NM_018706.7(DHTKD1):c.2185G>A (p.Gly729Arg) AND 2-aminoadipic 2-oxoadipic aciduria

Germline classification:: Pathogenic/Likely pathogenic (8 submissions)
Last evaluated:: Jan 31, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000032764.30

Allele description [Variation Report for NM_018706.7(DHTKD1):c.2185G>A (p.Gly729Arg)]

NM_018706.7(DHTKD1):c.2185G>A (p.Gly729Arg)

Gene:

DHTKD1:dehydrogenase E1 and transketolase domain containing 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10p14

Genomic location:

Preferred name:

NM_018706.7(DHTKD1):c.2185G>A (p.Gly729Arg)

Other names:

DHTKD1, GLY729ARG (rs117225135); NM_018706.6:c.2185G>A(p.Gly729Arg)

HGVS:

NC_000010.11:g.12112930G>A
NG_033248.1:g.49014G>A
NM_018706.7:c.2185G>AMANE SELECT
NP_061176.4:p.Gly729Arg
NC_000010.10:g.12154929G>A
NM_018706.5:c.2185G>A
NM_018706.6:c.2185G>A
Q96HY7:p.Gly729Arg

Protein change:

G729R; GLY729ARG

Links:

UniProtKB: Q96HY7#VAR_069585; OMIM: 614984.0002; dbSNP: rs117225135

NCBI 1000 Genomes Browser:

rs117225135

Molecular consequence:

NM_018706.7:c.2185G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: 2-aminoadipic 2-oxoadipic aciduria (AAKAD)
Synonyms:: Aminoadipic aciduria; ALPHA-AMINOADIPIC AND ALPHA-KETOADIPIC ACIDURIA
Identifiers:: MONDO: MONDO:0008774; MedGen: C1859817; Orphanet: 79154; OMIM: 204750

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000056528	OMIM	no assertion criteria provided	Pathogenic (Dec 7, 2012)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV000644177	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 31, 2024)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 23141293, 25860818, 26141459, 28492532
SCV000787452	SIB Swiss Institute of Bioinformatics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 16, 2018)	germline	curation	PubMed (2) [See all records that cite these PMIDs] 23141293, 25741868
SCV000787771	Institute of Human Genetics, Cologne University	no assertion criteria provided	Pathogenic (Apr 25, 2018)	germline	clinical testing
SCV001522987	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002034773	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSLVariantClassificationCriteria RUGD 01 April 2020)	Likely pathogenic (Aug 20, 2021)	unknown	clinical testing	PubMed (5) [See all records that cite these PMIDs] 23141293, 25860818, 26141459, 32303640, 32695416 Citation Link,
SCV002555875	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Pathogenic (Jun 1, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 25326637, 23141293, 25860818, 32303640 Citation Link,
SCV004177074	Clinical Genomics Laboratory, Washington University in St. Louis	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 2, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing, curation
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

New Cases of DHTKD1 Mutations in Patients with 2-Ketoadipic Aciduria.

Stiles AR, Venturoni L, Mucci G, Elbalalesy N, Woontner M, Goodman S, Abdenur JE.

JIMD Rep. 2016;25:15-19. Epub 2015 Jul 5.

PubMed [citation]

PMID:: 26141459
PMCID:: PMC5059180

See all PubMed Citations (8)

Details of each submission

From OMIM, SCV000056528.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In 2 patients with 2-aminoadipic 2-oxoadipic aciduria (AAKAD; 204750), Danhauser et al. (2012) identified a heterozygous G-to-A transition at nucleotide 2185 of the DHTKD1 gene resulting in a gly-to-arg substitution at codon 729 (G729R). In 1 patient the G729R mutation was found in compound heterozygosity with a mutation involving the initiator methionine (614984.0001), and in the other patient a premature termination mutation was found (R410X; 614984.0003). In the first patient the G729R mutation occurred de novo and in the second it was maternally transmitted. Gly729 is evolutionarily conserved from Homo sapiens to C. elegans and D. melanogaster. This mutation (rs117225135) was found in the NHLBI Exome Variant Server with a minor allele frequency of 0.17%, corresponding to 19 heterozygous but no homozygous carriers among 5,379 individuals.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Invitae, SCV000644177.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

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 2-aminoadipic 2-oxoadipic aciduria (PMID: 23141293, 25860818, 26141459; Invitae). 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From SIB Swiss Institute of Bioinformatics, SCV000787452.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (2)

Description

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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Institute of Human Genetics, Cologne University, SCV000787771.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV001522987.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Illumina Laboratory Services, Illumina, SCV002034773.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002555875.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

Variant summary: DHTKD1 c.2185G>A (p.Gly729Arg) results in a non-conservative amino acid change located in the Transketolase-like, pyrimidine-binding domain of the encoded protein sequence. Four 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. These data indicate that the variant is likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal activity in catalytic efficiency for NADH production. Twelve clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments (pathogenic/likely pathogenic n=9, VUS n=3). Based on the evidence outlined above, the variant was classified as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Clinical Genomics Laboratory, Washington University in St. Louis, SCV004177074.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 20, 2024

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