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NM_000262.3(NAGA):c.983T>C (p.Met328Thr)

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Interpretation:
Uncertain significance​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: May 26, 2021)
Last evaluated:
Oct 12, 2020
Accession:
VCV000596276.5
Variation ID:
596276
Description:
single nucleotide variant
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NM_000262.3(NAGA):c.983T>C (p.Met328Thr)

Allele ID
587337
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
22q13.2
Genomic location
22: 42061042 (GRCh38) GRCh38 UCSC
22: 42457046 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000022.10:g.42457046A>G
NC_000022.11:g.42061042A>G
NG_009247.1:g.14801T>C
... more HGVS
Protein change
M328T
Other names
-
Canonical SPDI
NC_000022.11:42061041:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00005
The Genome Aggregation Database (gnomAD), exomes 0.00004
Exome Aggregation Consortium (ExAC) 0.00005
The Genome Aggregation Database (gnomAD) 0.00006
Trans-Omics for Precision Medicine (TOPMed) 0.00006
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Links
dbSNP: rs140356002
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 Mar 17, 2020 RCV000732043.4
Uncertain significance 1 criteria provided, single submitter Oct 12, 2020 RCV001305248.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
NAGA - - GRCh38
GRCh37
105 158

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Uncertain significance
(Feb 21, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Affected status: unknown
Allele origin: germline
Eurofins NTD, LLC
Accession: SCV000859919.1
Submitted: (Sep 19, 2018)
Other databases
http://www.egl-eurofins.com/emvc… http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=NAGA
Number of individuals with the variant: 1
Zygosity: 1 Single Heterozygote
Sex: mixed
Uncertain significance
(Oct 12, 2020)
criteria provided, single submitter
Method: clinical testing
Alpha-N-acetylgalactosaminidase deficiency type 1
Affected status: unknown
Allele origin: germline
Invitae
Accession: SCV001494577.1
Submitted: (Jan 07, 2021)
Comment:
This sequence change replaces methionine with threonine at codon 328 of the NAGA protein (p.Met328Thr). The methionine residue is weakly conserved and there is a … (more)
Uncertain significance
(Mar 17, 2020)
criteria provided, single submitter
Method: clinical testing
Not provided
Affected status: unknown
Allele origin: germline
Mayo Clinic Laboratories,Mayo Clinic
Accession: SCV001713911.1
Submitted: (May 26, 2021)
Number of individuals with the variant: 1

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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=NAGA - - - -

Text-mined citations for rs140356002...

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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 Dec 12, 2021