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_001110792.2(MECP2):c.429C>G (p.Ala143=)

CA170296

143557 (ClinVar)

Gene: MECP2

Condition: Rett syndrome

Inheritance Mode: X-linked inheritance

Link to MONDO

UUID: e88ae85c-2226-49e9-b2fd-d8bf822acbfc

HGVS expressions

NM_001110792.2:c.429C>G

NM_001110792.2(MECP2):c.429C>G (p.Ala143=)

NC_000023.11:g.154031435G>C

CM000685.2:g.154031435G>C

NC_000023.10:g.153296886G>C

CM000685.1:g.153296886G>C

NC_000023.9:g.152950080G>C

NG_007107.2:g.110693C>G

NG_007107.3:g.110669C>G

ENST00000303391.11:c.393C>G

ENST00000453960.7:c.429C>G

ENST00000637917.1:n.26C>G

ENST00000303391.10:c.393C>G

ENST00000369957.5:c.*447C>G

ENST00000407218.5:c.429C>G

ENST00000453960.6:c.429C>G

ENST00000486506.5:n.2741C>G

ENST00000611468.1:c.381C>G

ENST00000619732.4:c.393C>G

ENST00000622433.4:c.381C>G

ENST00000628176.2:c.393C>G

NM_001110792.1:c.429C>G

NM_001316337.1:c.114C>G

NM_004992.3:c.393C>G

NM_001316337.2:c.114C>G

NM_001369391.2:c.114C>G

NM_001369392.2:c.114C>G

NM_001369393.2:c.114C>G

NM_001369394.1:c.114C>G

NM_001369394.2:c.114C>G

NM_001386137.1:c.-168C>G

NM_001386138.1:c.-168C>G

NM_001386139.1:c.-168C>G

NM_004992.4:c.393C>G

Benign

BA1 BP7 BP4

PP4 BS2

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.393C>G (p.Ala131=) variant in MECP2 (NM_004992.3) is 0.1698% in the Ashkenazi Jewish 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 c.393C>G (p.Ala131=) 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.393C>G (p.Ala131=) variant in MECP2 is classified as Benign based on the ACMG/AMP criteria (BA1, BP4, BP7).

BA1

The allele frequency of the c.393C>G (p.Ala131=) variant in MECP2 is 0.1698%% in the Ashkenazi Jewish 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).

BP7

The silent c.393C>G (p.Ala131=) variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide (BP4, BP7).

BP4

The silent c.393C>G (p.Ala131=) variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide (BP4, BP7).

PP4

The c.393C>G variant in MECP2 was identified in the hemizygous state in a male with a Prader-Willi-like phenotype (PMID 14560307). The c.393C>G variant was identified in an individual from an autism cohort as well as in a healthy control (PMID 17427193).

BS2

The c.393C>G variant in MECP2 was identified in a healthy control (PMID 17427193). The control group consisted of healthy adults and children and it is unknown whether this variant was identified in an adult or a child.

Approved on: 2021-10-26

Published on: 2021-12-27

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