ClinVar Genomic variation as it relates to human health
NM_014989.7(RIMS1):c.2024T>C (p.Ile675Thr)
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.2024T>C (p.Ile675Thr)
Variation ID: 1449441 Accession: VCV001449441.8
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 6q13 6: 72242380 (GRCh38) [ NCBI UCSC ] 6: 72952083 (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 28, 2022 May 1, 2024 Apr 22, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_014989.7:c.2024T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_055804.2:p.Ile675Thr missense NM_001168407.2:c.446T>C NP_001161879.1:p.Ile149Thr missense NM_001168408.2:c.446T>C NP_001161880.1:p.Ile149Thr missense NM_001168409.2:c.203T>C NP_001161881.1:p.Ile68Thr missense NM_001168410.2:c.401T>C NP_001161882.1:p.Ile134Thr missense NM_001350414.2:c.446T>C NP_001337343.1:p.Ile149Thr missense NM_001350415.2:c.446T>C NP_001337344.1:p.Ile149Thr missense NM_001350416.2:c.446T>C NP_001337345.1:p.Ile149Thr missense NM_001350417.2:c.446T>C NP_001337346.1:p.Ile149Thr missense NM_001350418.2:c.446T>C NP_001337347.1:p.Ile149Thr missense NM_001350419.2:c.446T>C NP_001337348.1:p.Ile149Thr missense NM_001350420.2:c.446T>C NP_001337349.1:p.Ile149Thr missense NM_001350421.2:c.377T>C NP_001337350.1:p.Ile126Thr missense NM_001350422.2:c.446T>C NP_001337351.1:p.Ile149Thr missense NM_001350423.2:c.446T>C NP_001337352.1:p.Ile149Thr missense NM_001350424.2:c.377T>C NP_001337353.1:p.Ile126Thr missense NM_001350425.2:c.446T>C NP_001337354.1:p.Ile149Thr missense NM_001350426.2:c.446T>C NP_001337355.1:p.Ile149Thr missense NM_001350427.2:c.446T>C NP_001337356.1:p.Ile149Thr missense NM_001350428.2:c.377T>C NP_001337357.1:p.Ile126Thr missense NM_001350429.2:c.446T>C NP_001337358.1:p.Ile149Thr missense NM_001350430.2:c.377T>C NP_001337359.1:p.Ile126Thr missense NM_001350431.2:c.446T>C NP_001337360.1:p.Ile149Thr missense NM_001350432.2:c.446T>C NP_001337361.1:p.Ile149Thr missense NM_001350433.2:c.446T>C NP_001337362.1:p.Ile149Thr missense NM_001350434.2:c.446T>C NP_001337363.1:p.Ile149Thr missense NM_001350435.2:c.446T>C NP_001337364.1:p.Ile149Thr missense NM_001350436.2:c.446T>C NP_001337365.1:p.Ile149Thr missense NM_001350437.2:c.377T>C NP_001337366.1:p.Ile126Thr missense NM_001350438.2:c.446T>C NP_001337367.1:p.Ile149Thr missense NM_001350439.2:c.446T>C NP_001337368.1:p.Ile149Thr missense NM_001350440.2:c.446T>C NP_001337369.1:p.Ile149Thr missense NM_001350441.2:c.446T>C NP_001337370.1:p.Ile149Thr missense NM_001350442.2:c.446T>C NP_001337371.1:p.Ile149Thr missense NM_001350443.2:c.446T>C NP_001337372.1:p.Ile149Thr missense NM_001350444.2:c.446T>C NP_001337373.1:p.Ile149Thr missense NM_001350445.2:c.446T>C NP_001337374.1:p.Ile149Thr missense NM_001350446.2:c.446T>C NP_001337375.1:p.Ile149Thr missense NM_001350447.2:c.446T>C NP_001337376.1:p.Ile149Thr missense NM_001350448.2:c.446T>C NP_001337377.1:p.Ile149Thr missense NM_001350449.2:c.446T>C NP_001337378.1:p.Ile149Thr missense NM_001350450.2:c.377T>C NP_001337379.1:p.Ile126Thr missense NM_001350452.2:c.446T>C NP_001337381.1:p.Ile149Thr missense NM_001350454.2:c.446T>C NP_001337383.1:p.Ile149Thr missense NM_001350455.2:c.446T>C NP_001337384.1:p.Ile149Thr missense NM_001350456.2:c.446T>C NP_001337385.1:p.Ile149Thr missense NM_001350457.2:c.446T>C NP_001337386.1:p.Ile149Thr missense NM_001350458.2:c.446T>C NP_001337387.1:p.Ile149Thr missense NM_001350459.2:c.377T>C NP_001337388.1:p.Ile126Thr missense NM_001350460.2:c.446T>C NP_001337389.1:p.Ile149Thr missense NM_001350461.2:c.203T>C NP_001337390.1:p.Ile68Thr missense NM_001350462.2:c.377T>C NP_001337391.1:p.Ile126Thr missense NM_001350463.2:c.203T>C NP_001337392.1:p.Ile68Thr missense NM_001350464.2:c.203T>C NP_001337393.1:p.Ile68Thr missense NM_001350465.2:c.203T>C NP_001337394.1:p.Ile68Thr missense NM_001350466.2:c.203T>C NP_001337395.1:p.Ile68Thr missense NM_001350467.2:c.203T>C NP_001337396.1:p.Ile68Thr missense NM_001350468.2:c.203T>C NP_001337397.1:p.Ile68Thr missense NM_001350469.2:c.203T>C NP_001337398.1:p.Ile68Thr missense NM_001350470.2:c.401T>C NP_001337399.1:p.Ile134Thr missense NM_001350471.2:c.377T>C NP_001337400.1:p.Ile126Thr missense NM_001350472.2:c.401T>C NP_001337401.1:p.Ile134Thr missense NM_001350473.2:c.401T>C NP_001337402.1:p.Ile134Thr missense NM_001350474.2:c.401T>C NP_001337403.1:p.Ile134Thr missense NM_014989.4:c.2024T>C NC_000006.12:g.72242380T>C NC_000006.11:g.72952083T>C NG_016209.1:g.360434T>C - Protein change
- I134T, I149T, I68T, I126T, I675T
- Other names
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- Canonical SPDI
- NC_000006.12:72242379:T:C
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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
Help
The frequency of the allele represented by this VCV record.
The Genome Aggregation Database (gnomAD) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00002
- Links
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 | ||
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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
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. |
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RIMS1 | Little evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
1138 | 1184 |
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. |
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Uncertain significance (1) |
criteria provided, single submitter
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Apr 22, 2023 | RCV002004604.5 | |
Uncertain significance (1) |
criteria provided, single submitter
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Jul 26, 2022 | RCV002286434.1 | |
Uncertain significance (1) |
criteria provided, single submitter
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Nov 2, 2021 | RCV004043920.1 |
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. |
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Uncertain significance
(Jul 26, 2022)
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criteria provided, single submitter
Method: clinical testing
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Cone-rod dystrophy 7
Affected status: yes
Allele origin:
unknown
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Institute of Human Genetics, University of Leipzig Medical Center
Accession: SCV002576474.1
First in ClinVar: Oct 01, 2022 Last updated: Oct 01, 2022 |
Comment:
_x000D_ Criteria applied: PP3
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Uncertain significance
(Apr 22, 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: SCV002230260.3
First in ClinVar: Mar 28, 2022 Last updated: Feb 20, 2024 |
Comment:
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 … (more)
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. 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 disruptive. ClinVar contains an entry for this variant (Variation ID: 1449441). This variant has not been reported in the literature in individuals affected with RIMS1-related conditions. This variant is present in population databases (rs762108313, gnomAD 0.002%). This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 675 of the RIMS1 protein (p.Ile675Thr). (less)
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Uncertain significance
(Nov 02, 2021)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV003588343.2
First in ClinVar: Feb 07, 2023 Last updated: May 01, 2024 |
Comment:
The c.2024T>C (p.I675T) alteration is located in exon 10 (coding exon 10) of the RIMS1 gene. This alteration results from a T to C substitution … (more)
The c.2024T>C (p.I675T) alteration is located in exon 10 (coding exon 10) of the RIMS1 gene. This alteration results from a T to C substitution at nucleotide position 2024, causing the isoleucine (I) at amino acid position 675 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. (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 rs762108313 ...
HelpRecord last updated Jun 02, 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.