ClinVar Genomic variation as it relates to human health
NM_018116.4(MSTO1):c.560G>A (p.Gly187Glu)
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.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_018116.4(MSTO1):c.560G>A (p.Gly187Glu)
Variation ID: 1018118 Accession: VCV001018118.6
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 1q22 1: 155611827 (GRCh38) [ NCBI UCSC ] 1: 155581618 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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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 Mar 14, 2021 Feb 28, 2024 Oct 3, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_018116.4:c.560G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_060586.2:p.Gly187Glu missense NM_001256532.1:c.560G>A NP_001243461.1:p.Gly187Glu missense NM_001256533.1:c.560G>A NP_001243462.1:p.Gly187Glu missense NM_001350772.1:c.560G>A NP_001337701.1:p.Gly187Glu missense NM_001350773.1:c.560G>A NP_001337702.1:p.Gly187Glu missense NM_001350774.1:c.560G>A NP_001337703.1:p.Gly187Glu missense NM_001350775.1:c.560G>A NP_001337704.1:p.Gly187Glu missense NM_001350776.1:c.395G>A NP_001337705.1:p.Gly132Glu missense NM_001350777.1:c.4G>A NP_001337706.1:p.Gly2Ser missense NM_001350778.1:c.4G>A NP_001337707.1:p.Gly2Ser missense NM_001350779.1:c.4G>A NP_001337708.1:p.Gly2Ser missense NM_001350780.1:c.26G>A NP_001337709.1:p.Gly9Glu missense NM_001350781.1:c.26G>A NP_001337710.1:p.Gly9Glu missense NM_001350782.1:c.26G>A NP_001337711.1:p.Gly9Glu missense NM_001350783.1:c.26G>A NP_001337712.1:p.Gly9Glu missense NM_001350784.1:c.-46G>A 5 prime UTR NM_001350785.1:c.-46G>A 5 prime UTR NM_001350786.1:c.26G>A NP_001337715.1:p.Gly9Glu missense NM_001350787.1:c.-46G>A 5 prime UTR NM_001350788.1:c.26G>A NP_001337717.1:p.Gly9Glu missense NM_001350789.1:c.-46G>A 5 prime UTR NR_046292.1:n.761G>A non-coding transcript variant NR_046293.1:n.703G>A non-coding transcript variant NR_046294.1:n.625G>A non-coding transcript variant NR_046295.1:n.563G>A non-coding transcript variant NR_146907.1:n.639G>A non-coding transcript variant NR_146908.1:n.639G>A non-coding transcript variant NC_000001.11:g.155611827G>A NC_000001.10:g.155581618G>A - Protein change
- G132E, G187E, G2S, G9E
- Other names
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- Canonical SPDI
- NC_000001.11:155611826:G:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe 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.
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Allele frequency
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The frequency of the allele represented by this VCV record.
The Genome Aggregation Database (gnomAD) 0.00004
The Genome Aggregation Database (gnomAD), exomes 0.00017
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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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. |
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MSTO1 | - | - |
GRCh38 GRCh37 |
153 | 178 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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
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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
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Uncertain significance (1) |
criteria provided, single submitter
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Oct 3, 2022 | RCV001317373.6 |
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
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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
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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
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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. |
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Uncertain significance
(Oct 03, 2022)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV001508032.4
First in ClinVar: Mar 14, 2021 Last updated: Feb 28, 2024 |
Comment:
Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of … (more)
Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 1018118). This missense change has been observed in individual(s) with clinical features of MSTO1-related disease (Invitae). This variant is present in population databases (no rsID available, gnomAD 0.09%). This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 187 of the MSTO1 protein (p.Gly187Glu). This variant also falls at the last nucleotide of exon 6, which is part of the consensus splice site for this exon. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (less)
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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. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. | Buratti E | Nucleic acids research | 2007 | PMID: 17576681 |
Statistical features of human exons and their flanking regions. | Zhang MQ | Human molecular genetics | 1998 | PMID: 9536098 |
Text-mined citations for rs1351785077 ...
HelpRecord last updated Feb 28, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.