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]

Link to SEPIO compliant JSON-LD document

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

PM6 PP4 PVS1 PM2_Supporting

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).

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)

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)

PVS1

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

PM2_Supporting

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

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