ClinVar Genomic variation as it relates to human health
NM_012424.6(RPS6KC1):c.768A>C (p.Glu256Asp)
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_012424.6(RPS6KC1):c.768A>C (p.Glu256Asp)
Variation ID: 1626969 Accession: VCV001626969.8
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 1q32.3 1: 213129822 (GRCh38) [ NCBI UCSC ] 1: 213303165 (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 Apr 8, 2022 Apr 15, 2024 Dec 11, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_012424.6:c.768A>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_036556.2:p.Glu256Asp missense NM_001136138.4:c.732A>C NP_001129610.1:p.Glu244Asp missense NM_001287218.3:c.225A>C NP_001274147.1:p.Glu75Asp missense NM_001287219.3:c.225A>C NP_001274148.1:p.Glu75Asp missense NM_001287220.3:c.-447A>C 5 prime UTR NM_001287221.3:c.225A>C NP_001274150.1:p.Glu75Asp missense NM_001349646.2:c.768A>C NP_001336575.1:p.Glu256Asp missense NM_001349647.2:c.472+12412A>C intron variant NM_001349648.2:c.225A>C NP_001336577.1:p.Glu75Asp missense NM_001349649.2:c.225A>C NP_001336578.1:p.Glu75Asp missense NM_001349650.2:c.225A>C NP_001336579.1:p.Glu75Asp missense NM_001349651.2:c.225A>C NP_001336580.1:p.Glu75Asp missense NM_001349652.2:c.225A>C NP_001336581.1:p.Glu75Asp missense NM_001349653.2:c.225A>C NP_001336582.1:p.Glu75Asp missense NM_001349654.2:c.225A>C NP_001336583.1:p.Glu75Asp missense NM_001349657.2:c.-57+25253A>C intron variant NM_001349658.2:c.-57+12412A>C intron variant NM_001349659.2:c.-520A>C 5 prime UTR NM_001349660.2:c.-440A>C 5 prime UTR NM_001349661.2:c.-440A>C 5 prime UTR NM_001349662.2:c.-440A>C 5 prime UTR NM_001349663.2:c.-287+25253A>C intron variant NM_001349664.2:c.-354A>C 5 prime UTR NM_001349665.2:c.-380+12412A>C intron variant NM_001349666.2:c.-447A>C 5 prime UTR NM_001349667.2:c.-447A>C 5 prime UTR NM_001349668.2:c.-447A>C 5 prime UTR NM_001349669.2:c.-447A>C 5 prime UTR NM_001349670.2:c.-354A>C 5 prime UTR NM_001349671.2:c.-447A>C 5 prime UTR NM_001349672.2:c.-447A>C 5 prime UTR NR_146207.2:n.932A>C non-coding transcript variant NR_146209.2:n.932A>C non-coding transcript variant NR_146210.2:n.1049A>C non-coding transcript variant NC_000001.11:g.213129822A>C NC_000001.10:g.213303165A>C - Protein change
- E244D, E256D, E75D
- Other names
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- Canonical SPDI
- NC_000001.11:213129821:A: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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0.00080 (C)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
1000 Genomes Project 30x 0.00062
1000 Genomes Project 0.00080
- 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
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. |
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RPS6KC1 | - | - |
GRCh38 GRCh37 |
247 | 275 |
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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Likely benign (2) |
criteria provided, multiple submitters, no conflicts
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Dec 11, 2023 | RCV002110904.7 |
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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Likely benign
(Dec 11, 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: SCV002436227.3
First in ClinVar: Apr 08, 2022 Last updated: Feb 20, 2024 |
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Likely benign
(Dec 01, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV004701499.2
First in ClinVar: Mar 10, 2024 Last updated: Apr 15, 2024 |
Comment:
RPS6KC1: BP4
Number of individuals with the variant: 1
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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 rs150727119 ...
HelpRecord last updated Apr 15, 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.