ClinVar Genomic variation as it relates to human health
NM_014989.7(RIMS1):c.4186A>G (p.Met1396Val)
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_014989.7(RIMS1):c.4186A>G (p.Met1396Val)
Variation ID: 954678 Accession: VCV000954678.7
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 6q13 6: 72333655 (GRCh38) [ NCBI UCSC ] 6: 73043358 (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 Jul 16, 2020 Feb 14, 2024 Aug 17, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_014989.7:c.4186A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_055804.2:p.Met1396Val missense NM_001168407.2:c.2146A>G NP_001161879.1:p.Met716Val missense NM_001168408.2:c.1741+41609A>G intron variant NM_001168409.2:c.1570+41609A>G intron variant NM_001168410.2:c.1768+41609A>G intron variant NM_001350414.2:c.2107A>G NP_001337343.1:p.Met703Val missense NM_001350415.2:c.2203A>G NP_001337344.1:p.Met735Val missense NM_001350416.2:c.2152A>G NP_001337345.1:p.Met718Val missense NM_001350417.2:c.1813+41609A>G intron variant NM_001350418.2:c.2125A>G NP_001337347.1:p.Met709Val missense NM_001350419.2:c.1585+41609A>G intron variant NM_001350420.2:c.2260A>G NP_001337349.1:p.Met754Val missense NM_001350421.2:c.2005A>G NP_001337350.1:p.Met669Val missense NM_001350422.2:c.1810+41609A>G intron variant NM_001350423.2:c.1894A>G NP_001337352.1:p.Met632Val missense NM_001350424.2:c.1672+41609A>G intron variant NM_001350425.2:c.2104A>G NP_001337354.1:p.Met702Val missense NM_001350426.2:c.1660+41609A>G intron variant NM_001350427.2:c.1738+41609A>G intron variant NM_001350428.2:c.1744+41609A>G intron variant NM_001350429.2:c.1924A>G NP_001337358.1:p.Met642Val missense NM_001350430.2:c.1741+41609A>G intron variant NM_001350431.2:c.2242A>G NP_001337360.1:p.Met748Val missense NM_001350432.2:c.1648+41609A>G intron variant NM_001350433.2:c.2233A>G NP_001337362.1:p.Met745Val missense NM_001350434.2:c.1888+41609A>G intron variant NM_001350435.2:c.2095A>G NP_001337364.1:p.Met699Val missense NM_001350436.2:c.2338A>G NP_001337365.1:p.Met780Val missense NM_001350437.2:c.2089A>G NP_001337366.1:p.Met697Val missense NM_001350438.2:c.1993+41609A>G intron variant NM_001350439.2:c.2077A>G NP_001337368.1:p.Met693Val missense NM_001350440.2:c.1657+41609A>G intron variant NM_001350441.2:c.2074A>G NP_001337370.1:p.Met692Val missense NM_001350442.2:c.1996+41609A>G intron variant NM_001350443.2:c.2047A>G NP_001337372.1:p.Met683Val missense NM_001350444.2:c.1921A>G NP_001337373.1:p.Met641Val missense NM_001350445.2:c.1894+41609A>G intron variant NM_001350446.2:c.2332A>G NP_001337375.1:p.Met778Val missense NM_001350447.2:c.1993A>G NP_001337376.1:p.Met665Val missense NM_001350448.2:c.2149A>G NP_001337377.1:p.Met717Val missense NM_001350449.2:c.1720+41609A>G intron variant NM_001350450.2:c.1669+41609A>G intron variant NM_001350454.2:c.2056A>G NP_001337383.1:p.Met686Val missense NM_001350455.2:c.1588+41609A>G intron variant NM_001350456.2:c.2329A>G NP_001337385.1:p.Met777Val missense NM_001350457.2:c.2086A>G NP_001337386.1:p.Met696Val missense NM_001350458.2:c.2155A>G NP_001337387.1:p.Met719Val missense NM_001350459.2:c.2008A>G NP_001337388.1:p.Met670Val missense NM_001350460.2:c.2026A>G NP_001337389.1:p.Met676Val missense NM_001350461.2:c.1876A>G NP_001337390.1:p.Met626Val missense NM_001350462.2:c.2191A>G NP_001337391.1:p.Met731Val missense NM_001350463.2:c.1831A>G NP_001337392.1:p.Met611Val missense NM_001350464.2:c.1834A>G NP_001337393.1:p.Met612Val missense NM_001350465.2:c.1498+41609A>G intron variant NM_001350466.2:c.1837A>G NP_001337395.1:p.Met613Val missense NM_001350467.2:c.1753A>G NP_001337396.1:p.Met585Val missense NM_001350468.2:c.1678A>G NP_001337397.1:p.Met560Val missense NM_001350469.2:c.1906A>G NP_001337398.1:p.Met636Val missense NM_001350470.2:c.1774+41609A>G intron variant NM_001350471.2:c.1987A>G NP_001337400.1:p.Met663Val missense NM_001350472.2:c.1693+41609A>G intron variant NM_001350473.2:c.1696+41609A>G intron variant NM_001350474.2:c.1879A>G NP_001337403.1:p.Met627Val missense NC_000006.12:g.72333655A>G NC_000006.11:g.73043358A>G NG_016209.1:g.451709A>G - Protein change
- M1396V, M641V, M665V, M699V, M703V, M709V, M754V, M778V, M626V, M627V, M642V, M663V, M676V, M686V, M696V, M702V, M717V, M780V, M560V, M585V, M632V, M669V, M683V, M692V, M697V, M718V, M731V, M735V, M748V, M611V, M612V, M613V, M636V, M670V, M693V, M716V, M719V, M745V, M777V
- Other names
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- Canonical SPDI
- NC_000006.12:72333654:A:G
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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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0.00020 (G)
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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) 0.00002
1000 Genomes Project 30x 0.00031
Trans-Omics for Precision Medicine (TOPMed) 0.00003
1000 Genomes Project 0.00020
- 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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RIMS1 | Little evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
1137 | 1186 |
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
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
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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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Aug 17, 2023 | RCV001227183.6 |
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
(Aug 17, 2023)
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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: SCV001399528.4
First in ClinVar: Jul 16, 2020 Last updated: Feb 14, 2024 |
Comment:
This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 1396 of the RIMS1 protein (p.Met1396Val). … (more)
This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 1396 of the RIMS1 protein (p.Met1396Val). This variant is present in population databases (rs200994612, gnomAD 0.006%). This missense change has been observed in individuals with clinical features of RIMS1-related conditions (Invitae). ClinVar contains an entry for this variant (Variation ID: 954678). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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
HelpThere are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for rs200994612 ...
HelpRecord last updated Feb 20, 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.