rs117225135
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 1P and 6B. PP5BP4BS1_SupportingBS2
The NM_018706.7(DHTKD1):c.2185G>A(p.Gly729Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00266 in 1,610,968 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_018706.7 missense
Scores
Clinical Significance
Conservation
Publications
- 2-aminoadipic 2-oxoadipic aciduriaInheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, ClinGen
- Charcot-Marie-Tooth disease axonal type 2QInheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet
Genome browser will be placed here
ACMG classification
Our verdict: Likely_benign. The variant received -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.00186 AC: 283AN: 152102Hom.: 1 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.00166 AC: 412AN: 248268 AF XY: 0.00176 show subpopulations
GnomAD4 exome AF: 0.00275 AC: 4009AN: 1458748Hom.: 11 Cov.: 31 AF XY: 0.00273 AC XY: 1983AN XY: 725616 show subpopulations
Age Distribution
GnomAD4 genome 0.00186 AC: 283AN: 152220Hom.: 1 Cov.: 33 AF XY: 0.00156 AC XY: 116AN XY: 74414 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
2-aminoadipic 2-oxoadipic aciduria Pathogenic:10
- -
This sequence variant is a single nucleotide substitution (G>A) at position 2185 of the coding sequence of the DHTKD1 gene that results in a glycine to arginine amino acid change at residue 729 of the DHTKD1 encoded protein, E1 component of 2-oxoglutarate dehydrogese. The Gly729 residue falls in the alpha/beta2 domain (PMID: 32695416) which plays a critical role in 2-oxoglutarate dehydrogese's role in DH production (PMID: 32303640). This is a previously reported variant (ClinVar) and is one of the more common variants associated with two rare metabolic disorders: 2-aminoadipic and alpha-ketoadipic aciduria (PMID: 32303640). When in the compound heterozygous or homozygous states, this variant has been observed in individuals with a range of neurological disorders including developmental delay, mild-to-severe intellectual disability, speech delay, ataxia, epilepsy, hypotonia, spil muscular atrophy, autism, and behavioral disorders (PMID: 23141293, 26141459, 25860818, 29858556, 30842647). This variant is rare in control population datasets (gnomAD database, 465 of 279,662 alleles, 0.17%). Multiple bioinformatic tools predict that this glycine to arginine amino acid change would be damaging, and the Gly729 residue is strongly conserved across the vertebrate species examined. Functiol studies indicate that this variant leads to increased 2-oxoadipate levels in cells (PMID: 23141293) and reduces the efficiency of the 2-oxoadipate dehydrogese complex in generating DH (PMID: 32303640). This reduction in efficiency is thought to be the result of this variant disrupting the protein-to-protein interactions within the 2-oxoadipate dehydrogese complex (PMID: 32303640); however other studies have concluded that this variant has no impact on protein stability or its interactions. Given this information, we consider this to be a likely pathogenic variant. ACMG Criteria: PM3, PP3, PS3 -
- -
This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 729 of the DHTKD1 protein (p.Gly729Arg). This variant is present in population databases (rs117225135, gnomAD 0.3%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with autosomal recessive 2-aminoadipic 2-oxoadipic aciduria (PMID: 23141293, 25860818, 26141459; internal data). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 39564). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. For these reasons, this variant has been classified as Pathogenic. -
This variant is interpreted as a Likely Pathogenic, for 2-aminoadipic 2-oxoadipic aciduria, Autosomal Recessive inheritance. The following ACMG Tag(s) were applied: PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PP3 => Multiple lines of computational evidence support a deleterious effect on the gene or gene product. PM6 => Assumed de novo, but without confirmation of paternity and maternity. PM3-Supporting => PM3 downgraded in strength to Supporting. PS3-Moderate => PS3 downgraded in strength to Moderate. -
- -
The DHTKD1 c.2185G>A (p.Gly729Arg) variant is a missense variant that has been reported in a total of seven individuals with alpha-aminoadipic and alpha-ketoadipic aciduria, including in a compound heterozygous state in six, including in one where the variant arose de novo, and in a heterozygous state without a second identified allele in one (Danhauser et al. 2012; Hagen et al. 2015; Stiles et al. 2016). One of the individuals who was compound heterozygous presented only with elevated metabolites and biotinidase deficiency; all others presented with more severe phenotypes that included features such as developmental delay, speech delay, intellectual disability, microcephaly, and seizures. Control data are unavailable for this variant, which is reported in the Genome Aggregation Database at a frequency of 0.002748 in the European (non-Finnish) population (version 2.1.1) and was identified in one individual in a homozygous state (version 3.1.1). The higher than expected allele frequency and the homozygous individual may be consistent with variable disease expressivity. In vitro analysis in fibroblasts from patients reported by Danhauser et al. (2012) showed elevated levels of 2-oxoadipate in cells and media when compared to wildtype control fibroblasts, and expression of wildtype DHTKD1 in patient fibroblasts rescued the phenotype and decreased the 2-oxoadipate concentrations to levels consistent with control fibroblasts. Zhang et al. (2020) demonstrated that the p.Gly729Arg variant causes a 50-fold decrease in catalytic efficiency for NADH production when assembled into the 2-oxoadipate dehydrogenase complex (OADHc) in vitro, and impacts the assembly of 2-oxoadipate dehydrogenase with dihydrolipoamide succinyl-transferase, leading to impaired channeling of OADHc intermediates. Bezerra et al. (2020) found that the p.Gly729Arg variant does not impact protein thermostability or overall protein stability. Based on the evidence, the p.Gly729Arg variant is classified as likely pathogenic for alpha-aminoadipic and alpha-ketoadipic aciduria. -
The DHTKD1 c.2185G>A (p.Gly729Arg) variant has been reported in seven individuals affected with alpha-aminoadipic and alpha ketoadipic aciduria (Danhauser K et al., PMID: 23141293; Duran M et al., PMID: 6434826; Hagen J et al., PMID: 25860818; Stiles AR et al., PMID: 26141459). Of those individuals, four were compound heterozygous for the variant and a pathogenic or likely pathogenic variant and all confirmed in trans (Danhauser K et al., PMID: 23141293; Duran M et al., PMID: 6434826; Hagen J et al., PMID: 25860818). The highest population minor allele frequency in the population database genome aggregation database (v.2.1.1) is 0.3% in European non-Finnish population. Although in vitro analysis indicates that the p.Gly729Arg variant does not disrupt protein stability or thermostability (Bezerra GA et al., PMID: 32695416), functional studies in patient fibroblasts show elevated levels of 2-oxoadipate that was rescued with the expression of wildtype DHTKD1 (Danhauser K et al., PMID: 23141293). This variant also results in decreased catalytic efficiency for NADH production which impairs channeling of 2-oxoadipate dehydrogenase complex (OADHc) intermediates (Zhang X et al., PMID: 32303640); both studies indicate that this variant impacts protein function. Computational predictors are conflicting as to the impact of this variant on DHTKD1 function. This variant has been reported in the ClinVar database as a pathogenic variant by four submitters, likely pathogenic by eight submitters and a variant of uncertain significance by three submitters. Based on available information and the ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), this variant is classified as likely pathogenic. -
- -
Variant summary: DHTKD1 c.2185G>A (p.Gly729Arg) results in a non-conservative amino acid change located in the Transketolase-like, pyrimidine-binding domain (IPR005475) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0017 in 248268 control chromosomes. c.2185G>A has been reported in the literature in individuals affected with 2-Aminoadipic 2-Oxoadipic Aciduria (examples: Danhauser_2012, Lee_2014, Hagen_2015). These data indicate that the variant is likely to be associated with disease. At least one publication reports experimental evidence that this variant impacts normal protein function (Zhang_2020). The following publications have been ascertained in the context of this evaluation (PMID: 23141293, 25860818, 25326637, 32303640). ClinVar contains an entry for this variant (Variation ID: 39564). Based on the evidence outlined above, the variant was classified as pathogenic. -
not provided Pathogenic:4Uncertain:2
The DHTKD1 c.2185G>A; p.Gly729Arg (rs117225135; ClinVar Variation ID: 39564) has been previously reported in association with 2-aminoadipic 2-oxoadipic aciduria in multiple unrelated individuals in the compound heterozygous state along with loss of function variants of DHTKD1 (Danhauser 2012, Hagen 2015, Stiles 2012, Dawidziuk 2021). Functional studies performed by Danhauser et al. in fibroblasts isolated from carriers of the p.Gly729Arg variant demonstrated defective lysine metabolism which was corrected by the addition of wild type DHTKD1. Additional functional analysis by Zhang et al (2020) further characterized the reduction in enzymatic activity associated with the substituted arginine. This variant is listed in the genome Aggregation Database (gnomAD) v2.1.1 with a non-Finnish European population frequency of 0.3% (identified on 352 out of 128,094 chromosomes). Based on available information, this variant is considered to be a pathogenic recessive allele for 2-aminoadipic 2-oxoadipic aciduria. Furthermore, as discussed in Hagen et al, it is unlikely to result in elevated risk for Charcot-Marie-Tooth disease. References: Danhauser et al. DHTKD1 mutations cause 2-aminoadipic and 2-oxoadipic aciduria. Am J Hum Genet. 2012 Dec 7;91(6):1082-7. Dawidziuk M et al. Exome Sequencing Reveals Novel Variants and Expands the Genetic Landscape for Congenital Microcephaly. Genes (Basel). 2021 Dec 18;12(12):2014. PMID: 34946966 Hagen et al. Genetic basis of alpha-aminoadipic and alpha-ketoadipic aciduria. J Inherit Metab Dis. 2015 Sep;38(5):873-9. Stiles AR et al. New Cases of DHTKD1 Mutations in Patients with 2-Ketoadipic Aciduria. JIMD Rep. 2016;25:15-19. PMID: 26141459 Zhang X et al. Structure-function analyses of the G729R 2-oxoadipate dehydrogenase genetic variant associated with a disorder of l-lysine metabolism. J Biol Chem. 2020 Jun 5;295(23):8078-8095. PMID: 32303640 -
Observed in multiple patients in published literature with 2-aminoadipic and 2-oxoadipic aciduria and phenotypes suspected to be related; however, some of these patients harbored other potential explanations for their clinical phenotypes or harbored only one variant in DHTKD1 (Danhauser et al., 2012; Hagen et al., 2015; Stiles et al., 2016); Published functional studies suggest a damaging effect on the function of the 2-oxoadipate dehydrogenase complex (Zhang et al., 2020); 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: 23141293, 26141459, 32303640, 25860818, 30842647, 34426522, 33946784, 35052424) -
- -
- -
BP4, PM3, PS3, PS4_moderate -
DHTKD1: PS3:Supporting, BS1:Supporting -
not specified Pathogenic:1Uncertain:1
- -
- -
Inborn genetic diseases Pathogenic:1
The c.2185G>A (p.G729R) alteration is located in exon 13 (coding exon 13) of the DHTKD1 gene. This alteration results from a G to A substitution at nucleotide position 2185, causing the glycine (G) at amino acid position 729 to be replaced by an arginine (R). Based on data from gnomAD, the A allele has an overall frequency of 0.17% (465/279662) total alleles studied. The highest observed frequency was 0.27% (352/128094) of European (non-Finnish) alleles. This variant has been identified in conjunction with other DHTKD1 variant(s) in individual(s) with features consistent with alpha-aminoadipic and alpha-ketoadipic aciduria (Danhauser, 2012; Hagen, 2015; Stiles, 2016). This amino acid position is well conserved in available vertebrate species. Experimental studies showed this variant has a damaging effect on protein function (Danhauser, 2012; Zhang, 2020). This alteration is predicted to be tolerated by in silico analysis. Based on the available evidence, this alteration is classified as likely pathogenic. -
Tip-toe gait Pathogenic:1
Hereditary motor sensory neuropathy (HMSN), also known as Charcot-Marie-Tooth Disease (CMT), is the most commonly inherited peripheral polyneuropathy. It constitutes a group of inherited, progressive, motor and sensory peripheral nerve disorders with properties of demyelination, axonal degeneration, or both. It is classified by clinical characteristics, modes of inheritance, electrophysiologic features, metabolic defects, and specific gene markers. Our patients all walk on tiptoe, so they show similar symptoms. When we genetically test them with our toe walking panel, we find that around 90 per cent of them have a genetic variant that explains their toe walking. These can be assigned, for example, to the area of myopathies (such as variants of the COL6A3 gene), the area of hereditary neuropathies (such as variants of the KMT2C gene) or the area of metabolic diseases (such as variants of the PYGM gene). In a smaller group of patients with almost identical symptoms, no abnormality is found in the genes of our panel, but spastic paraplegia can be detected. In another small group of our toe walkers, no abnormalities can be detected in the genes analysed in our toe walking panel, nor do they suffer from spastic paraplegia, as is also the case with healthy children. In contrast to these, however, they show a tiptoe gait. These patients suffer from infantile cerebral palsy, in which toe walking can also be observed. -
DHTKD1-related disorder Pathogenic:1
The DHTKD1 c.2185G>A variant is predicted to result in the amino acid substitution p.Gly729Arg. This variant has been reported in the compound heterozygous and homozygous states in several individuals diagnosed with 2-aminoadipic 2-oxoadipic aciduria (Danhauser et al. 2012. PubMed ID: 23141293; Hagen et al. 2015. PubMed ID: 25860818; Stiles et al. 2015. PubMed ID: 26141459; Boonsawat et al. 2019. PubMed ID: 30842647). This variant is reported in 0.27% of alleles in individuals of European (Non-Finnish) descent in gnomAD, including several homozygous individuals in the most recent dataset (https://gnomad.broadinstitute.org/variant/10-12112930-G-A?dataset=gnomad_r4), indicating this variant is relatively common. These population data suggest there may be reduced expressivity of disease when this variant is present in the homozygous state. Given the evidence, we interpret this variant as likely pathogenic. -
Charcot-Marie-Tooth disease type 2A2 Uncertain:1
- -
Inborn disorder of lysine and hydroxylysine metabolism Uncertain:1
The p.Gly729Arg variant in DHTKD1 has been reported in 3 compound heterozygous individuals with 2-aminoadipic & 2-oxoadipic aciduria, one occurrence noted to be de novo (Danhauser 2012, Lee 2014) and has also been identified in 0.23% (151/66498) of European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs117225135). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. In vitro functional studies provide some evidence that the p.Gly729Arg variant may impact protein function (Danhauser 2012). However, these types of assays may not accurately represent biological function. In addition, computational prediction tools and conservation analysis do not provide strong support for or against an impact to the protein. In summary, the clinical significance of the p.Gly729Arg variant is uncertain. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at