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]

Variant: NM_001110792.2(MECP2):c.90C>G (p.Leu30=)

Curation Version - 1.0
Curation History
JSON LD for Version 1.0

CA243345

196403 (ClinVar)

Gene: MECP2

Condition: Rett syndrome

Inheritance Mode: X-linked inheritance

Link to MONDO

UUID: 3cf99e7b-af13-40f4-bad6-d0c3c12b6f7f

Approved on: 2023-06-15

Published on: 2023-06-21

HGVS expressions

NM_001110792.2:c.90C>G

NM_001110792.2(MECP2):c.90C>G (p.Leu30=)

NC_000023.11:g.154032530G>C

CM000685.2:g.154032530G>C

NC_000023.10:g.153297981G>C

CM000685.1:g.153297981G>C

NC_000023.9:g.152951175G>C

NG_007107.2:g.109598C>G

NG_007107.3:g.109574C>G

ENST00000303391.11:c.54C>G

ENST00000453960.7:c.90C>G

ENST00000611468.2:n.302C>G

ENST00000630151.2:c.54C>G

ENST00000637533.1:n.85C>G

ENST00000675526.1:c.*447C>G

ENST00000676382.1:n.247C>G

ENST00000303391.10:c.54C>G

ENST00000369957.5:c.*108C>G

ENST00000407218.5:c.90C>G

ENST00000415944.3:c.54C>G

ENST00000453960.6:c.90C>G

ENST00000460227.4:n.1203C>G

ENST00000463644.5:n.993C>G

ENST00000481807.3:n.340C>G

ENST00000486506.5:n.2402C>G

ENST00000488293.4:n.1103C>G

ENST00000496908.5:n.185C>G

ENST00000611468.1:c.42C>G

ENST00000619732.4:c.54C>G

ENST00000622433.4:c.42C>G

ENST00000625300.1:n.279C>G

ENST00000626422.2:n.764C>G

ENST00000628176.2:c.54C>G

ENST00000630151.1:c.54C>G

ENST00000631210.1:n.333C>G

NM_001110792.1:c.90C>G

NM_001316337.1:c.-226C>G

NM_004992.3:c.54C>G

NM_001316337.2:c.-226C>G

NM_001369391.2:c.-226C>G

NM_001369392.2:c.-226C>G

NM_001369393.2:c.-226C>G

NM_001369394.1:c.-226C>G

NM_001369394.2:c.-226C>G

NM_001386137.1:c.-507C>G

NM_001386138.1:c.-507C>G

NM_001386139.1:c.-507C>G

NM_004992.4:c.54C>G

Benign

BA1 BP4 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.54C>G p.Leu18= variant in MECP2 (NM_004992.1) is 0.042% in the 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). The silent p.Leu18= variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide (BP4, BP7). In summary, the c.54C>G p.Leu18= variant in MECP2 is classified as Benign based on the ACMG/AMP criteria (BA1, BP4, BP7).

BA1

The allele frequency of the c.54C>G p.(Leu18=) variant in MECP2 (NM_004992.1) is 0.042% in the 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.

BP4

The silent p.(Leu18=) variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide.

BP7

The silent p.(Leu18=) 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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