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.1169C>T (p.Ala390Val)

CA170175

143341 (ClinVar)

Gene: MECP2

Condition: Rett syndrome

Inheritance Mode: X-linked inheritance

Link to MONDO

UUID: 48fda9a4-d1f4-4f66-a6a1-63af8a81c8b4

Approved on: 2022-05-10

Published on: 2022-06-28

HGVS expressions

NM_001110792.2:c.1169C>T

NM_001110792.2(MECP2):c.1169C>T (p.Ala390Val)

NC_000023.11:g.154030695G>A

CM000685.2:g.154030695G>A

NC_000023.10:g.153296146G>A

CM000685.1:g.153296146G>A

NC_000023.9:g.152949340G>A

NG_007107.2:g.111433C>T

NG_007107.3:g.111409C>T

ENST00000303391.11:c.1133C>T

ENST00000453960.7:c.1169C>T

ENST00000303391.10:c.1133C>T

ENST00000407218.5:c.*505C>T

ENST00000453960.6:c.1169C>T

ENST00000619732.4:c.1133C>T

ENST00000628176.2:c.*505C>T

NM_001110792.1:c.1169C>T

NM_001316337.1:c.854C>T

NM_004992.3:c.1133C>T

NM_001316337.2:c.854C>T

NM_001369391.2:c.854C>T

NM_001369392.2:c.854C>T

NM_001369393.2:c.854C>T

NM_001369394.1:c.854C>T

NM_001369394.2:c.854C>T

NM_001386137.1:c.464C>T

NM_001386138.1:c.464C>T

NM_001386139.1:c.464C>T

NM_004992.4:c.1133C>T

Benign

BS2 BS1

BP4

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 p.Ala378Val (NM_004992) variant in MECP2 is 0.014% in East Asian sub population in gnomAD, which is high enough to meet BS1 criteria based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BS1). The p.Ala378Val variant is observed in at least 2 unaffected individuals (PMID 15737703)(BS2). In summary, the p.Ala378Val variant in MECP2 is classified as Benign based on the ACMG/AMP criteria (BS1, BS2).

BS2

The p.Ala378Val variant is observed in at least 2 unaffected individuals (PMID 15737703) (BS2)

BS1

The allele frequency of the p.Ala378Val variant in MECP2 is 0.014% in East Asian sub population in gnomAD, which is high enough to be classified as likely benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions.

BP4

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

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