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Variant: NM_014297.5(ETHE1):c.505+1G>T

CA406175434

504502 (ClinVar)

Gene: ETHE1
Condition: ethylmalonic encephalopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: c248dbb2-b387-486b-a99c-64bd8d7c165b
Approved on: 2021-07-27
Published on: 2021-07-27

HGVS expressions

NM_014297.5:c.505+1G>T
NM_014297.5(ETHE1):c.505+1G>T
ENST00000292147.7:c.505+1G>T
ENST00000292147.6:c.505+1G>T
ENST00000594342.5:c.*68+1G>T
ENST00000598330.1:c.*68+1G>T
ENST00000600651.5:c.505+1G>T
NM_014297.3:c.505+1G>T
NM_001320867.1:c.472+1G>T
NM_001320868.1:c.136+1G>T
NM_001320869.1:c.211+1G>T
NM_014297.4:c.505+1G>T
NM_001320867.2:c.472+1G>T
NM_001320868.2:c.136+1G>T
NM_001320869.2:c.211+1G>T
NC_000019.10:g.43511436C>A
CM000681.2:g.43511436C>A
NC_000019.9:g.44015588C>A
CM000681.1:g.44015588C>A
NC_000019.8:g.48707428C>A
NG_008141.1:g.20809G>T
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Pathogenic

Met criteria codes 4
PP4_Moderate PM2 PVS1 PM3_Supporting
Not Met criteria codes 7
BA1 BS4 BS1 BS2 BP5 BP2 PP1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The c.505+1G>T variant (NM_014297.5) in ETHE1 occurs within the canonical splice donor/acceptor site (+1) of exon/intron 4 boundary (exon 4/7). It is predicted to cause aberrant splicing, resulting in a frameshift leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1; PMID: 14732903). This prediction is supported by the absence of protein on Western blot of fibroblasts from patient J who was homozygous for this variant (PMID: 14732903). This variant is absent from gnomAD v2.1.1 (PM2). This variant was originally reported in a homozygote with developmental delay, petechiae, orthostatic acrocyanosis, chronic diarrhea, and ethylmalonic aciduria which is a phenotype highly specific to ethylmalonic encephalopathy (PP4_moderate; PMID: 14732903 patient J). While there are at least four homozygotes with ethylmalonic encephalopathy reported to date, parental linkage analyses have only been performed in one of these patients to confirm the variants were in trans (PM3_supporting; Total Score- 0.5; PMID: 14732903, PMID: 22584649, PMID: 18593870). In summary, this variant meets the criteria to be classified as pathogenic for Autosomal Recessive Ethylmalonic Encephalopathy. ACMG/AMP criteria applied, as specified by the ClinGen ETHE1 VCEP (version 1.0): PVS1, PM2, PM3_supporting, PP4_Moderate. Approved 7/6/2021.
Met criteria codes
PP4_Moderate
Patient J, homozygous per paper "All patients had clinical and biochemical features typical of the disease" "EE is characterized by neurodevelopmental delay and regression, prominent pyramidal and extrapyramidal signs, recurrent petechiae, orthostatic acrocyanosis (fig. 1a), and chronic diarrhea, leading to death in the first decade of life."
PM2
Not present in gnomAD 6/20/2021
PVS1
505+1G>T occurs on the exon/intron 4 boundary, predicted to lead to NMD through abberant splicing, which was corroborated via Western Blot in Tiranti et al 2004
PM3_Supporting
4 homozygotes in literature, 1 in Tiranti et al 2004, 2 in Mineri et al 2008, 1 in Dweikat et al no parental testing so unable to score. Only Tiranti et al 2004 reported linkage studies confirming in trans. Utilized ClinGen SVI v.10 scoring guidelines for PM3 TOTAL = 0.5 (Homozygote confirmed in trans; PMID 14732903)
Not Met criteria codes
BA1
Not present in gnomAD 6/20/2021
BS4
No such family studies performed
BS1
Not present in gnomAD 6/20/2021
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No such case found
BP2
No such case found
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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