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NM_007357.3(COG2):c.1765G>A (p.Val589Ile)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
2 (Most recent: Sep 10, 2021)
Last evaluated:
May 4, 2021
Accession:
VCV000775694.5
Variation ID:
775694
Description:
single nucleotide variant
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NM_007357.3(COG2):c.1765G>A (p.Val589Ile)

Allele ID
696568
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q42.2
Genomic location
1: 230688533 (GRCh38) GRCh38 UCSC
1: 230824279 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.230824279G>A
NC_000001.11:g.230688533G>A
NM_001145036.2:c.1762G>A NP_001138508.1:p.Val588Ile missense
NM_007357.3:c.1765G>A MANE Select NP_031383.1:p.Val589Ile missense
Protein change
V588I, V589I
Other names
-
Canonical SPDI
NC_000001.11:230688532:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.02137 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00614
Trans-Omics for Precision Medicine (TOPMed) 0.02012
1000 Genomes Project 0.02137
Exome Aggregation Consortium (ExAC) 0.00706
The Genome Aggregation Database (gnomAD) 0.01764
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01945
Links
dbSNP: rs34109129
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Dec 31, 2019 RCV000955891.2
Benign 1 criteria provided, single submitter May 4, 2021 RCV001638021.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
COG2 - - GRCh38
GRCh37
107 145

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
Congenital disorder of glycosylation, type IIq
Allele origin: germline
Invitae
Accession: SCV001102626.2
Submitted: (Jan 29, 2020)
Evidence details
Benign
(May 04, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001852031.1
Submitted: (Sep 10, 2021)
Evidence details

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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs34109129...

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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 Sep 29, 2021