NC_000007.13:g.(?_107002458)_(107204434_?)del AND COG5-congenital disorder of glycosylation

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 2, 2021
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:: RCV001983028.2

Allele description

NC_000007.13:g.(?_107002458)_(107204434_?)del

Genes:: GPR22:G protein-coupled receptor 22 [Gene - OMIM - HGNC]
DUS4L:dihydrouridine synthase 4 like [Gene - HGNC]
COG5:component of oligomeric golgi complex 5 [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 7q22.3
Genomic location:: Chr7: 107002458 - 107204434 (on Assembly GRCh37)
Preferred name:: NC_000007.13:g.(?_107002458)_(107204434_?)del
HGVS:: NC_000007.13:g.(?_107002458)_(107204434_?)del
This HGVS expression did not pass validation

Condition(s)

Name:: COG5-congenital disorder of glycosylation
Synonyms:: CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIi; Congenital disorder of glycosylation type 2i; CDG IIi; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0013325; MedGen: C3150876; Orphanet: 263487; OMIM: 613612

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002238553	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 2, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 23228021, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002238553

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 2, 2021)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

COG5-CDG: expanding the clinical spectrum.

Rymen D, Keldermans L, Race V, Régal L, Deconinck N, Dionisi-Vici C, Fung CW, Sturiale L, Rosnoblet C, Foulquier F, Matthijs G, Jaeken J.

Orphanet J Rare Dis. 2012 Dec 10;7:94. doi: 10.1186/1750-1172-7-94. Erratum in: Orphanet J Rare Dis. 2013;8:120.

PubMed [citation]

PMID:: 23228021
PMCID:: PMC3697985

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, SCV002238553.2

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

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 1-10 of the COG5 gene, which includes the initiator codon. The 5' end of this event is unknown as it extends beyond the assayed region for this gene and therefore may encompass additional genes. The 3' boundary is likely confined to intron 10 of the COG5 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in COG5 are known to be pathogenic (PMID: 23228021). This variant has not been reported in the literature in individuals affected with COG5-related conditions. 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

Last Updated: Feb 13, 2023

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