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NC_000001.10:g.(?_19199339)_(22987879_?)dup AND Congenital disorder of glycosylation type Ir

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 29, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV003113321.3

Allele description

NC_000001.10:g.(?_19199339)_(22987879_?)dup

Genes:
  • HTR6:5-hydroxytryptamine receptor 6 [Gene - OMIM - HGNC]
  • EPHA8:EPH receptor A8 [Gene - OMIM - HGNC]
  • EMC1:ER membrane protein complex subunit 1 [Gene - OMIM - HGNC]
  • MICOS10-NBL1:MICOS10-NBL1 readthrough [Gene - HGNC]
  • MRTO4:MRT4 homolog, ribosome maturation factor [Gene - OMIM - HGNC]
  • NBL1:NBL1, DAN family BMP antagonist [Gene - OMIM - HGNC]
  • NBPF3:NBPF member 3 [Gene - OMIM - HGNC]
  • OTUD3:OTU deubiquitinase 3 [Gene - OMIM - HGNC]
  • PINK1:PTEN induced kinase 1 [Gene - OMIM - HGNC]
  • RAP1GAP:RAP1 GTPase activating protein [Gene - OMIM - HGNC]
  • SH2D5:SH2 domain containing 5 [Gene - HGNC]
  • UBXN10:UBX domain protein 10 [Gene - OMIM - HGNC]
  • WNT4:Wnt family member 4 [Gene - OMIM - HGNC]
  • ALDH4A1:aldehyde dehydrogenase 4 family member A1 [Gene - OMIM - HGNC]
  • AKR7L:aldo-keto reductase family 7 like (gene/pseudogene) [Gene - OMIM - HGNC]
  • AKR7A2:aldo-keto reductase family 7 member A2 [Gene - OMIM - HGNC]
  • AKR7A3:aldo-keto reductase family 7 member A3 [Gene - OMIM - HGNC]
  • ALPL:alkaline phosphatase, biomineralization associated [Gene - OMIM - HGNC]
  • CAMK2N1:calcium/calmodulin dependent protein kinase II inhibitor 1 [Gene - OMIM - HGNC]
  • CAPZB:capping actin protein of muscle Z-line subunit beta [Gene - OMIM - HGNC]
  • CDC42:cell division cycle 42 [Gene - OMIM - HGNC]
  • CELA3A:chymotrypsin like elastase 3A [Gene - OMIM - HGNC]
  • CELA3B:chymotrypsin like elastase 3B [Gene - OMIM - HGNC]
  • C1QA:complement C1q A chain [Gene - OMIM - HGNC]
  • C1QB:complement C1q B chain [Gene - OMIM - HGNC]
  • C1QC:complement C1q C chain [Gene - OMIM - HGNC]
  • CDA:cytidine deaminase [Gene - OMIM - HGNC]
  • DDOST:dolichyl-diphosphooligosaccharide--protein glycosyltransferase non-catalytic subunit [Gene - OMIM - HGNC]
  • ECE1:endothelin converting enzyme 1 [Gene - OMIM - HGNC]
  • EIF4G3:eukaryotic translation initiation factor 4 gamma 3 [Gene - OMIM - HGNC]
  • FAM43B:family with sequence similarity 43 member B [Gene - HGNC]
  • HSPG2:heparan sulfate proteoglycan 2 [Gene - OMIM - HGNC]
  • HP1BP3:heterochromatin protein 1 binding protein 3 [Gene - OMIM - HGNC]
  • IFFO2:intermediate filament family orphan 2 [Gene - HGNC]
  • KIF17:kinesin family member 17 [Gene - OMIM - HGNC]
  • LDLRAD2:low density lipoprotein receptor class A domain containing 2 [Gene - HGNC]
  • MUL1:mitochondrial E3 ubiquitin protein ligase 1 [Gene - OMIM - HGNC]
  • MICOS10:mitochondrial contact site and cristae organizing system subunit 10 [Gene - OMIM - HGNC]
  • PLA2G2A:phospholipase A2 group IIA [Gene - OMIM - HGNC]
  • PLA2G2C:phospholipase A2 group IIC [Gene - HGNC]
  • PLA2G2D:phospholipase A2 group IID [Gene - OMIM - HGNC]
  • PLA2G2E:phospholipase A2 group IIE [Gene - OMIM - HGNC]
  • PLA2G2F:phospholipase A2 group IIF [Gene - OMIM - HGNC]
  • PLA2G5:phospholipase A2 group V [Gene - OMIM - HGNC]
  • RNF186:ring finger protein 186 [Gene - OMIM - HGNC]
  • SLC66A1:solute carrier family 66 member 1 [Gene - OMIM - HGNC]
  • TMCO4:transmembrane and coiled-coil domains 4 [Gene - HGNC]
  • UBR4:ubiquitin protein ligase E3 component n-recognin 4 [Gene - OMIM - HGNC]
  • USP48:ubiquitin specific peptidase 48 [Gene - OMIM - HGNC]
  • VWA5B1:von Willebrand factor A domain containing 5B1 [Gene - HGNC]
  • ZBTB40:zinc finger and BTB domain containing 40 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
1p36.13-36.12
Genomic location:
Chr1: 19199339 - 22987879 (on Assembly GRCh37)
Preferred name:
NC_000001.10:g.(?_19199339)_(22987879_?)dup
HGVS:
NC_000001.10:g.(?_19199339)_(22987879_?)dup

Condition(s)

Name:
Congenital disorder of glycosylation type Ir (CDG1R)
Synonyms:
DDOST-congenital disorder of glycosylation
Identifiers:
MONDO: MONDO:0013789; MedGen: C3281084; Orphanet: 300536; OMIM: 614507

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003794778Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jul 29, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV003794778.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals affected with DDOST-related conditions. A copy number gain of the genomic region encompassing the full coding sequence of the DDOST gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 17, 2024