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NM_000036.2(AMPD1):c.1373G>A (p.Arg458His)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely pathogenic(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Aug 7, 2020
Accession:
VCV000018273.2
Variation ID:
18273
Description:
single nucleotide variant
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NM_000036.2(AMPD1):c.1373G>A (p.Arg458His)

Allele ID
33312
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p13.2
Genomic location
1: 114677465 (GRCh38) GRCh38 UCSC
1: 115220086 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.115220086C>T
NC_000001.11:g.114677465C>T
NM_000036.2:c.1373G>A NP_000027.2:p.Arg458His missense
... more HGVS
Protein change
R454H, R458H
Other names
R425H
Canonical SPDI
NC_000001.11:114677464:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00220 (T)

Allele frequency
1000 Genomes Project 0.00220
The Genome Aggregation Database (gnomAD) 0.00048
Trans-Omics for Precision Medicine (TOPMed) 0.00055
Exome Aggregation Consortium (ExAC) 0.00077
Links
ClinGen: CA128025
UniProtKB: P23109#VAR_013272
OMIM: 102770.0003
dbSNP: rs121912682
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Nov 10, 2014 RCV000173624.1
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Aug 7, 2020 RCV000019935.34
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
AMPD1 - - GRCh38
GRCh37
113 125

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Nov 10, 2014)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000224749.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Aug 07, 2020)
criteria provided, single submitter
Method: clinical testing
Muscle AMP deaminase deficiency
Allele origin: germline
Invitae
Accession: SCV001723691.1
Submitted: (Jan 07, 2021)
Evidence details
Likely pathogenic
(Mar 18, 2016)
criteria provided, single submitter
Method: reference population
Muscle AMP deaminase deficiency
Allele origin: germline
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center
Accession: SCV000267211.1
Submitted: (Apr 14, 2016)
Evidence details
Publications
PubMed (1)
Pathogenic
(Dec 01, 2000)
no assertion criteria provided
Method: literature only
MYOPATHY DUE TO MYOADENYLATE DEAMINASE DEFICIENCY
Allele origin: germline
OMIM
Accession: SCV000040233.5
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (2)

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
First missense mutations (R388W and R425H) of AMPD1 accompanied with myopathy found in a Japanese patient. Morisaki H Human mutation 2000 PMID: 11102975
Myoadenylate deaminase deficiency with progressive muscle weakness and atrophy caused by new missense mutations in AMPD1 gene: case report in a Japanese patient. Abe M Neuromuscular disorders : NMD 2000 PMID: 10996775
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=AMPD1 - - - -

Text-mined citations for rs121912682...

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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 Jun 14, 2021