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.62+1G>A

CA274678

189776 (ClinVar)

Gene: MECP2

Condition: Rett syndrome

Inheritance Mode: X-linked inheritance

Link to MONDO

UUID: f7ac5581-6bde-4913-928f-17df401b9645

Approved on: 2021-12-22

Published on: 2021-12-27

HGVS expressions

NM_001110792.2:c.62+1G>A

NM_001110792.2(MECP2):c.62+1G>A

NC_000023.11:g.154097603C>T

CM000685.2:g.154097603C>T

NC_000023.10:g.153363060C>T

CM000685.1:g.153363060C>T

NC_000023.9:g.153016254C>T

NG_007107.2:g.44519G>A

NG_007107.3:g.44501G>A

ENST00000303391.11:c.-99+1G>A

ENST00000453960.7:c.62+1G>A

ENST00000676382.1:n.22+1G>A

ENST00000303391.10:c.-99+1G>A

ENST00000369957.5:c.-99+1G>A

ENST00000407218.5:c.62+1G>A

ENST00000453960.6:c.62+1G>A

ENST00000619732.4:c.-99+1G>A

ENST00000627864.1:n.77+1G>A

ENST00000628176.2:c.-99+1G>A

ENST00000631210.1:n.305+7178G>A

NM_001110792.1:c.62+1G>A

NM_001316337.1:c.-546+1G>A

NM_004992.3:c.-99+1G>A

NM_001316337.2:c.-546+1G>A

NM_001369391.2:c.-841+1G>A

NM_001369392.2:c.-490+1G>A

NM_001369393.2:c.-366+1G>A

NM_001386137.1:c.-771+1G>A

NM_001386138.1:c.-659+1G>A

NM_001386139.1:c.-535+1G>A

NM_004992.4:c.-99+1G>A

Pathogenic

PM2_Supporting PP4 PM6 PVS1

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.62+1G>A (NM_001110792.2) variant in MECP2 is predicted to affect a canonical splice site and lead to a truncated or absent protein in a gene where loss-of-function is an established mechanism. There is significant evidence that loss of this region of the gene is pathogenic (PVS1). The c.62+1G>A variant in MECP2 has been reported as a de novo occurrence (biological parentage unconfirmed) in an individual with Rett syndrome (PMID 15737703) (PM6, PP4). The c.62+1G>A variant in MECP2 is absent from gnomAD (PM2_supporting). In summary, the c.62+1G>A variant in MECP2 is classified as pathogenic for Rett syndrome based on the ACMG/AMP criteria (PVS1, PM6, PP4, PM2_supporting).

PM2_Supporting

The c.62+1 G>A variant in MECP2 is absent from gnomAD

PP4

The c.62+1 G>A variant in MECP2 has been reported in an individual with a clinical phenotype suggestive of Rett syndrome (PMID 15737703)

PM6

The c.62+1 G>A variant in MECP2 has been reported as a de novo occurrence (biological parentage unconfirmed) in an individual with Rett syndrome (PMID 15737703)

PVS1

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

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