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.1466G>C (p.Ser489Thr)

CA170245

143475 (ClinVar)

Gene: MECP2

Condition: Rett syndrome

Inheritance Mode: X-linked inheritance

Link to MONDO

UUID: 32d53fd8-0652-4c83-ba6a-b7a791fb3b20

Approved on: 2021-12-13

Published on: 2021-12-27

HGVS expressions

NM_001110792.2:c.1466G>C

NM_001110792.2(MECP2):c.1466G>C (p.Ser489Thr)

NC_000023.11:g.154030398C>G

CM000685.2:g.154030398C>G

NC_000023.10:g.153295849C>G

CM000685.1:g.153295849C>G

NC_000023.9:g.152949043C>G

NG_007107.2:g.111730G>C

NG_007107.3:g.111706G>C

ENST00000303391.11:c.1430G>C

ENST00000453960.7:c.1466G>C

ENST00000303391.10:c.1430G>C

ENST00000453960.6:c.1466G>C

ENST00000619732.4:c.1430G>C

ENST00000628176.2:c.*802G>C

NM_001110792.1:c.1466G>C

NM_001316337.1:c.1151G>C

NM_004992.3:c.1430G>C

NM_001316337.2:c.1151G>C

NM_001369391.2:c.1151G>C

NM_001369392.2:c.1151G>C

NM_001369393.2:c.1151G>C

NM_001369394.1:c.1151G>C

NM_001369394.2:c.1151G>C

NM_001386137.1:c.761G>C

NM_001386138.1:c.761G>C

NM_001386139.1:c.761G>C

NM_004992.4:c.1430G>C

Uncertain Significance

BS2 PM2_Supporting

BP2

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 p.Ser477Thr (NM_004992.3) variant is observed in at least 2 unaffected individuals (PMID 12655490)(BS2). The p.Ser477Thr variant is observed in the MECP2 gene where a second pathogenic variant in the same gene is present in the patient (PMID 12655490); however, it is unknown if the variants are in cis or trans (BP5 - not met). The p.Ser477Thr variant in MECP2 is absent from gnomAD (PM2_supporting). In summary, the p.Ser477Thr variant in MECP2 is classified as a variant of uncertain significance based on the ACMG/AMP criteria (BS2, PM2_supporting).

BS2

The p.Ser477Thr variant is observed in at least 2 unaffected individuals (PMID 12655490)

PM2_Supporting

The p.Ser477Thr variant in MECP2 is absent from gnomAD

BP2

The p.Ser477Thr variant is observed in the MECP2 gene where a second pathogenic variant in the same gene is present in the patient (PMID 12655490); however, it is unknown if the variants are in cis or trans.

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