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NM_003859.3(DPM1):c.494+9A>G AND Congenital disorder of glycosylation type 1E

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 12, 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:
RCV002648168.2

Allele description

NM_003859.3(DPM1):c.494+9A>G

Genes:
ADNP-AS1:ADNP antisense RNA 1 [Gene - HGNC]
DPM1:dolichyl-phosphate mannosyltransferase subunit 1, catalytic [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
20q13.13
Genomic location:
Preferred name:
NM_003859.3(DPM1):c.494+9A>G
HGVS:
  • NC_000020.11:g.50942022T>C
  • NG_008923.1:g.21502A>G
  • NM_001317034.1:c.494+9A>G
  • NM_001317035.1:c.494+9A>G
  • NM_001317036.1:c.494+9A>G
  • NM_003859.3:c.494+9A>GMANE SELECT
  • NC_000020.10:g.49558559T>C
Molecular consequence:
  • NM_001317034.1:c.494+9A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001317035.1:c.494+9A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001317036.1:c.494+9A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_003859.3:c.494+9A>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Congenital disorder of glycosylation type 1E (CDG1E)
Synonyms:
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Ie; CDG Ie; CDG 1E; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0012123; MedGen: C1837396; Orphanet: 79322; OMIM: 608799

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003523330Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(May 12, 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, SCV003523330.2

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

Description

This sequence change falls in intron 6 of the DPM1 gene. It does not directly change the encoded amino acid sequence of the DPM1 protein. This variant is present in population databases (rs774832271, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with DPM1-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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.

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

Last Updated: Feb 14, 2024