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_004992.3(MECP2):c.608C>T (p.Thr203Met)

CA148319

95198 (ClinVar)

Gene: MECP2
Condition: Rett syndrome
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: 49670d6c-9ef7-465b-a280-333556f92e42
Approved on: 2021-03-26
Published on: 2021-05-17

HGVS expressions

NM_004992.3:c.608C>T
NM_004992.3(MECP2):c.608C>T (p.Thr203Met)
NC_000023.11:g.154031220G>A
CM000685.2:g.154031220G>A
NC_000023.10:g.153296671G>A
CM000685.1:g.153296671G>A
NC_000023.9:g.152949865G>A
NG_007107.2:g.110908C>T
NG_007107.3:g.110884C>T
ENST00000303391.11:c.608C>T
ENST00000453960.7:c.644C>T
ENST00000637917.1:n.65+176C>T
ENST00000303391.10:c.608C>T
ENST00000407218.5:c.535C>T
ENST00000453960.6:c.644C>T
ENST00000619732.4:c.608C>T
ENST00000622433.4:c.596C>T
ENST00000628176.2:c.499C>T
NM_001110792.1:c.644C>T
NM_001316337.1:c.329C>T
NM_001110792.2:c.644C>T
NM_001316337.2:c.329C>T
NM_001369391.2:c.329C>T
NM_001369392.2:c.329C>T
NM_001369393.2:c.329C>T
NM_001369394.1:c.329C>T
NM_001369394.2:c.329C>T
NM_001386137.1:c.-62C>T
NM_001386138.1:c.-62C>T
NM_001386139.1:c.-62C>T
NM_004992.4:c.608C>T

Benign

Met criteria codes 4
BA1 BS2 BP4 BP5

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 allele frequency of the p.Thr203Met variant in MECP2 is 0.07% in gnomAD, which is high enough to be classified as benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BA1). The p.Thr203Met variant is observed in at least 2 unaffected individuals (internal database) (BS2). Computational analysis prediction tools suggest that the p.Thr203Met variant does not have a deleterious impact; however this information does not predict clinical significance on its own (BP4). The p.Thr203Met variant is found in a patient with an alternate molecular basis of disease (internal database) (BP5). In summary, the p.Thr203Met variant in MECP2 is classified as benign based on the ACMG/AMP criteria (BA1, BS2, BP4, BP5).
Met criteria codes
BA1
The allele frequency of the p.Thr203Met variant in MECP2 is 0.07% in gnomAD, which is high enough to be classified as benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions.
BS2
The p.Thr203Met variant is observed in at least 2 unaffected individuals (internal database)
BP4
Computational analysis prediction tools suggest that the p.Thr203Met variant does not have a deleterious impact; however this information does not predict clinical significance on its own
BP5
The p.Thr203Met variant is found in a patient with an alternate molecular basis of disease (internal database)
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