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.968C>T (p.Thr323Met)

CA170409

36496 (ClinVar)

Gene: MECP2
Condition: Rett syndrome
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: cf504ba2-3f8d-472c-88e2-1bf8fcf65ee5
Approved on: 2022-02-18
Published on: 2024-03-13

HGVS expressions

NM_001110792.2:c.968C>T
NM_001110792.2(MECP2):c.968C>T (p.Thr323Met)
NC_000023.11:g.154030896G>A
CM000685.2:g.154030896G>A
NC_000023.10:g.153296347G>A
CM000685.1:g.153296347G>A
NC_000023.9:g.152949541G>A
NG_007107.2:g.111232C>T
NG_007107.3:g.111208C>T
ENST00000303391.11:c.932C>T
ENST00000453960.7:c.968C>T
ENST00000637917.1:c.106C>T
ENST00000303391.10:c.932C>T
ENST00000407218.5:c.*304C>T
ENST00000453960.6:c.968C>T
ENST00000619732.4:c.932C>T
ENST00000622433.4:c.918C>T
ENST00000628176.2:c.*304C>T
NM_001110792.1:c.968C>T
NM_001316337.1:c.653C>T
NM_004992.3:c.932C>T
NM_001316337.2:c.653C>T
NM_001369391.2:c.653C>T
NM_001369392.2:c.653C>T
NM_001369393.2:c.653C>T
NM_001369394.1:c.653C>T
NM_001369394.2:c.653C>T
NM_001386137.1:c.263C>T
NM_001386138.1:c.263C>T
NM_001386139.1:c.263C>T
NM_004992.4:c.932C>T

Benign

Met criteria codes 4
BP5 PP3 BS2 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 allele frequency of the p.Thr311Met variant in MECP2 (NM_004992.3) is 0.022% and 0.01% in "Other" and South Asian sub population in gnomAD, which is high enough to meet the BS1 criteria based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BS1). The p.Thr311Met variant is observed in at least 2 unaffected individuals (GeneDx internal database) (BS2) and found in 2 patients with an alternate molecular basis of disease (Baylor Genetics internal database, Invitae internal database) (BP5). Computational prediction analysis tools suggests a deleterious impact; however, this information does not predict clinical significance on its own (PP3). As this variant meets 2 strong and 1 supporting benign criteria it can be classified as benign even though in silico predictions meet PP3. In summary, the p.Thr311Met variant in MECP2 is classified as benign for Rett syndrome based on the ACMG/AMP criteria (BS1, BS2, BP5).
Met criteria codes
BP5
The p.Thr311Met variant in MECP2 is found in 2 patients with an alternate molecular basis of disease (Baylor Genetics internal database, Invitae internal database).
PP3
Computational prediction analysis tools suggests a deleterious impact; however, this information does not predict clinical significance on its own.
BS2
The p.Thr311Met variant is observed in at least 2 unaffected individual (GeneDx internal database).
BS1
The allele frequency of the p.Thr311Met variant in MECP2 is 0.022% and 0.01% in "Other" and South 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.
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