NM_014297.5:c.488G>A

Variant names:

• chr19-43511454-C-T
• rs745656120
• NM_014297.5:c.488G>A

Variant summary

Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PP4_Moderate PM3_Strong PM5 PS3_Supporting PP3

This summary comes from the ClinGen Evidence Repository: The c.488G>A (NM_014297.5) variant in ETHE1 is a missense variant predicted to cause substitution of arginine by glutamine at amino acid 163 (p.R163Q). The highest population minor allele frequency for this variant in gnomAD v2.1.1 is 0.00005 (13/251,458 alleles) in the general population, which is higher than the ClinGen ETHE1 threshold < 0.00002 for PM2, thus it does not meet this criterion. This variant was originally reported in two compound heterozygous (c.131_132delAG; p. E44fsX105) relatives who both had developmental delay, petechiae, orthostatic acrocyanosis, chronic diarrhea, and ethylmalonic aciduria which is a phenotype highly specific to ethylmalonic encephalopathy (PP4_moderate; PMID:14732903). This variant has been detected in at least 9 patients reported in the literature with ethylmalonic encephalopathy, however, many of the cases are not scoreable according to the SVI recommendation for in trans criterion for PM3, as parental phasing was not performed or the second variant was a VUS (PMID:18593870; PMID:16183799, PMID:30298498). After review of scoreable cases, it was determined by the ETHE1 VCEP that four reported cases were scorable. A single relative from family L from PMID:14732903 was awarded 1.0 as this patient was a compound heterozygote for an upstream truncating variant (c.131_132delAG; p. E44fsX105), which was confirmed in trans by segregation analysis. Additionally, while the p.E44fsX105 has not been formally curated at this time, given that the p.E44fsX105 is a truncating variant that is predicted to undergo nonsense mediated decay, it is also a strong candidate for a pathogenic classification; the VCEP agreed that this was justification to score this case as 1.0. Patients reported in PMID:22020834 and PMID:27771676 were each awarded 0.25 for their respective VUS’s, which were also confirmed in trans. A homozygous patient reported in PMID:27391121 in whom homozygosity was confirmed via trio WES including parental samples was scored 0.5. This was confirmed by Baylor Genetics who performed the testing for this study (PM3_Strong; Total score- 2.0). ETHE1 encodes persulfide dioxygenase. Persulfide dioxygenase activity measured in recombinant human ETHE1 proteins (both wild-type and p.R163Q) expressed in E.Coli (purified to homogeneity) showed that the p.R163Q recombinant E.Coli only exhibited ~10% of wild-type catalytic activity, indicating that this variant impacts protein function (PS3_supporting; PMID:25198162). One other missense variant [c.487C>T, p.R163W; PMID 14732903, PMID 16828325, PMID 16183799, PMID 28698729; ClinVar Variation ID: 2317], in the same codon has been classified as pathogenic for ethylmalonic encephalopathy by the ClinGen ETHE1 VCEP (PM5). The computational predictor [REVEL] gives a score of 0.928, which is above the threshold of 0.75, evidence that correlates with impact on ETHE1 function (PP3). 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): PM3_strong, PP4_Moderate, PS3_supporting, PM5, PP3. Approved 7/12/2021. LINK:https://erepo.genome.network/evrepo/ui/classification/CA320215/MONDO:0011229/014

• Frequency:
  • Genomes: 𝑓 0.000020 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000025 (0 hom.)
• Consequence: ETHE1 NM_014297.5 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:10 U:1 O:1
• Conservation: PhyloP100: 6.47
• Publications: 13 publications found

Genes affected

ETHE1 (HGNC:23287): (ETHE1 persulfide dioxygenase) This gene encodes a member of the metallo beta-lactamase family of iron-containing proteins involved in the mitochondrial sulfide oxidation pathway. The encoded protein catalyzes the oxidation of a persulfide substrate to sulfite. Certain mutations in this gene cause ethylmalonic encephalopathy, an infantile metabolic disorder affecting the brain, gastrointestinal tract and peripheral vessels. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2016]

ETHE1 Gene-Disease associations (from GenCC):

• ethylmalonic encephalopathy

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae)
• Leigh syndrome

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen

ACMG classification

Our verdict: Pathogenic. The variant received 10 ACMG points.

• PS3: For more information check the summary or visit ClinGen Evidence Repository.
• PM3: For more information check the summary or visit ClinGen Evidence Repository.
• PM5: For more information check the summary or visit ClinGen Evidence Repository.
• PP3: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014297.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ETHE1	NM_014297.5	MANE Select	c.488G>A	p.Arg163Gln	missense	Exon 4 of 7	NP_055112.2
	ETHE1	NM_001320867.2		c.455G>A	p.Arg152Gln	missense	Exon 4 of 7	NP_001307796.1
	ETHE1	NM_001320869.2		c.194G>A	p.Arg65Gln	missense	Exon 2 of 5	NP_001307798.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ETHE1	ENST00000292147.7	TSL:1 MANE Select	c.488G>A	p.Arg163Gln	missense	Exon 4 of 7	ENSP00000292147.1
	ETHE1	ENST00000600651.5	TSL:1	c.488G>A	p.Arg163Gln	missense	Exon 4 of 6	ENSP00000469037.1
	ETHE1	ENST00000594342.5	TSL:2	n.*51G>A		non_coding_transcript_exon	Exon 3 of 6	ENSP00000469652.1

Frequencies

GnomAD3 genomes AF: 0.0000197 AC: 3 AN: 152178 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000197

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000517 AC: 13 AN: 251458 AF XY: 0.0000441

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000347

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000253 AC: 37 AN: 1461876 Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20 AN XY: 727238

African (AFR) AF: 0.0000299 AC: 1 AN: 33480

American (AMR) AF: 0.000246 AC: 11 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26134

East Asian (EAS) AF: 0.0000252 AC: 1 AN: 39698

South Asian (SAS) AF: 0.0000464 AC: 4 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53420

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.0000162 AC: 18 AN: 1111998

Other (OTH) AF: 0.0000331 AC: 2 AN: 60396

GnomAD4 genome AF: 0.0000197 AC: 3 AN: 152178 Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2 AN XY: 74340

African (AFR) AF: 0.00 AC: 0 AN: 41448

American (AMR) AF: 0.000197 AC: 3 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5204

South Asian (SAS) AF: 0.00 AC: 0 AN: 4832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10612

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68032

Other (OTH) AF: 0.00 AC: 0 AN: 2090

Alfa AF: 0.00000466 Hom.: 0

Bravo AF: 0.0000227

ExAC AF: 0.0000330 AC: 4

EpiCase AF: 0.00

EpiControl AF: 0.0000593

ClinVar

ClinVar submissions as Germline

Significance: Pathogenic

Revision: reviewed by expert panel

Pathogenic	VUS	Benign	Condition
10	1	-	Ethylmalonic encephalopathy (12)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.87
BayesDel_addAF	Pathogenic	0.34	D
BayesDel_noAF	Pathogenic	0.56
CADD	Pathogenic	33
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.90	D
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.94
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Pathogenic	1.0	D
M_CAP	Uncertain	0.22	D
MetaRNN	Pathogenic	0.98	D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	4.7	H
PhyloP100		6.5
PrimateAI	Uncertain	0.78	T
PROVEAN	Uncertain	-3.9	D
REVEL	Pathogenic	0.93
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Polyphen		1.0	D
Vest4		0.87
MutPred		0.98		Loss of methylation at R163 (P = 0.0695)
MVP		0.98
MPC		1.6
ClinPred		1.0	D
GERP RS		5.0
Varity_R		0.96
gMVP		0.93
Mutation Taster		=3/97	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs745656120; hg19: chr19-44015606; COSMIC: COSV52678756; COSMIC: COSV52678756;