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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
ClinVar Genomic variation as it relates to human health
NM_014989.7(RIMS1):c.3941T>C (p.Leu1314Pro)
Germline
Classification
Help
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.
(2)
Help
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.
Benign
2
criteria provided, multiple submitters, no conflicts
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_014989.7(RIMS1):c.3941T>C (p.Leu1314Pro)
Variation ID: 357855 Accession: VCV000357855.13
- Type and length
-
single nucleotide variant, 1 bp
- Location
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Cytogenetic: 6q13 6: 72307348 (GRCh38) [ NCBI UCSC ] 6: 73017051 (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 Dec 6, 2016 Feb 14, 2024 Nov 18, 2023 - HGVS
-
... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_014989.7:c.3941T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_055804.2:p.Leu1314Pro missense NM_001168407.2:c.1901T>C NP_001161879.1:p.Leu634Pro missense NM_001168408.2:c.1741+15302T>C intron variant NM_001168409.2:c.1570+15302T>C intron variant NM_001168410.2:c.1768+15302T>C intron variant NM_001350414.2:c.1862T>C NP_001337343.1:p.Leu621Pro missense NM_001350415.2:c.1985T>C NP_001337344.1:p.Leu662Pro missense NM_001350416.2:c.1934T>C NP_001337345.1:p.Leu645Pro missense NM_001350417.2:c.1813+15302T>C intron variant NM_001350418.2:c.1907T>C NP_001337347.1:p.Leu636Pro missense NM_001350419.2:c.1585+15302T>C intron variant NM_001350420.2:c.2015T>C NP_001337349.1:p.Leu672Pro missense NM_001350421.2:c.1760T>C NP_001337350.1:p.Leu587Pro missense NM_001350422.2:c.1810+15302T>C intron variant NM_001350423.2:c.1676T>C NP_001337352.1:p.Leu559Pro missense NM_001350424.2:c.1672+15302T>C intron variant NM_001350425.2:c.1859T>C NP_001337354.1:p.Leu620Pro missense NM_001350426.2:c.1660+15302T>C intron variant NM_001350427.2:c.1738+15302T>C intron variant NM_001350428.2:c.1744+15302T>C intron variant NM_001350429.2:c.1679T>C NP_001337358.1:p.Leu560Pro missense NM_001350430.2:c.1741+15302T>C intron variant NM_001350431.2:c.1997T>C NP_001337360.1:p.Leu666Pro missense NM_001350432.2:c.1648+15302T>C intron variant NM_001350433.2:c.1988T>C NP_001337362.1:p.Leu663Pro missense NM_001350434.2:c.1888+15302T>C intron variant NM_001350435.2:c.1850T>C NP_001337364.1:p.Leu617Pro missense NM_001350436.2:c.2093T>C NP_001337365.1:p.Leu698Pro missense NM_001350437.2:c.1844T>C NP_001337366.1:p.Leu615Pro missense NM_001350438.2:c.1993+15302T>C intron variant NM_001350439.2:c.1832T>C NP_001337368.1:p.Leu611Pro missense NM_001350440.2:c.1657+15302T>C intron variant NM_001350441.2:c.1829T>C NP_001337370.1:p.Leu610Pro missense NM_001350442.2:c.1996+15302T>C intron variant NM_001350443.2:c.1829T>C NP_001337372.1:p.Leu610Pro missense NM_001350444.2:c.1676T>C NP_001337373.1:p.Leu559Pro missense NM_001350445.2:c.1894+15302T>C intron variant NM_001350446.2:c.2087T>C NP_001337375.1:p.Leu696Pro missense NM_001350447.2:c.1748T>C NP_001337376.1:p.Leu583Pro missense NM_001350448.2:c.1904T>C NP_001337377.1:p.Leu635Pro missense NM_001350449.2:c.1720+15302T>C intron variant NM_001350450.2:c.1669+15302T>C intron variant NM_001350454.2:c.1811T>C NP_001337383.1:p.Leu604Pro missense NM_001350455.2:c.1588+15302T>C intron variant NM_001350456.2:c.2084T>C NP_001337385.1:p.Leu695Pro missense NM_001350457.2:c.1841T>C NP_001337386.1:p.Leu614Pro missense NM_001350458.2:c.1910T>C NP_001337387.1:p.Leu637Pro missense NM_001350459.2:c.1763T>C NP_001337388.1:p.Leu588Pro missense NM_001350460.2:c.1781T>C NP_001337389.1:p.Leu594Pro missense NM_001350461.2:c.1658T>C NP_001337390.1:p.Leu553Pro missense NM_001350462.2:c.1946T>C NP_001337391.1:p.Leu649Pro missense NM_001350463.2:c.1586T>C NP_001337392.1:p.Leu529Pro missense NM_001350464.2:c.1589T>C NP_001337393.1:p.Leu530Pro missense NM_001350465.2:c.1498+15302T>C intron variant NM_001350466.2:c.1619T>C NP_001337395.1:p.Leu540Pro missense NM_001350467.2:c.1508T>C NP_001337396.1:p.Leu503Pro missense NM_001350468.2:c.1433T>C NP_001337397.1:p.Leu478Pro missense NM_001350469.2:c.1661T>C NP_001337398.1:p.Leu554Pro missense NM_001350470.2:c.1774+15302T>C intron variant NM_001350471.2:c.1742T>C NP_001337400.1:p.Leu581Pro missense NM_001350472.2:c.1693+15302T>C intron variant NM_001350473.2:c.1696+15302T>C intron variant NM_001350474.2:c.1634T>C NP_001337403.1:p.Leu545Pro missense NC_000006.12:g.72307348T>C NC_000006.11:g.73017051T>C NG_016209.1:g.425402T>C - Protein change
- L1314P, L554P, L581P, L587P, L588P, L634P, L636P, L637P, L649P, L663P, L695P, L696P, L540P, L553P, L559P, L560P, L604P, L611P, L614P, L617P, L621P, L635P, L662P, L698P, L503P, L530P, L545P, L594P, L620P, L478P, L529P, L583P, L610P, L615P, L645P, L666P, L672P
- Other names
- -
- Canonical SPDI
- NC_000006.12:72307347: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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0.00200 (C)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
-
The Genome Aggregation Database (gnomAD), exomes 0.00015
The Genome Aggregation Database (gnomAD) 0.00018
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00025
Trans-Omics for Precision Medicine (TOPMed) 0.00030
Exome Aggregation Consortium (ExAC) 0.00035
1000 Genomes Project 30x 0.00172
1000 Genomes Project 0.00200
- 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 | ||
|---|---|---|---|---|---|---|
| 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. |
|||
| RIMS1 | Little evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
1141 | 1188 | |
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. |
|---|---|---|---|---|
| Benign (1) |
criteria provided, single submitter
|
Jan 12, 2018 | RCV000303373.5 | |
| Benign (1) |
criteria provided, single submitter
|
Nov 18, 2023 | RCV000899846.9 |
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. |
|
|---|---|---|---|---|---|
|
Benign
(Jan 12, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Cone-rod dystrophy 7
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV000464678.3
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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. (less)
|
|
|
Benign
(Nov 18, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001044135.6
First in ClinVar: Dec 17, 2019 Last updated: Feb 14, 2024 |
|
Comment:
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:
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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Citations for germline classification of this variant
Help| There 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 rs201798320 ...
HelpThese 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 Sep 29, 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.