ClinVar Genomic variation as it relates to human health
NM_020975.6(RET):c.1927_1929del (p.Leu643del)
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_020975.6(RET):c.1927_1929del (p.Leu643del)
Variation ID: 2121795 Accession: VCV002121795.2
- Type and length
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Deletion, 3 bp
- Location
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Cytogenetic: 10q11.21 10: 43114525-43114527 (GRCh38) [ NCBI UCSC ] 10: 43609973-43609975 (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 Feb 8, 2023 Feb 20, 2024 Dec 14, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_020975.6:c.1927_1929del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_066124.1:p.Leu643del inframe deletion NM_000323.2:c.1927_1929delCTC NP_000314.1:p.Leu643del inframe indel NM_001355216.2:c.1165_1167delCTC NP_001342145.1:p.Leu389del inframe indel NM_001406743.1:c.1927_1929delCTC NP_001393672.1:p.Leu643del inframe indel NM_001406744.1:c.1927_1929delCTC NP_001393673.1:p.Leu643del inframe indel NM_001406759.1:c.1927_1929delCTC NP_001393688.1:p.Leu643del inframe indel NM_001406760.1:c.1927_1929delCTC NP_001393689.1:p.Leu643del inframe indel NM_001406761.1:c.1798_1800delCTC NP_001393690.1:p.Leu600del inframe indel NM_001406762.1:c.1798_1800delCTC NP_001393691.1:p.Leu600del inframe indel NM_001406764.1:c.1798_1800delCTC NP_001393693.1:p.Leu600del inframe indel NM_001406766.1:c.1639_1641delCTC NP_001393695.1:p.Leu547del inframe indel NM_001406767.1:c.1639_1641delCTC NP_001393696.1:p.Leu547del inframe indel NM_001406769.1:c.1531_1533delCTC NP_001393698.1:p.Leu511del inframe indel NM_001406770.1:c.1639_1641delCTC NP_001393699.1:p.Leu547del inframe indel NM_001406771.1:c.1489_1491delCTC NP_001393700.1:p.Leu497del inframe indel NM_001406772.1:c.1531_1533delCTC NP_001393701.1:p.Leu511del inframe indel NM_001406773.1:c.1489_1491delCTC NP_001393702.1:p.Leu497del inframe indel NM_001406774.1:c.1402_1404delCTC NP_001393703.1:p.Leu468del inframe indel NM_001406775.1:c.1201_1203delCTC NP_001393704.1:p.Leu401del inframe indel NM_001406776.1:c.1201_1203delCTC NP_001393705.1:p.Leu401del inframe indel NM_001406777.1:c.1201_1203delCTC NP_001393706.1:p.Leu401del inframe indel NM_001406778.1:c.1201_1203delCTC NP_001393707.1:p.Leu401del inframe indel NM_001406779.1:c.1030_1032delCTC NP_001393708.1:p.Leu344del inframe indel NM_001406780.1:c.1030_1032delCTC NP_001393709.1:p.Leu344del inframe indel NM_001406781.1:c.1030_1032delCTC NP_001393710.1:p.Leu344del inframe indel NM_001406782.1:c.1030_1032delCTC NP_001393711.1:p.Leu344del inframe indel NM_001406783.1:c.901_903delCTC NP_001393712.1:p.Leu301del inframe indel NM_001406784.1:c.937_939delCTC NP_001393713.1:p.Leu313del inframe indel NM_001406785.1:c.910_912delCTC NP_001393714.1:p.Leu304del inframe indel NM_001406786.1:c.901_903delCTC NP_001393715.1:p.Leu301del inframe indel NM_001406788.1:c.742_744delCTC NP_001393717.1:p.Leu248del inframe indel NM_001406789.1:c.742_744delCTC NP_001393718.1:p.Leu248del inframe indel NM_001406790.1:c.742_744delCTC NP_001393719.1:p.Leu248del inframe indel NM_001406791.1:c.622_624delCTC NP_001393720.1:p.Leu208del inframe indel NM_001406792.1:c.478_480delCTC NP_001393721.1:p.Leu160del inframe indel NM_001406793.1:c.478_480delCTC NP_001393722.1:p.Leu160del inframe indel NM_001406794.1:c.478_480delCTC NP_001393723.1:p.Leu160del inframe indel NM_020629.2:c.1927_1929delCTC NP_065680.1:p.Leu643del inframe indel NM_020630.7:c.1927_1929delCTC NP_065681.1:p.Leu643del inframe indel NC_000010.11:g.43114527_43114529del NC_000010.10:g.43609975_43609977del NG_007489.1:g.42459_42461del LRG_518:g.42459_42461del LRG_518t1:c.1927_1929del LRG_518p1:p.Leu643del LRG_518t2:c.1927_1929del LRG_518p2:p.Leu643del - Protein change
- L208del, L389del, L600del, L160del, L468del, L248del, L301del, L304del, L344del, L401del, L547del, L313del, L497del, L511del, L643del
- Other names
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- Canonical SPDI
- NC_000010.11:43114524:TCCTC:TC
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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.
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- 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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RET | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
3382 | 3500 |
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
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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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Dec 14, 2023 | RCV003049336.2 |
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
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
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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
(Dec 14, 2023)
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criteria provided, single submitter
Method: clinical testing
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Multiple endocrine neoplasia, type 2
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV003339730.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024 |
Comment:
This variant, c.1927_1929del, results in the deletion of 1 amino acid(s) of the RET protein (p.Leu643del), but otherwise preserves the integrity of the reading frame. … (more)
This variant, c.1927_1929del, results in the deletion of 1 amino acid(s) of the RET protein (p.Leu643del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with RET-related conditions. ClinVar contains an entry for this variant (Variation ID: 2121795). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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 this variant ...
HelpRecord last updated Feb 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.