.1:c.313T>C

NM_001354543.1:c.313T>C

NM_001354544.1:c.313T>C

NM_001354545.1:c.373T>C

NM_001354546.1:c.196T>C

NM_001354547.1:c.313T>C

NM_001354548.1:c.313T>C

NM_001354549.1:c.313T>C

NM_001354550.1:c.361+3664T>C

NM_001354551.1:c.301+3664T>C

NM_130838.3:c.313T>C

NM_130839.4:c.373T>C

NR_146177.1:n.18393-19795A>G

NR_148916.1:n.921T>C

NM_001354506.2:c.313T>C

NM_001354507.2:c.313T>C

NM_001354508.2:c.313T>C

NM_001354509.2:c.313T>C

NM_001354511.2:c.313T>C

NM_001354512.2:c.313T>C

NM_001354513.2:c.313T>C

NM_001354523.2:c.313T>C

NM_001354538.2:c.373T>C

NM_001354539.2:c.313T>C

NM_001354540.2:c.313T>C

NM_001354541.2:c.313T>C

NM_001354542.2:c.313T>C

NM_001354543.2:c.313T>C

NM_001354544.2:c.313T>C

NM_001354545.2:c.373T>C

NM_001354546.2:c.196T>C

NM_001354547.2:c.313T>C

NM_001354548.2:c.313T>C

NM_001354549.2:c.313T>C

NM_001354550.2:c.361+3664T>C

NM_001354551.2:c.301+3664T>C

NM_001374461.1:c.313T>C

NM_130838.4:c.313T>C

NR_148916.2:n.889T>C

Benign

BA1

BP7

Evidence Links 0

Expert Panel

Rett and Angelman-like Disorders VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Rett and Angelman-like Disorders VCEP

The allele frequency of the c.313T>C p.(Leu105=) variant in UBE3A (NM_130838.2) is 7.5% in African/African-American sub population in gnomAD, 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). In summary, the c.313T>C p.(Leu105=) variant in UBE3A is classified as Benign based on the ACMG/AMP criteria (BA1).

BA1

The allele frequency of the p.Leu105= variant in UBE3A is 7.5% in African/African-American sub population in gnomAD, 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.

BP7

The silent p.Leu105= variant is not predicted to affect splicing using multiple computational tools, however this affects a highly conserved nucleotide (PhastCons 1.0, PhlyoP 3.28) therefore BP7 cannot be applied.

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