ClinVar Genomic variation as it relates to human health
NM_001352702.2(PTK2):c.2109C>T (p.Asp703=)
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_001352702.2(PTK2):c.2109C>T (p.Asp703=)
Variation ID: 785268 Accession: VCV000785268.5
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 8q24.3 8: 140735295 (GRCh38) [ NCBI UCSC ] 8: 141745394 (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 Dec 17, 2019 Sep 29, 2024 Dec 31, 2019 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001352702.2:c.2109C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001339631.1:p.Asp703= synonymous NM_001199649.2:c.1986C>T NP_001186578.1:p.Asp662= synonymous NM_001316342.2:c.1686C>T NP_001303271.1:p.Asp562= synonymous NM_001352694.2:c.1986C>T NP_001339623.1:p.Asp662= synonymous NM_001352695.2:c.2088C>T NP_001339624.1:p.Asp696= synonymous NM_001352696.2:c.1686C>T NP_001339625.1:p.Asp562= synonymous NM_001352697.2:c.2241C>T NP_001339626.1:p.Asp747= synonymous NM_001352698.2:c.2148C>T NP_001339627.1:p.Asp716= synonymous NM_001352699.2:c.2109C>T NP_001339628.1:p.Asp703= synonymous NM_001352700.2:c.2109C>T NP_001339629.1:p.Asp703= synonymous NM_001352701.2:c.2109C>T NP_001339630.1:p.Asp703= synonymous NM_001352703.2:c.2109C>T NP_001339632.1:p.Asp703= synonymous NM_001352704.2:c.2088C>T NP_001339633.1:p.Asp696= synonymous NM_001352705.2:c.2064C>T NP_001339634.1:p.Asp688= synonymous NM_001352706.2:c.2025C>T NP_001339635.1:p.Asp675= synonymous NM_001352707.2:c.2025C>T NP_001339636.1:p.Asp675= synonymous NM_001352708.2:c.2025C>T NP_001339637.1:p.Asp675= synonymous NM_001352709.2:c.2025C>T NP_001339638.1:p.Asp675= synonymous NM_001352710.2:c.2025C>T NP_001339639.1:p.Asp675= synonymous NM_001352711.2:c.2022C>T NP_001339640.1:p.Asp674= synonymous NM_001352712.2:c.2109C>T NP_001339641.1:p.Asp703= synonymous NM_001352713.2:c.2007C>T NP_001339642.1:p.Asp669= synonymous NM_001352714.2:c.2007C>T NP_001339643.1:p.Asp669= synonymous NM_001352715.2:c.2004C>T NP_001339644.1:p.Asp668= synonymous NM_001352716.2:c.2001C>T NP_001339645.1:p.Asp667= synonymous NM_001352717.2:c.2004C>T NP_001339646.1:p.Asp668= synonymous NM_001352718.2:c.1986C>T NP_001339647.1:p.Asp662= synonymous NM_001352719.2:c.1986C>T NP_001339648.1:p.Asp662= synonymous NM_001352720.2:c.1986C>T NP_001339649.1:p.Asp662= synonymous NM_001352721.2:c.2025C>T NP_001339650.1:p.Asp675= synonymous NM_001352722.2:c.2025C>T NP_001339651.1:p.Asp675= synonymous NM_001352723.2:c.2025C>T NP_001339652.1:p.Asp675= synonymous NM_001352724.2:c.2025C>T NP_001339653.1:p.Asp675= synonymous NM_001352725.2:c.1986C>T NP_001339654.1:p.Asp662= synonymous NM_001352726.2:c.1917C>T NP_001339655.1:p.Asp639= synonymous NM_001352727.2:c.2025C>T NP_001339656.1:p.Asp675= synonymous NM_001352728.2:c.1878C>T NP_001339657.1:p.Asp626= synonymous NM_001352729.2:c.1917C>T NP_001339658.1:p.Asp639= synonymous NM_001352730.2:c.1770C>T NP_001339659.1:p.Asp590= synonymous NM_001352731.2:c.1770C>T NP_001339660.1:p.Asp590= synonymous NM_001352732.2:c.1770C>T NP_001339661.1:p.Asp590= synonymous NM_001352733.2:c.1749C>T NP_001339662.1:p.Asp583= synonymous NM_001352734.2:c.1770C>T NP_001339663.1:p.Asp590= synonymous NM_001352735.2:c.1707C>T NP_001339664.1:p.Asp569= synonymous NM_001352736.2:c.1701C>T NP_001339665.1:p.Asp567= synonymous NM_001352737.2:c.1749C>T NP_001339666.1:p.Asp583= synonymous NM_001352738.2:c.1686C>T NP_001339667.1:p.Asp562= synonymous NM_001352739.2:c.1668C>T NP_001339668.1:p.Asp556= synonymous NM_001352740.2:c.1665C>T NP_001339669.1:p.Asp555= synonymous NM_001352741.2:c.1647C>T NP_001339670.1:p.Asp549= synonymous NM_001352742.2:c.1623C>T NP_001339671.1:p.Asp541= synonymous NM_001352743.2:c.1686C>T NP_001339672.1:p.Asp562= synonymous NM_001352744.2:c.1578C>T NP_001339673.1:p.Asp526= synonymous NM_001352745.2:c.1560C>T NP_001339674.1:p.Asp520= synonymous NM_001352746.2:c.1515C>T NP_001339675.1:p.Asp505= synonymous NM_001352747.2:c.564C>T NP_001339676.1:p.Asp188= synonymous NM_005607.5:c.2052C>T NP_005598.3:p.Asp684= synonymous NM_153831.4:c.1986C>T NP_722560.1:p.Asp662= synonymous NR_148036.2:n.2388C>T non-coding transcript variant NR_148037.2:n.2419C>T non-coding transcript variant NR_148038.2:n.2137C>T non-coding transcript variant NR_148039.2:n.2029C>T non-coding transcript variant NC_000008.11:g.140735295G>A NC_000008.10:g.141745394G>A NG_029467.2:g.271019C>T - Protein change
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- Other names
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- Canonical SPDI
- NC_000008.11:140735294:G:A
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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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0.00499 (A)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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Trans-Omics for Precision Medicine (TOPMed) 0.00542
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00554
The Genome Aggregation Database (gnomAD), exomes 0.00123
Exome Aggregation Consortium (ExAC) 0.00153
The Genome Aggregation Database (gnomAD) 0.00482
1000 Genomes Project 0.00499
1000 Genomes Project 30x 0.00562
- 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. |
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| PTK2 | - | - |
GRCh38 GRCh37 |
60 | 116 | |
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 (2) |
criteria provided, multiple submitters, no conflicts
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Dec 31, 2019 | RCV000967107.5 |
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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|---|---|---|---|---|---|
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Benign
(Dec 31, 2019)
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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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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001114478.2
First in ClinVar: Dec 17, 2019 Last updated: May 04, 2020 |
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Benign
(-)
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criteria provided, single submitter
Method: not provided
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not provided
(Unknown mechanism)
Affected status: yes
Allele origin:
germline
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Breakthrough Genomics, Breakthrough Genomics
Accession: SCV005271571.1
First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024 |
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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
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 rs139495370 ...
HelpRecord 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.