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.1007T>C (p.Met336Thr)

CA279176

217366 (ClinVar)

Gene: UBE3A

Condition: Angelman syndrome

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

Link to MONDO

UUID: aeb1dbbf-844f-4b79-aa1f-1195bf541052

Approved on: 2022-06-30

Published on: 2022-06-30

HGVS expressions

NM_130839.5:c.1007T>C

NM_130839.5(UBE3A):c.1007T>C (p.Met336Thr)

NC_000015.10:g.25371167A>G

CM000677.2:g.25371167A>G

NC_000015.9:g.25616314A>G

CM000677.1:g.25616314A>G

NC_000015.8:g.23167407A>G

NG_009268.1:g.72815T>C

ENST00000438097.6:c.947T>C

ENST00000625778.3:c.947T>C

ENST00000635914.1:c.947T>C

ENST00000637886.1:c.1007T>C

ENST00000638011.1:c.947T>C

ENST00000638155.1:c.947T>C

ENST00000648336.2:c.1007T>C

ENST00000649550.1:c.947T>C

ENST00000650110.1:c.1016T>C

ENST00000675000.1:n.1682T>C

ENST00000675177.1:c.830T>C

ENST00000675593.1:n.3703T>C

ENST00000232165.7:c.947T>C

ENST00000397954.6:c.1016T>C

ENST00000428984.6:c.947T>C

ENST00000438097.5:c.947T>C

ENST00000566215.5:c.947T>C

ENST00000614096.4:c.1007T>C

ENST00000625778.2:c.947T>C

ENST00000630424.2:c.947T>C

NM_000462.3:c.1016T>C

NM_130838.1:c.947T>C

NM_130839.2:c.1007T>C

NM_000462.5:c.1016T>C

NM_001354505.1:c.1007T>C

NM_001354506.1:c.947T>C

NM_001354507.1:c.947T>C

NM_001354508.1:c.947T>C

NM_001354509.1:c.947T>C

NM_001354511.1:c.947T>C

NM_001354512.1:c.947T>C

NM_001354513.1:c.947T>C

NM_001354523.1:c.947T>C

NM_001354526.1:c.947T>C

NM_001354538.1:c.1007T>C

NM_001354539.1:c.947T>C

NM_001354540.1:c.947T>C

NM_001354541.1:c.947T>C

NM_001354542.1:c.947T>C

NM_001354543.1:c.947T>C

NM_001354544.1:c.947T>C

NM_001354545.1:c.1007T>C

NM_001354546.1:c.830T>C

NM_001354547.1:c.947T>C

NM_001354548.1:c.947T>C

NM_001354549.1:c.947T>C

NM_001354550.1:c.361+4298T>C

NM_001354551.1:c.301+4298T>C

NM_130838.3:c.947T>C

NM_130839.4:c.1007T>C

NR_146177.1:n.18393-20429A>G

NR_148916.1:n.1555T>C

NM_001354506.2:c.947T>C

NM_001354507.2:c.947T>C

NM_001354508.2:c.947T>C

NM_001354509.2:c.947T>C

NM_001354511.2:c.947T>C

NM_001354512.2:c.947T>C

NM_001354513.2:c.947T>C

NM_001354523.2:c.947T>C

NM_001354538.2:c.1007T>C

NM_001354539.2:c.947T>C

NM_001354540.2:c.947T>C

NM_001354541.2:c.947T>C

NM_001354542.2:c.947T>C

NM_001354543.2:c.947T>C

NM_001354544.2:c.947T>C

NM_001354545.2:c.1007T>C

NM_001354546.2:c.830T>C

NM_001354547.2:c.947T>C

NM_001354548.2:c.947T>C

NM_001354549.2:c.947T>C

NM_001354550.2:c.361+4298T>C

NM_001354551.2:c.301+4298T>C

NM_001374461.1:c.947T>C

NM_130838.4:c.947T>C

NR_148916.2:n.1523T>C

Uncertain Significance

PS2 PP4

PS4 BP4 PP3 PM2 BS1

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 c.947T>C p.(Met316Thr) variant in UBE3A (NM_130838.2) is present in gnomAD v2.1.1 at a frequency of 0.003% in the Latino/Admixed sub population (no criteria met). The p.(Met316Thr) variant in UBE3A has been reported as a de novo occurrence (biological parentage confirmed) in an individual with Angelman syndrome (PMID 27864847) (PS2, PP4), however the gnomAD frequency of this variant means that the PS4 criterion cannot be applied. Computational prediction analysis tools are inconclusive for this variant. In summary, the c.947T>C p.(Met316Thr) variant in UBE3A is classified as a variant of uncertain significance based on the ACMG/AMP criteria (PS2, PP4).

PS2

The p.Met316Thr variant in UBE3A has been reported as a de novo occurrence (biological parentage confirmed) in an individual with Angelman syndrome (PMID 27864847).

PP4

The p.Met316Thr variant in UBE3A has been reported in an individual with a clinical phenotype suggestive of Angelman syndrome (PMID 27864847).

PS4

The p.Met316Thr variant has been observed in at least 1 individual with Angelman syndrome (PMID 27864847), however the gnomAD frequency of this variant means that the PS4 criteria cannot be applied if further probands are reported.

BP4

Computational prediction analysis tools are inconclusive for this variant.

PP3

Computational prediction analysis tools are inconclusive for this variant.

PM2

The p.Met316Thr variant in UBE3A is present in gnomAD v2.1.1 at a frequency of 0.003% in the Latino/Admixed sub population (no criteria met).

BS1

The p.Met316Thr variant in UBE3A is present in gnomAD v2.1.1 at a frequency of 0.003% in the Latino/Admixed sub population (no criteria met).

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