The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

  • See Evidence submitted by expert panel for details.

Variant: NM_014297.5(ETHE1):c.487C>T (p.Arg163Trp)

CA115479

2317 (ClinVar)

Gene: ETHE1
Condition: ethylmalonic encephalopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: fee72906-744e-40b2-a972-1025f79f0db5
Approved on: 2021-05-06
Published on: 2021-05-06

HGVS expressions

NM_014297.5:c.487C>T
NM_014297.5(ETHE1):c.487C>T (p.Arg163Trp)
ENST00000292147.7:c.487C>T
ENST00000292147.6:c.487C>T
ENST00000594342.5:c.*50C>T
ENST00000598330.1:c.*50C>T
ENST00000600651.5:c.487C>T
NM_014297.3:c.487C>T
NM_001320867.1:c.454C>T
NM_001320868.1:c.118C>T
NM_001320869.1:c.193C>T
NM_014297.4:c.487C>T
NM_001320867.2:c.454C>T
NM_001320868.2:c.118C>T
NM_001320869.2:c.193C>T
NC_000019.10:g.43511455G>A
CM000681.2:g.43511455G>A
NC_000019.9:g.44015607G>A
CM000681.1:g.44015607G>A
NC_000019.8:g.48707447G>A
NG_008141.1:g.20790C>T

Pathogenic

Met criteria codes 6
PS3_Supporting PP3 PP4_Moderate PP1_Strong PM5 PM3_Strong
Not Met criteria codes 11
BA1 BP4 BP1 BP2 BS2 BS1 BS4 PP2 PM2 PS1 PS4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Mitochondrial Diseases VCEP
The ETHE1 c.487C>T mutation is a missense mutation at the 163 amino acid position where one other pathogenic mutation has been reported (c.488G>A) indicating that this residue is critical to the function of the protein (PM5_moderate). There are multiple lines of computational evidence supporting a deleterious effect (PP3_supporting). Functional studies performed in ETHE1 isolated from E-coli cells demonstrated 10 fold reduced ETHE1 catalytic activity when compared to controls (PS3_supporting; PMID:25198162). The c.487C>T mutation has been reported in four unrelated affected individuals including three who were homozygous for the mutation (PMID:16183799; PMID:16828325; PMID:28698729) and one proband where the c. 487C>T was found in trans with another reportedly pathogenic ETHE1 mutation (PMID:18593870) (PM3_strong). One of these patients demonstrated a clinical phenotype specific to ethylmalonic encephalopathy including chronic diarrhea, petechiae, acrocyanosis, and developmental delay in addition to the biochemical findings urinary ethylmalonic acid and elevated blood C4-acylcarnitine esters and blood C5-acylcarnitines (PP4_moderate; PMID: 16828325). A larger family including 7 children has been reported where homozygous c.487C>T mutation was identified in the three affected siblings and segregated with disease in the unaffected siblings (PP1_strong; PMID:14732903). In summary, this variant meets criteria to be classified as pathogenic for ethylmalonic encephalopathy in an autosomal recessive manner. ETHE1-specific ACMG/AMP criteria applied PM5_moderate; PP3_supporting; PS3_supporting; PM3_strong; PP4_moderate; PP1_strong.
Met criteria codes
PS3_Supporting
ETHE1 activity was determined according to its capacity to oxidize glutathione persulfide. This mutation shown <10% activity relative to control
PP3
Revel score of 0.954 meets criteria (>0.75)
PP4_Moderate
Multiple individuals either meeting clinical or biochemical criteria consistent with EE
PP1_Strong
Three affected children and Four unaffected children; linkage analysis tracks with mutated allele. LOD score of 2.31 assigned to this family
PM5
c.488 G>A has been classified as pathogenic and is present in the same amino acid residue.
PM3_Strong
Multiple patients reported with a total score of 2 pts leading to a strong classification
Not Met criteria codes
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
This rule is not used. Missense mutations have been identified in affected individuals
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
Missense mutations have been identified in affected individuals
PM2
Found at an allele frequency of 0.00023.
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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