VCV000094072.50 - ClinVar

NM_002435.3(MPI):c.982C>T (p.Arg328Trp)

Germline

Classification

criteria provided, multiple submitters, no conflicts. Learn more about how ClinVar calculates review status.

Benign/Likely benign

8 out of 10 submissions contributed to this classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_002435.3(MPI):c.982C>T (p.Arg328Trp)

Variation ID: 94072 Accession: VCV000094072.50

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 15q24.1 15: 74897148 (GRCh38) [ NCBI UCSC ] 15: 75189489 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Jun 8, 2016	Apr 13, 2025	Jan 2, 2025

HGVS

Nucleotide	Protein	Molecular consequence
NM_002435.3:c.982C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_002426.1:p.Arg328Trp	missense
NM_001289155.2:c.845-364C>T		intron variant
NM_001289156.2:c.832C>T	NP_001276085.1:p.Arg278Trp	missense
NM_001289157.2:c.799C>T	NP_001276086.1:p.Arg267Trp	missense
NM_001330372.2:c.922C>T	NP_001317301.1:p.Arg308Trp	missense
NC_000015.10:g.74897148C>T
NC_000015.9:g.75189489C>T
NG_008921.1:g.12080C>T

... more HGVS ... less HGVS

Protein change

R328W, R267W, R278W, R308W

Other names

Canonical SPDI

NC_000015.10:74897147:C:T

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

0.00140 (T)

Allele frequency Help The frequency of the allele represented by this VCV record.

The Genome Aggregation Database (gnomAD) 0.00577

Exome Aggregation Consortium (ExAC) 0.00610

1000 Genomes Project 0.00140

1000 Genomes Project 30x 0.00187

Trans-Omics for Precision Medicine (TOPMed) 0.00527

NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00639

The Genome Aggregation Database (gnomAD), exomes 0.00554

Links

ClinGen: CA147584 dbSNP: rs117089191 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
MPI		-	-	GRCh38 GRCh37	534	584

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not specified	Benign/Likely benign (2)	criteria provided, multiple submitters, no conflicts	Feb 12, 2021	RCV000080017.22
not provided	Benign/Likely benign (4)	criteria provided, multiple submitters, no conflicts	Sep 1, 2024	RCV000224183.30
MPI-congenital disorder of glycosylation	Benign/Likely benign (3)	criteria provided, multiple submitters, no conflicts	Jan 2, 2025	RCV001083811.23
MPI-related disorder	Benign (1)	no assertion criteria provided	Mar 19, 2020	RCV003905051.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Likely Benign (Nov 24, 2015) C Contributing to aggregate classification	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	not provided Affected status: not provided Allele origin: germline	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics Accession: SCV000280776.1 First in ClinVar: Jun 08, 2016 Last updated: Jun 08, 2016	Comment: Converted during submission to Likely benign.
Likely benign (Jan 13, 2018) C Contributing to aggregate classification	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019) Method: clinical testing	MPI-congenital disorder of glycosylation Affected status: unknown Allele origin: germline	Illumina Laboratory Services, Illumina Accession: SCV000393950.3 First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020	Comment: This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more) This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. (less)
Benign (Sep 01, 2024) C Contributing to aggregate classification	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2) Method: clinical testing	not provided Affected status: yes Allele origin: germline	CeGaT Center for Human Genetics Tuebingen Accession: SCV002563268.18 First in ClinVar: Aug 23, 2022 Last updated: Mar 22, 2025	Comment: MPI: BS1, BS2 Number of individuals with the variant: 9
Benign (Oct 16, 2012) C Contributing to aggregate classification	criteria provided, single submitter (EGL Classification Definitions 2015) Method: clinical testing	not specified Affected status: unknown Allele origin: germline	Eurofins Ntd Llc (ga) Accession: SCV000111910.9 First in ClinVar: Jan 17, 2014 Last updated: Apr 13, 2025	Other databases http://www.egl-eurofins.com/emvc… http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=MPI Number of individuals with the variant: 4 Zygosity: Single Heterozygote Sex: mixed
Benign (Jul 29, 2021) C Contributing to aggregate classification	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV000522331.4 First in ClinVar: Mar 08, 2017 Last updated: Dec 19, 2017	Comment: This variant is associated with the following publications: (PMID: 23806237)
Likely benign (Feb 12, 2021) C Contributing to aggregate classification	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	not specified Affected status: no Allele origin: germline	Genetic Services Laboratory, University of Chicago Accession: SCV002064641.1 First in ClinVar: Jan 29, 2022 Last updated: Jan 29, 2022
Likely benign (-) C Contributing to aggregate classification	criteria provided, single submitter (ACMG Guidelines, 2015) Method: not provided	not provided (Autosomal recessive inheritance) Affected status: yes Allele origin: germline	Breakthrough Genomics, Breakthrough Genomics Accession: SCV005211060.1 First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024
Benign (Jan 02, 2025) C Contributing to aggregate classification	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	MPI-congenital disorder of glycosylation Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV000645200.8 First in ClinVar: Dec 26, 2017 Last updated: Feb 25, 2025
Benign (Nov 15, 2019) N Not contributing to aggregate classification	no assertion criteria provided Method: clinical testing	Congenital disorder of glycosylation type 1b Affected status: unknown Allele origin: germline	Natera, Inc. Accession: SCV002089788.1 First in ClinVar: Apr 23, 2022 Last updated: Apr 23, 2022
Benign (Mar 19, 2020) N Not contributing to aggregate classification	no assertion criteria provided Method: clinical testing	MPI-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004718027.2 First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024	Comment: This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

Comment:

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

Germline Functional Evidence

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.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=MPI	-	-	-	-

Text-mined citations for rs117089191 ...

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 13, 2025

ClinVar Genomic variation as it relates to human health

NM_002435.3(MPI):c.982C>T (p.Arg328Trp)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs117089191 ...