ClinVar Genomic variation as it relates to human health
NM_001382273.1(TNK2):c.1667_1668delinsAT (p.Gly556Asp)
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_001382273.1(TNK2):c.1667_1668delinsAT (p.Gly556Asp)
Variation ID: 2814607 Accession: VCV002814607.1
- Type and length
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Indel, 2 bp
- Location
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Cytogenetic: 3q29 3: 195868630-195868631 (GRCh38) [ NCBI UCSC ] 3: 195595501-195595502 (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 20, 2024 Feb 20, 2024 Jan 4, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001382273.1:c.1667_1668delinsAT MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001369202.1:p.Gly556Asp missense NM_001010938.2:c.1739_1740delinsAT NP_001010938.2:p.Gly580Asp missense NM_001308046.2:c.1718_1719delinsAT NP_001294975.1:p.Gly573Asp missense NM_001382271.1:c.1718_1719delinsAT NP_001369200.1:p.Gly573Asp missense NM_001382272.1:c.1739_1740delinsAT NP_001369201.1:p.Gly580Asp missense NM_001382274.1:c.1667_1668delinsAT NP_001369203.1:p.Gly556Asp missense NM_001382275.1:c.1763_1764delinsAT NP_001369204.1:p.Gly588Asp missense NM_001386164.1:c.1622_1623delinsAT NP_001373093.1:p.Gly541Asp missense NM_001387707.1:c.1763_1764delinsAT NP_001374636.1:p.Gly588Asp missense NM_001387708.1:c.1694_1695delinsAT NP_001374637.1:p.Gly565Asp missense NM_001387709.1:c.1622_1623delinsAT NP_001374638.1:p.Gly541Asp missense NM_001387710.1:c.1622_1623delinsAT NP_001374639.1:p.Gly541Asp missense NM_001387711.1:c.1622_1623delinsAT NP_001374640.1:p.Gly541Asp missense NM_001387712.1:c.1622_1623delinsAT NP_001374641.1:p.Gly541Asp missense NM_001387713.1:c.1622_1623delinsAT NP_001374642.1:p.Gly541Asp missense NM_001387714.1:c.1622_1623delinsAT NP_001374643.1:p.Gly541Asp missense NM_001387715.1:c.1694_1695delinsAT NP_001374644.1:p.Gly565Asp missense NM_001387716.1:c.1667_1668delinsAT NP_001374645.1:p.Gly556Asp missense NM_001387717.1:c.1667_1668delinsAT NP_001374646.1:p.Gly556Asp missense NM_001387718.1:c.1667_1668delinsAT NP_001374647.1:p.Gly556Asp missense NM_001387719.1:c.1622_1623delinsAT NP_001374648.1:p.Gly541Asp missense NM_001387720.1:c.1622_1623delinsAT NP_001374649.1:p.Gly541Asp missense NM_001387721.1:c.1622_1623delinsAT NP_001374650.1:p.Gly541Asp missense NM_005781.5:c.1622_1623delinsAT NP_005772.3:p.Gly541Asp missense NR_170678.1:n.1914_1915delinsAT non-coding transcript variant NR_170679.1:n.2218_2219delinsAT non-coding transcript variant NR_170680.1:n.1925_1926delinsAT non-coding transcript variant NR_170681.1:n.1880_1881delinsAT non-coding transcript variant NR_170682.1:n.2192_2193delinsAT non-coding transcript variant NR_170683.1:n.2147_2148delinsAT non-coding transcript variant NR_170684.1:n.1560_1561delinsAT non-coding transcript variant NR_170685.1:n.2063_2064delinsAT non-coding transcript variant NR_170686.1:n.1931_1932delinsAT non-coding transcript variant NR_170687.1:n.1906_1907delinsAT non-coding transcript variant NR_170688.1:n.2147_2148delinsAT non-coding transcript variant NR_170689.1:n.1661_1662delinsAT non-coding transcript variant NR_170690.1:n.1472_1473delinsAT non-coding transcript variant NR_170691.1:n.1819_1820delinsAT non-coding transcript variant NR_170692.1:n.1429_1430delinsAT non-coding transcript variant NC_000003.12:g.195868630_195868631delinsAT NC_000003.11:g.195595501_195595502delinsAT NG_029779.1:g.45379_45380delinsAT - Protein change
- G580D, G588D, G556D, G565D, G573D, G541D
- Other names
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- Canonical SPDI
- NC_000003.12:195868629:GC:AT
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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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TNK2 | - | - |
GRCh38 GRCh37 |
310 | 369 |
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
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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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Jan 4, 2024 | RCV003683004.1 |
Submissions - Germline
Classification
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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
(Jan 04, 2024)
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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: SCV004410934.1
First in ClinVar: Feb 20, 2024 Last updated: Feb 20, 2024 |
Comment:
This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 619 of the TNK2 protein … (more)
This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 619 of the TNK2 protein (p.Gly619Asp). This variant is present in population databases (no rsID available, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with TNK2-related conditions. 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. 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.