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.633C>G (p.Pro211=)

CA10558582

698693 (ClinVar)

Gene: MECP2

Condition: Rett syndrome

Inheritance Mode: X-linked inheritance

Link to MONDO

UUID: da88ee76-9d03-4ca5-9bd0-5f9d646bc984

Approved on: 2023-10-13

Published on: 2023-12-08

HGVS expressions

NM_001110792.2:c.633C>G

NM_001110792.2(MECP2):c.633C>G (p.Pro211=)

NC_000023.11:g.154031231G>C

CM000685.2:g.154031231G>C

NC_000023.10:g.153296682G>C

CM000685.1:g.153296682G>C

NC_000023.9:g.152949876G>C

NG_007107.2:g.110897C>G

NG_007107.3:g.110873C>G

ENST00000303391.11:c.597C>G

ENST00000453960.7:c.633C>G

ENST00000637917.1:c.65+165C>G

ENST00000303391.10:c.597C>G

ENST00000407218.5:c.524C>G

ENST00000453960.6:c.633C>G

ENST00000619732.4:c.597C>G

ENST00000622433.4:c.585C>G

ENST00000628176.2:c.488C>G

NM_001110792.1:c.633C>G

NM_001316337.1:c.318C>G

NM_004992.3:c.597C>G

NM_001316337.2:c.318C>G

NM_001369391.2:c.318C>G

NM_001369392.2:c.318C>G

NM_001369393.2:c.318C>G

NM_001369394.1:c.318C>G

NM_001369394.2:c.318C>G

NM_001386137.1:c.-73C>G

NM_001386138.1:c.-73C>G

NM_001386139.1:c.-73C>G

NM_004992.4:c.597C>G

Benign

BP5 BP4 BS1 BS2

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.597C>G (p.Pro199=) variant in MECP2 (NM_004992.3) is 0.013% in East Asian 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 (BS1). The p.Pro199= variant is observed in at least 6 unaffected individuals (internal database - Invitae) (BS2). Splice prediction analysis, using multiple computational tools does not suggest an impact to splicing (BP4). The p.Pro199= variant is found in at least 2 individuals with an alternate molecular basis of disease (internal database - Invitae) (BP5). In summary, the p.Pro199= variant in MECP2 is classified as Benign based on the ACMG/AMP criteria (BS1, BS2, BP4, BP5).

BP5

The p.Pro199= variant is found in at least 2 individuals with an alternate molecular basis of disease (internal database - Invitae) (BP5).

BP4

Splice prediction analysis, using multiple computational tools does not suggest an impact to splicing (BP4).

BS1

BS2

The p.Pro199= variant is observed in at least 6 unaffected individuals (internal database - Invitae) (BS2).

BP7

PhastCons 1.00, phyloP 2.96

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