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NM_002435.3(MPI):c.414G>A (p.Met138Ile)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 20, 2020
Accession:
VCV000449251.6
Variation ID:
449251
Description:
single nucleotide variant
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NM_002435.3(MPI):c.414G>A (p.Met138Ile)

Allele ID
445420
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q24.1
Genomic location
15: 74892729 (GRCh38) GRCh38 UCSC
15: 75185070 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.74892729G>A
NC_000015.9:g.75185070G>A
NM_002435.3:c.414G>A MANE Select NP_002426.1:p.Met138Ile missense
... more HGVS
Protein change
M138I, M118I, M88I
Other names
-
Canonical SPDI
NC_000015.10:74892728:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00180 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00238
The Genome Aggregation Database (gnomAD) 0.00226
Exome Aggregation Consortium (ExAC) 0.00059
1000 Genomes Project 0.00180
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00246
The Genome Aggregation Database (gnomAD), exomes 0.00053
Links
ClinGen: CA7662433
dbSNP: rs150217523
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 Jun 22, 2017 RCV000523642.3
Likely benign 2 criteria provided, single submitter Nov 20, 2020 RCV001083362.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
MPI - - GRCh38
GRCh37
213 249

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jun 22, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000617147.2
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The M138I variant in the MPI gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. This … (more)
Likely benign
(Nov 20, 2020)
criteria provided, single submitter
Method: clinical testing
MPI-CDG
Allele origin: germline
Invitae
Accession: SCV001005085.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Oct 28, 2019)
no assertion criteria provided
Method: clinical testing
Congenital disorder of glycosylation type 1b
Allele origin: germline
Natera, Inc.
Accession: SCV001454926.1
Submitted: (Dec 28, 2020)
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 rs150217523...

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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 May 16, 2021