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.1191_1202del (p.Leu398_Pro401del)

CA274655

189751 (ClinVar)

Gene: MECP2
Condition: Rett syndrome
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: 053ac9bf-6950-4700-905e-85fcf3efd862
Approved on: 2022-12-09
Published on: 2022-12-23

HGVS expressions

NM_001110792.2:c.1191_1202del
NM_001110792.2(MECP2):c.1191_1202del (p.Leu398_Pro401del)
NC_000023.11:g.154030668_154030679del
CM000685.2:g.154030668_154030679del
NC_000023.10:g.153296119_153296130del
CM000685.1:g.153296119_153296130del
NC_000023.9:g.152949313_152949324del
NG_007107.2:g.111455_111466del
NG_007107.3:g.111431_111442del
ENST00000303391.11:c.1155_1166del
ENST00000453960.7:c.1191_1202del
ENST00000303391.10:c.1155_1166del
ENST00000407218.5:c.*527_*538del
ENST00000453960.6:c.1191_1202del
ENST00000619732.4:c.1155_1166del
ENST00000628176.2:c.*527_*538del
NM_001110792.1:c.1191_1202del
NM_001316337.1:c.876_887del
NM_004992.3:c.1155_1166del
NM_001316337.2:c.876_887del
NM_001369391.2:c.876_887del
NM_001369392.2:c.876_887del
NM_001369393.2:c.876_887del
NM_001369394.1:c.876_887del
NM_001369394.2:c.876_887del
NM_001386137.1:c.486_497del
NM_001386138.1:c.486_497del
NM_001386139.1:c.486_497del
NM_004992.4:c.1155_1166del
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Benign

Met criteria codes 3
BS2 BS1 BP5
Not Met criteria codes 1
PS4

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.Leu386_Pro389del variant in MECP2 (NM_004992.3) is 0.019% in Latino/Admixed American 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.Leu386_Pro389del variant is observed in 3 unaffected individuals (internal database) (BS2). The p.Leu386_Pro389del variant is found in 2 patients with an alternate molecular basis of disease (internal database) (BP5). The p.Leu386_Pro389del variant has been observed in 2 individuals with neurological disorders (PMID: 19914908, 23262346) (PS4 not met). In summary, the p.Leu386_Pro389del variant in MECP2 is classified as Benign based on the ACMG/AMP criteria (BS1, BS2, BP5).
Met criteria codes
BS2
The p.Leu386_Pro389del variant in MECP2 (NM_004992.3) is observed in 3 unaffected individuals (internal database) (BS2).
BS1
The allele frequency of the p.Leu386_Pro389del variant in MECP2 (NM_004992.3) is 0.019% in Latino/Admixed American 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).
BP5
The p.Leu386_Pro389del variant in MECP2 (NM_004992.3) is found in 2 patient with an alternate molecular basis of disease (internal database).
Not Met criteria codes
PS4
The p.Leu386_Pro389del variant in MECP2 (NM_004992.3) has been observed in 2 individuals with neurological disorders (PMID: 19914908, 23262346).
Curation History
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