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_014297.5(ETHE1):c.505+1G>A

CA308743496

496427 (ClinVar)

Gene: ETHE1
Condition: ethylmalonic encephalopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: 447c8ee6-9867-4f18-a748-0ceb86576e20
Approved on: 2021-07-27
Published on: 2021-07-27

HGVS expressions

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

Met criteria codes 4
PP4_Moderate PM3_Supporting PVS1 PM2
Not Met criteria codes 6
BS2 BS1 PS2 PP1 BA1 PM6

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>A 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). There is another pathogenic variant at this position (c.505+1G>T) for which Western blot analyses provided supportive evidence for nonsense mediated decay (PMID: 14732903). The highest population minor allele frequency in gnomAD v2.1.1 is 0.000008 (2/251,460 alleles) in the general population, which is lower than the ClinGen ETHE1 threshold < 0.00002 for PM2, meeting this criterion (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 O). While there are at least 2 homozygotes of this variant with ethylmalonic encephalopathy reported to date, parental analyses have only been performed in one of these patients to confirm the variants were in trans (PM3_supporting; PMID: 29526615). 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 O Tiranti et al. 2004: "All patients had clinical and biochemical features typical of the disease"
PM3_Supporting
Utilized ClinGen SVI v.10 scoring guidelines for PM3 TOTAL = 0.5 (Homozygote confirmed in trans; PMID 29526615). Unable to count patient O in Tiranti et al 2004 as this was a singleton case
PVS1
This variant is predicted to result in abnormal splicing >50bp upstream of the last exon/intron junction (c.505+1G>A occurs at exon/intron 4) and LOF due to nonsense mediated decay. Absence of protein was confirmed for the c.505+1G>T mutation in Tiranti et al 2004 via Western blot. Splice AI predicts a high confidence (delta score 0.96) splice donor loss at this site
PM2
Present in 2 alleles in gnomAD (AF =0.00001, no homozygotes) which is below established AF threshold of 0.00002
Not Met criteria codes
BS2
No homozygotes in gnomAD
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No de novo cases reported to date
PP1
Boyer et al. 2018 reports patient 1's sibling who had a classic presentation of ethylmalonic encephalopathy with all clinical and biochemical features. However, this sibling passed away several years prior to the study and mutation status was not confirmed.
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No de novo cases reported to date
Curation History
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