Evidence Repository
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.1477G>A (p.Val493Met)

CA208886

36492 (ClinVar)

Gene: MECP2
Condition: Rett syndrome
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: 15f6f99d-7268-4eee-9cb6-ad481b36ae07

HGVS expressions

NM_001110792.2:c.1477G>A
NM_001110792.2(MECP2):c.1477G>A (p.Val493Met)
NC_000023.11:g.154030387C>T
CM000685.2:g.154030387C>T
NC_000023.10:g.153295838C>T
CM000685.1:g.153295838C>T
NC_000023.9:g.152949032C>T
NG_007107.2:g.111741G>A
NG_007107.3:g.111717G>A
ENST00000303391.11:c.1441G>A
ENST00000453960.7:c.1477G>A
ENST00000303391.10:c.1441G>A
ENST00000453960.6:c.1477G>A
ENST00000619732.4:c.1441G>A
ENST00000628176.2:c.*813G>A
NM_001110792.1:c.1477G>A
NM_001316337.1:c.1162G>A
NM_004992.3:c.1441G>A
NM_001316337.2:c.1162G>A
NM_001369391.2:c.1162G>A
NM_001369392.2:c.1162G>A
NM_001369393.2:c.1162G>A
NM_001369394.1:c.1162G>A
NM_001369394.2:c.1162G>A
NM_001386137.1:c.772G>A
NM_001386138.1:c.772G>A
NM_001386139.1:c.772G>A
NM_004992.4:c.1441G>A

Likely Benign

Met criteria codes 2
BS2 BP5
Not Met criteria codes 2
PS4 BS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Rett and Angelman-like Disorders VCEP
The p.Val481Met variant in MECP2 (NM_004992.3) is observed in at least 2 unaffected individuals (GeneDx internal database) (BS2). The p.Val481Met variant in MECP2 is present in gnomAD v2.1.1 at a frequency of 0.007% in the Latino/Admixed American sub population including 2 hemizygous males (not sufficient for BS1). The p.Val481Met variant is found in a patient with an alternate molecular basis of disease (Invitae internal database) (BP5). The p.Val481Met variant has been observed in 1 individual with a Rett like disorder (PMID 22277191) and 1 individual with nonspecific neurological phenotypes (PMID 29655203) (Not sufficient for PS4_supporting). In summary, the p.Val481Met variant in MECP2 is classified as likely benign based on the ACMG/AMP criteria (BS2, BP5).
Met criteria codes
BS2
The p.Val481Met variant is observed in at least 2 unaffected individuals (GeneDx internal database).
BP5
The p.Val481Met variant is found in a patient with an alternate molecular basis of disease (Invitae internal database).
Not Met criteria codes
PS4
The p.Val481Met variant has been observed in 1 individual with a Rett like disorder (PMID 22277191) and 1 individual with nonspecific neurological phenotypes (PMID 29655203) (Not sufficient for PS4_supporting).
BS1
The p.Val481Met variant in GENE is present in gnomAD v2.1.1 at a frequency of 0.007% in the Latino/Admixed American sub population including 2 hemizygous males.
Approved on: 2022-02-18
Published on: 2022-06-30
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