NM_004453.4(ETFDH):c.250G>A (p.Ala84Thr)
criteria provided, multiple submitters, no conflicts. Learn more about how ClinVar calculates review status.
Pathogenic (10)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_004453.4(ETFDH):c.250G>A (p.Ala84Thr)
Variation ID: 12028 Accession: VCV000012028.48
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 4q32.1 4: 158682269 (GRCh38) [ NCBI UCSC ] 4: 159603421 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 4, 2013 Apr 4, 2026 Jan 18, 2026 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_004453.4:c.250G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_004444.2:p.Ala84Thr missense NM_001281737.2:c.109G>A NP_001268666.1:p.Ala37Thr missense NM_001281738.1:c.67G>A NP_001268667.1:p.Ala23Thr missense NM_004453.2:c.250G>A NC_000004.12:g.158682269G>A NC_000004.11:g.159603421G>A NG_007078.2:g.14928G>A Q16134:p.Ala84Thr - Protein change
- A84T, A23T, A37T
- Other names
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- Canonical SPDI
- NC_000004.12:158682268:G:A
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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0.00020 (A)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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The Genome Aggregation Database (gnomAD) 0.00004
The Genome Aggregation Database (gnomAD) 0.00005
The Genome Aggregation Database (gnomAD), exomes 0.00005
Trans-Omics for Precision Medicine (TOPMed) 0.00007
The Genome Aggregation Database (gnomAD), exomes 0.00014
1000 Genomes Project 30x 0.00016
Exome Aggregation Consortium (ExAC) 0.00016
1000 Genomes Project 0.00020
- Links
Genes
| Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
|---|---|---|---|---|---|---|
| HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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| ETFDH | Gene associated with autosomal recessive phenotype | Not yet evaluated |
GRCh38 GRCh37 |
1107 | 1156 | |
Conditions - Germline
| Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Pathogenic (1) |
no assertion criteria provided
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Dec 1, 2010 | RCV000012808.23 | |
| Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Jan 27, 2022 | RCV000224728.6 | |
| Pathogenic (8) |
criteria provided, multiple submitters, no conflicts
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Jan 18, 2026 | RCV000553294.25 | |
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See cases
|
no classifications from unflagged records (1) |
no classifications from unflagged records
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May 24, 2024 | RCV003231099.3 |
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Glutaric acidemia type 2C
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Pathogenic (1) |
criteria provided, single submitter
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Nov 4, 2025 | RCV006638616.1 |
Submissions - Germline
| Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
Expand all rows
Collapse all rows
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Oct 30, 2015)
C
Contributing to aggregate classification
|
criteria provided, single submitter
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not provided |
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics
Accession: SCV000281570.2
First in ClinVar: Jun 08, 2016 Last updated: Jun 08, 2016 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: not provided
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: not provided
Platform type: Sequencing
Platform name: Illumina
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Pathogenic
(-)
C
Contributing to aggregate classification
|
criteria provided, single submitter
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Multiple acyl-CoA dehydrogenase deficiency |
Juno Genomics, Hangzhou Juno Genomics, Inc
Accession: SCV005416471.2
First in ClinVar: Nov 30, 2024 Last updated: Oct 05, 2025 |
Comment:
show
Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.;Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc).;For recessive disorders, detected in trans with a pathogenic variant. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
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Pathogenic
(Jan 03, 2022)
C
Contributing to aggregate classification
|
criteria provided, single submitter
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Multiple acyl-CoA dehydrogenase deficiency |
3billion
Accession: SCV002058808.1
First in ClinVar: Jan 15, 2022 Last updated: Jan 15, 2022 |
Comment:
show
Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000012028, PMID:19249206, PS1_S). The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least one similarly affected unrelated individual (3billion dataset, PM3_M). A different missense change at the same codon has been reported to be associated with ETFDH related disorder (PMID:23628458, PM5_P). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.886, 3CNET: 0.925, PP3_P). A missense variant is a common mechanism associated with Glutaric acidemia IIC (PP2_P). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000127, PM2_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Clinical Features:
Global developmental delay (present) , Abnormal facial shape (present) , Hepatic steatosis (present) , Generalized hypotonia (present) , Mild intellectual disability (present) , Intellectual disability (present)
Zygosity: 1 Single Heterozygote
Platform type: whole exome sequencing
Platform name: NovaSeq
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Pathogenic
(Jan 27, 2022)
C
Contributing to aggregate classification
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criteria provided, single submitter
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not provided |
GeneDx
Accession: SCV001814073.3
First in ClinVar: Sep 08, 2021 Last updated: Mar 04, 2023 |
Comment:
show
Functional studies in an A84T knock-in mouse model found this variant was associated with lower steady state levels of ETF:QO protein and increased acylcarnitine concentration in muscle that was riboflavin-dependent, consistent with findings in muscle cells from affected individuals (Xu J et al., 2018); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 27060313, 20370797, 25119904, 24357026, 21347544, 22013910, 19249206, 27000805, 24522293, 19265687, 29961769, 29615056, 28950901, 31058673, 31852447, 32190638, 27935074, 32778825, 33639866, 32005694, 33589341, 29046209, 27270537, 30709034, 30232818) (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
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Pathogenic
(Dec 13, 2023)
C
Contributing to aggregate classification
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criteria provided, single submitter
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Multiple acyl-CoA dehydrogenase deficiency |
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV004241078.1
First in ClinVar: Feb 04, 2024 Last updated: Feb 04, 2024 |
Comment:
show
Variant summary: ETFDH c.250G>A (p.Ala84Thr) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00014 in 251434 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in ETFDH causing Glutaric Aciduria, Type 2c (0.00014 vs 0.0011), allowing no conclusion about variant significance. c.250G>A has been reported in the literature in multiple individuals affected with lateonset multiple acylcoenzyme A dehydrogenation deficiency, including as a homozygote or heterozygote phenotype without second variants reported (e.g. Liu_2016). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence demonstrating an impact on protein function in Etfdh-(h)A84T knock-in mice, showing reduced protein levels in muscle and liver with vitamin B2 deficiency, and clinical and biochemical profiles similar to human patients affected with riboflavin-responsive multiple acylcoenzyme A dehydrogenation deficiency (e.g. Xu_2018). The following publications have been ascertained in the context of this evaluation (PMID: 27270537, 30232818). Eight submitters have cited clinical-significance assessments for this variant to ClinVar after 2014, classifying the variant as pathogenic (n=7) or likely pathogenic (n=1). Based on the evidence outlined above, the variant was classified as pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
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Pathogenic
(Mar 30, 2024)
C
Contributing to aggregate classification
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criteria provided, single submitter
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Multiple acyl-CoA dehydrogenase deficiency |
Baylor Genetics
Accession: SCV004194765.2
First in ClinVar: Dec 30, 2023 Last updated: Jun 17, 2024 |
Observation: 1
Collection method: clinical testing
Allele origin: unknown
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: unknown
Affected status: unknown
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Pathogenic
(Nov 04, 2025)
C
Contributing to aggregate classification
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criteria provided, single submitter
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Glutaric acidemia type 2C
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Natera, Inc.
Accession: SCV001452018.2
First in ClinVar: Jan 02, 2021 Last updated: Apr 04, 2026 |
Comment:
show
The c.250G>A variant in ETFDH is a missense variant predicted to cause substitution of alanine to threonine at amino acid 84. This variant is rare in the general population with a frequency below the threshold expected for the associated phenotype(s). This variant has been observed in one or more individuals affected with the associated recessive disease, as either homozygous or compound heterozygous with a second variant (PMID: 23628458, 20138856, 19265687). Additionally, this variant has been observed to segregate in affected family members (PMID: 20138856). Computational prediction algorithms indicate this variant is likely to affect gene or protein function. Given the available evidence, this variant is classified as Pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
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Pathogenic
(May 06, 2024)
C
Contributing to aggregate classification
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criteria provided, single submitter
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Multiple acyl-CoA dehydrogenase deficiency |
Fulgent Genetics, Fulgent Genetics
Accession: SCV002796479.2
First in ClinVar: Dec 31, 2022 Last updated: Jan 25, 2025 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
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Pathogenic
(Apr 27, 2021)
C
Contributing to aggregate classification
|
criteria provided, single submitter
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Multiple acyl-CoA dehydrogenase deficiency |
Revvity Omics, Revvity
Accession: SCV002022219.4
First in ClinVar: Nov 29, 2021 Last updated: Sep 06, 2025 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
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Pathogenic
(Jan 18, 2026)
C
Contributing to aggregate classification
|
criteria provided, single submitter
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Multiple acyl-CoA dehydrogenase deficiency |
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000631958.9
First in ClinVar: Dec 26, 2017 Last updated: Feb 23, 2026 |
Comment:
show
This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 84 of the ETFDH protein (p.Ala84Thr). This variant is present in population databases (rs121964954, gnomAD 0.2%). This missense change has been observed in individuals with late-onset, riboflavine-responsive form of MADD (PMID: 19249206, 20370797, 21347544, 22013910, 24357026, 27000805, 27270537). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 12028). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt ETFDH protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects ETFDH function (PMID: 27935074). For these reasons, this variant has been classified as Pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
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Pathogenic
(Dec 01, 2010)
N
Not contributing to aggregate classification
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no assertion criteria provided
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GLUTARIC ACIDEMIA IIC |
OMIM
Accession: SCV000033048.2
First in ClinVar: Apr 04, 2013 Last updated: Jul 15, 2021 |
Observation: 1
Collection method: literature only
Allele origin: germline
Affected status: not provided
Observation 1
Collection method: literature only
Allele origin: germline
Affected status: not provided
Comment on evidence:
In 4 Taiwanese patients from 3 unrelated families with glutaric acidemia IIC (MADD; 231680), Liang et al. (2009) identified a 250G-A transition in exon 3 … (more)
In 4 Taiwanese patients from 3 unrelated families with glutaric acidemia IIC (MADD; 231680), Liang et al. (2009) identified a 250G-A transition in exon 3 of the ETFDH gene, resulting in an ala84-to-thr (A84T) substitution. One patient was homozygous for the mutation, whereas the other 3 were compound heterozygous for A84T and either a 524G-T transversion, resulting in an arg175-to-leu (R175L; 231675.0004) substitution (2 sibs) or a 380T-A transversion, resulting in a leu127-to-his (L127H; 231675.0005) substitution. All 3 mutations affected highly conserved residues in the FAD-binding domain. The R175L and L127H mutations were not identified in 200 Taiwanese control chromosomes. The A84T variant was identified in 1 of 200 Taiwanese control chromosomes but not in 100 Japanese, 100 Korean, and 100 Thai control chromosomes. No specific haplotype could be linked to the A84T variant. Lan et al. (2010) identified homozygosity for the A84T mutation in 6 of 7 Han Taiwanese patients with MADD. The patients had a variable phenotype. The age at diagnosis ranged from 7 to 43 years, and the patients' ages at the time of the report were between 22 and 44 years. All had a history of episodic myalgia and limb weakness predominantly affecting the proximal muscles during an acute stage of myopathy. Four had dysphagia and 2 had respiratory failure. Serum creatine kinase was increased during the acute attacks. Three had 1 episode, whereas 4 had recurrent episodes. Four patients had extramuscular features. All except 1 regained normal muscle strength after the acute stage. Trigger factors in some patients included prolonged fasting and exercise. Blood analysis showed increased acylcarnitines ranging from C8 to C16. A seventh Han Taiwanese patient with the disorder was compound heterozygous for A84T and a 524G-A transition in the ETFDH gene, resulting in an arg175-to-his (R175H; 231675.0006) substitution in a highly conserved residue in the FAD-binding domain. (less)
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Likely pathogenic
(Jun 07, 2017)
N
Not contributing to aggregate classification
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no assertion criteria provided
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Multiple acyl-CoA dehydrogenase deficiency |
SingHealth Duke-NUS Institute of Precision Medicine
Accession: SCV000853129.1
First in ClinVar: Nov 25, 2018 Last updated: Nov 25, 2018 |
Observation: 1
Collection method: curation
Allele origin: germline
Affected status: no
Observation 1
Collection method: curation
Allele origin: germline
Affected status: no
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Uncertain significance
(-)
N
Not contributing to aggregate classification
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Flagged submission
flagged submission
Reason: Outlier claim with insufficient supporting evidence
Source: ClinGen
|
See cases
(Autosomal recessive inheritance)
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Pediatric Department, Xiangya Hospital, Central South University
Accession: SCV002760204.1
First in ClinVar: Jun 10, 2023 Last updated: Jun 10, 2023 |
Observation: 1
Collection method: clinical testing
Allele origin: inherited
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: inherited
Affected status: yes
Clinical Features:
Muscle weakness (present) , Abnormality of the liver (present)
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| Flagged submissions do not contribute to the aggregate classification or review status for the variant. Learn more | |||||
Citations for germline classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| ETFDH Mutations and Flavin Adenine Dinucleotide Homeostasis Disturbance Are Essential for Developing Riboflavin-Responsive Multiple Acyl-Coenzyme A Dehydrogenation Deficiency. | Xu J | Annals of neurology | 2018 | PMID: 30232818 |
| Neurite growth could be impaired by ETFDH mutation but restored by mitochondrial cofactors. | Liang WC | Muscle & nerve | 2017 | PMID: 27935074 |
| Skeletal Muscle Magnetic Resonance Imaging of the Lower Limbs in Late-onset Lipid Storage Myopathy with Electron Transfer Flavoprotein Dehydrogenase Gene Mutations. | Liu XY | Chinese medical journal | 2016 | PMID: 27270537 |
| Significant clinical heterogeneity with similar ETFDH genotype in three Chinese patients with late-onset multiple acyl-CoA dehydrogenase deficiency. | Fu HX | Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology | 2016 | PMID: 27000805 |
| Clinical features and ETFDH mutation spectrum in a cohort of 90 Chinese patients with late-onset multiple acyl-CoA dehydrogenase deficiency. | Xi J | Journal of inherited metabolic disease | 2014 | PMID: 24357026 |
| Increased muscle coenzyme Q10 in riboflavin responsive MADD with ETFDH gene mutations due to secondary mitochondrial proliferation. | Wen B | Molecular genetics and metabolism | 2013 | PMID: 23628458 |
| Computational analysis of a novel mutation in ETFDH gene highlights its long-range effects on the FAD-binding motif. | Er TK | BMC structural biology | 2011 | PMID: 22013910 |
| Molecular analysis of 51 unrelated pedigrees with late-onset multiple acyl-CoA dehydrogenation deficiency (MADD) in southern China confirmed the most common ETFDH mutation and high carrier frequency of c.250G>A. | Wang ZQ | Journal of molecular medicine (Berlin, Germany) | 2011 | PMID: 21347544 |
| High frequency of ETFDH c.250G>A mutation in Taiwanese patients with late-onset lipid storage myopathy. | Lan MY | Clinical genetics | 2010 | PMID: 20370797 |
| High resolution melting analysis facilitates mutation screening of ETFDH gene: applications in riboflavin-responsive multiple acyl-CoA dehydrogenase deficiency. | Er TK | Clinica chimica acta; international journal of clinical chemistry | 2010 | PMID: 20138856 |
| Novel mutations in ETFDH gene in Chinese patients with riboflavin-responsive multiple acyl-CoA dehydrogenase deficiency. | Law LK | Clinica chimica acta; international journal of clinical chemistry | 2009 | PMID: 19265687 |
| ETFDH mutations, CoQ10 levels, and respiratory chain activities in patients with riboflavin-responsive multiple acyl-CoA dehydrogenase deficiency. | Liang WC | Neuromuscular disorders : NMD | 2009 | PMID: 19249206 |
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Text-mined citations for rs121964954 ...
HelpRecord last updated Apr 13, 2026
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.
