VCV002426489.6 - ClinVar

NC_000010.10:g.(?_12111033)_(12148415_?)del

Germline

Classification

criteria provided, single submitter. Learn more about how ClinVar calculates review status.

Pathogenic
Pathogenic (1)

This classification is based on the single submission received

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.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NC_000010.10:g.(?_12111033)_(12148415_?)del

Variation ID: 2426489 Accession: VCV002426489.6

Type and length

Deletion, 37,383 bp

Location

Cytogenetic: 10p14 10: 12111033-12148415 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	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	Feb 13, 2023	Jun 9, 2024	Nov 6, 2021

HGVS

Nucleotide	Protein	Molecular consequence
NC_000010.10:g.(?_12111033)_(12148415_?)del

Protein change

Other names

Canonical SPDI

Global minor allele frequency (GMAF) Help The 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.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

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
Gene	OMIM	HI score Help 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.
DHTKD1		-	-	GRCh38 GRCh37	1060	1124

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.
2-aminoadipic 2-oxoadipic aciduria	Pathogenic (1)	criteria provided, single submitter	Nov 6, 2021	RCV003119931.5

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.
Pathogenic (Nov 06, 2021) C Contributing to aggregate classification	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	2-aminoadipic 2-oxoadipic aciduria	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003795195.3 First in ClinVar: Feb 13, 2023 Last updated: Jun 09, 2024	Publications: PubMed (2) PubMed: 23141293‚ 25860818 Comment: show For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with DHTKD1-related conditions. This variant is a gross deletion of the genomic region encompassing exon(s) 1-11 of the DHTKD1 gene, which includes the initiator codon. This deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DHTKD1 are known to be pathogenic (PMID: 23141293, 25860818). (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

Comment:

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with DHTKD1-related conditions. This variant is a gross deletion of the genomic region encompassing exon(s) 1-11 of the DHTKD1 gene, which includes the initiator codon. This deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DHTKD1 are known to be pathogenic (PMID: 23141293, 25860818).

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Genetic basis of alpha-aminoadipic and alpha-ketoadipic aciduria.	Hagen J	Journal of inherited metabolic disease	2015	PMID: 25860818
DHTKD1 mutations cause 2-aminoadipic and 2-oxoadipic aciduria.	Danhauser K	American journal of human genetics	2012	PMID: 23141293

Text-mined citations for this variant ...

Record last updated Apr 13, 2026