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NM_018297.4(NGLY1):c.659G>A (p.Gly220Asp)

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Interpretation:
Uncertain significance​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
2 (Most recent: Jan 7, 2021)
Last evaluated:
Sep 17, 2019
Accession:
VCV000571965.3
Variation ID:
571965
Description:
single nucleotide variant
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NM_018297.4(NGLY1):c.659G>A (p.Gly220Asp)

Allele ID
561346
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3p24.2
Genomic location
3: 25739799 (GRCh38) GRCh38 UCSC
3: 25781290 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000003.11:g.25781290C>T
NC_000003.12:g.25739799C>T
NM_018297.4:c.659G>A MANE Select NP_060767.2:p.Gly220Asp missense
... more HGVS
Protein change
G220D, G178D
Other names
-
Canonical SPDI
NC_000003.12:25739798:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00004
Trans-Omics for Precision Medicine (TOPMed) 0.00006
The Genome Aggregation Database (gnomAD), exomes 0.00007
The Genome Aggregation Database (gnomAD) 0.00003
Links
dbSNP: rs748862974
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Sep 17, 2019 RCV000693243.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
NGLY1 - - GRCh38
GRCh37
354 374

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Congenital disorder of deglycosylation
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000897084.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Uncertain significance
(Sep 17, 2019)
criteria provided, single submitter
Method: clinical testing
Congenital disorder of deglycosylation
Allele origin: germline
Invitae
Accession: SCV000821103.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces glycine with aspartic acid at codon 220 of the NGLY1 protein (p.Gly220Asp). The glycine residue is moderately conserved and there is … (more)

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
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868

Text-mined citations for rs748862974...

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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 Apr 12, 2021