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NM_018714.3(COG1):c.2365G>A (p.Glu789Lys)

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Interpretation:
Conflicting interpretations of pathogenicity​

Uncertain significance(1); Likely benign(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
2
First in ClinVar:
Dec 17, 2019
Most recent Submission:
May 16, 2022
Last evaluated:
Nov 29, 2021
Accession:
VCV000784701.8
Variation ID:
784701
Description:
single nucleotide variant
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NM_018714.3(COG1):c.2365G>A (p.Glu789Lys)

Allele ID
715670
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q25.1
Genomic location
17: 73203776 (GRCh38) GRCh38 UCSC
17: 71199915 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_018714.3:c.2365G>A MANE Select NP_061184.1:p.Glu789Lys missense
NC_000017.11:g.73203776G>A
NC_000017.10:g.71199915G>A
NG_008971.1:g.15743G>A
Protein change
E789K
Other names
-
Canonical SPDI
NC_000017.11:73203775:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00030
Exome Aggregation Consortium (ExAC) 0.00017
The Genome Aggregation Database (gnomAD) 0.00021
The Genome Aggregation Database (gnomAD), exomes 0.00023
Trans-Omics for Precision Medicine (TOPMed) 0.00026
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00038
Links
dbSNP: rs201867802
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Nov 29, 2021 RCV000966463.8
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
COG1 - - GRCh38
GRCh37
238 275

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
COG1 congenital disorder of glycosylation
Affected status: unknown
Allele origin: germline
Illumina Laboratory Services,Illumina
Accession: SCV001281462.1
First in ClinVar: May 31, 2020
Last updated: May 31, 2020
Publications:
PubMed (1)
PubMed: 23806237
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Nov 29, 2021)
criteria provided, single submitter
Method: clinical testing
COG1 congenital disorder of glycosylation
Affected status: unknown
Allele origin: germline
Invitae
Accession: SCV001113788.3
First in ClinVar: Dec 17, 2019
Last updated: May 16, 2022

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Molecular diagnostic testing for congenital disorders of glycosylation (CDG): detection rate for single gene testing and next generation sequencing panel testing. Jones MA Molecular genetics and metabolism 2013 PMID: 23806237

Text-mined citations for rs201867802...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Aug 24, 2022