ClinVar Genomic variation as it relates to human health
NM_001352702.2(PTK2):c.2563C>T (p.Arg855Ter)
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.2563C>T (p.Arg855Ter)
Variation ID: 2571628 Accession: VCV002571628.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 8q24.3 8: 140700950 (GRCh38) [ NCBI UCSC ] 8: 141711049 (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 Jul 17, 2023 Jul 16, 2023 Mar 24, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001352702.2:c.2563C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001339631.1:p.Arg855Ter nonsense NM_001199649.2:c.2440C>T NP_001186578.1:p.Arg814Ter nonsense NM_001316342.2:c.2140C>T NP_001303271.1:p.Arg714Ter nonsense NM_001352694.2:c.2440C>T NP_001339623.1:p.Arg814Ter nonsense NM_001352695.2:c.2542C>T NP_001339624.1:p.Arg848Ter nonsense NM_001352696.2:c.2140C>T NP_001339625.1:p.Arg714Ter nonsense NM_001352697.2:c.2695C>T NP_001339626.1:p.Arg899Ter nonsense NM_001352698.2:c.2602C>T NP_001339627.1:p.Arg868Ter nonsense NM_001352699.2:c.2563C>T NP_001339628.1:p.Arg855Ter nonsense NM_001352700.2:c.2563C>T NP_001339629.1:p.Arg855Ter nonsense NM_001352701.2:c.2563C>T NP_001339630.1:p.Arg855Ter nonsense NM_001352703.2:c.2563C>T NP_001339632.1:p.Arg855Ter nonsense NM_001352704.2:c.2542C>T NP_001339633.1:p.Arg848Ter nonsense NM_001352705.2:c.2518C>T NP_001339634.1:p.Arg840Ter nonsense NM_001352706.2:c.2479C>T NP_001339635.1:p.Arg827Ter nonsense NM_001352707.2:c.2479C>T NP_001339636.1:p.Arg827Ter nonsense NM_001352708.2:c.2479C>T NP_001339637.1:p.Arg827Ter nonsense NM_001352709.2:c.2479C>T NP_001339638.1:p.Arg827Ter nonsense NM_001352710.2:c.2479C>T NP_001339639.1:p.Arg827Ter nonsense NM_001352711.2:c.2476C>T NP_001339640.1:p.Arg826Ter nonsense NM_001352712.2:c.2563C>T NP_001339641.1:p.Arg855Ter nonsense NM_001352713.2:c.2461C>T NP_001339642.1:p.Arg821Ter nonsense NM_001352714.2:c.2461C>T NP_001339643.1:p.Arg821Ter nonsense NM_001352715.2:c.2458C>T NP_001339644.1:p.Arg820Ter nonsense NM_001352716.2:c.2455C>T NP_001339645.1:p.Arg819Ter nonsense NM_001352717.2:c.2458C>T NP_001339646.1:p.Arg820Ter nonsense NM_001352718.2:c.2440C>T NP_001339647.1:p.Arg814Ter nonsense NM_001352719.2:c.2440C>T NP_001339648.1:p.Arg814Ter nonsense NM_001352720.2:c.2440C>T NP_001339649.1:p.Arg814Ter nonsense NM_001352721.2:c.2479C>T NP_001339650.1:p.Arg827Ter nonsense NM_001352722.2:c.2479C>T NP_001339651.1:p.Arg827Ter nonsense NM_001352723.2:c.2479C>T NP_001339652.1:p.Arg827Ter nonsense NM_001352724.2:c.2479C>T NP_001339653.1:p.Arg827Ter nonsense NM_001352725.2:c.2440C>T NP_001339654.1:p.Arg814Ter nonsense NM_001352726.2:c.2371C>T NP_001339655.1:p.Arg791Ter nonsense NM_001352727.2:c.2479C>T NP_001339656.1:p.Arg827Ter nonsense NM_001352728.2:c.2332C>T NP_001339657.1:p.Arg778Ter nonsense NM_001352729.2:c.2371C>T NP_001339658.1:p.Arg791Ter nonsense NM_001352730.2:c.2224C>T NP_001339659.1:p.Arg742Ter nonsense NM_001352731.2:c.2224C>T NP_001339660.1:p.Arg742Ter nonsense NM_001352732.2:c.2224C>T NP_001339661.1:p.Arg742Ter nonsense NM_001352733.2:c.2203C>T NP_001339662.1:p.Arg735Ter nonsense NM_001352734.2:c.2224C>T NP_001339663.1:p.Arg742Ter nonsense NM_001352735.2:c.2161C>T NP_001339664.1:p.Arg721Ter nonsense NM_001352736.2:c.2155C>T NP_001339665.1:p.Arg719Ter nonsense NM_001352737.2:c.2203C>T NP_001339666.1:p.Arg735Ter nonsense NM_001352738.2:c.2140C>T NP_001339667.1:p.Arg714Ter nonsense NM_001352739.2:c.2122C>T NP_001339668.1:p.Arg708Ter nonsense NM_001352740.2:c.2119C>T NP_001339669.1:p.Arg707Ter nonsense NM_001352741.2:c.2101C>T NP_001339670.1:p.Arg701Ter nonsense NM_001352742.2:c.2077C>T NP_001339671.1:p.Arg693Ter nonsense NM_001352743.2:c.2140C>T NP_001339672.1:p.Arg714Ter nonsense NM_001352744.2:c.2032C>T NP_001339673.1:p.Arg678Ter nonsense NM_001352745.2:c.2014C>T NP_001339674.1:p.Arg672Ter nonsense NM_001352746.2:c.1969C>T NP_001339675.1:p.Arg657Ter nonsense NM_001352747.2:c.1018C>T NP_001339676.1:p.Arg340Ter nonsense NM_001352749.2:c.370C>T NP_001339678.1:p.Arg124Ter nonsense NM_001352750.2:c.370C>T NP_001339679.1:p.Arg124Ter nonsense NM_001352751.2:c.370C>T NP_001339680.1:p.Arg124Ter nonsense NM_001352752.2:c.370C>T NP_001339681.1:p.Arg124Ter nonsense NM_001387584.1:c.2101C>T NP_001374513.1:p.Arg701Ter nonsense NM_001387585.1:c.2440C>T NP_001374514.1:p.Arg814Ter nonsense NM_001387586.1:c.2440C>T NP_001374515.1:p.Arg814Ter nonsense NM_001387587.1:c.2440C>T NP_001374516.1:p.Arg814Ter nonsense NM_001387590.1:c.1993C>T NP_001374519.1:p.Arg665Ter nonsense NM_001387591.1:c.2101C>T NP_001374520.1:p.Arg701Ter nonsense NM_001387592.1:c.1498C>T NP_001374521.1:p.Arg500Ter nonsense NM_001387603.1:c.2101C>T NP_001374532.1:p.Arg701Ter nonsense NM_001387604.1:c.1498C>T NP_001374533.1:p.Arg500Ter nonsense NM_001387605.1:c.2101C>T NP_001374534.1:p.Arg701Ter nonsense NM_001387606.1:c.2122C>T NP_001374535.1:p.Arg708Ter nonsense NM_001387607.1:c.2140C>T NP_001374536.1:p.Arg714Ter nonsense NM_001387608.1:c.2101C>T NP_001374537.1:p.Arg701Ter nonsense NM_001387609.1:c.2101C>T NP_001374538.1:p.Arg701Ter nonsense NM_001387610.1:c.1918C>T NP_001374539.1:p.Arg640Ter nonsense NM_001387611.1:c.2119C>T NP_001374540.1:p.Arg707Ter nonsense NM_001387612.1:c.2101C>T NP_001374541.1:p.Arg701Ter nonsense NM_001387613.1:c.2101C>T NP_001374542.1:p.Arg701Ter nonsense NM_001387614.1:c.2440C>T NP_001374543.1:p.Arg814Ter nonsense NM_001387615.1:c.2371C>T NP_001374544.1:p.Arg791Ter nonsense NM_001387616.1:c.1498C>T NP_001374545.1:p.Arg500Ter nonsense NM_001387617.1:c.1498C>T NP_001374546.1:p.Arg500Ter nonsense NM_001387618.1:c.2101C>T NP_001374547.1:p.Arg701Ter nonsense NM_001387619.1:c.2332C>T NP_001374548.1:p.Arg778Ter nonsense NM_001387620.1:c.2140C>T NP_001374549.1:p.Arg714Ter nonsense NM_001387621.1:c.1498C>T NP_001374550.1:p.Arg500Ter nonsense NM_001387622.1:c.2458C>T NP_001374551.1:p.Arg820Ter nonsense NM_001387623.1:c.2101C>T NP_001374552.1:p.Arg701Ter nonsense NM_001387624.1:c.2455C>T NP_001374553.1:p.Arg819Ter nonsense NM_001387625.1:c.2440C>T NP_001374554.1:p.Arg814Ter nonsense NM_001387627.1:c.2458C>T NP_001374556.1:p.Arg820Ter nonsense NM_001387628.1:c.2440C>T NP_001374557.1:p.Arg814Ter nonsense NM_001387629.1:c.1516C>T NP_001374558.1:p.Arg506Ter nonsense NM_001387630.1:c.1918C>T NP_001374559.1:p.Arg640Ter nonsense NM_001387631.1:c.2455C>T NP_001374560.1:p.Arg819Ter nonsense NM_001387632.1:c.2440C>T NP_001374561.1:p.Arg814Ter nonsense NM_001387633.1:c.2461C>T NP_001374562.1:p.Arg821Ter nonsense NM_001387634.1:c.2458C>T NP_001374563.1:p.Arg820Ter nonsense NM_001387635.1:c.1993C>T NP_001374564.1:p.Arg665Ter nonsense NM_001387636.1:c.2440C>T NP_001374565.1:p.Arg814Ter nonsense NM_001387637.1:c.2440C>T NP_001374566.1:p.Arg814Ter nonsense NM_001387638.1:c.2440C>T NP_001374567.1:p.Arg814Ter nonsense NM_001387639.1:c.2479C>T NP_001374568.1:p.Arg827Ter nonsense NM_001387640.1:c.2563C>T NP_001374569.1:p.Arg855Ter nonsense NM_001387641.1:c.2479C>T NP_001374570.1:p.Arg827Ter nonsense NM_001387642.1:c.2440C>T NP_001374571.1:p.Arg814Ter nonsense NM_001387643.1:c.2572C>T NP_001374572.1:p.Arg858Ter nonsense NM_001387644.1:c.2581C>T NP_001374573.1:p.Arg861Ter nonsense NM_001387645.1:c.2440C>T NP_001374574.1:p.Arg814Ter nonsense NM_001387646.1:c.2572C>T NP_001374575.1:p.Arg858Ter nonsense NM_001387647.1:c.2440C>T NP_001374576.1:p.Arg814Ter nonsense NM_001387648.1:c.2572C>T NP_001374577.1:p.Arg858Ter nonsense NM_001387649.1:c.2611C>T NP_001374578.1:p.Arg871Ter nonsense NM_001387650.1:c.2572C>T NP_001374579.1:p.Arg858Ter nonsense NM_001387652.1:c.2101C>T NP_001374581.1:p.Arg701Ter nonsense NM_001387653.1:c.2332C>T NP_001374582.1:p.Arg778Ter nonsense NM_001387654.1:c.2101C>T NP_001374583.1:p.Arg701Ter nonsense NM_001387655.1:c.2440C>T NP_001374584.1:p.Arg814Ter nonsense NM_001387656.1:c.2440C>T NP_001374585.1:p.Arg814Ter nonsense NM_001387657.1:c.2440C>T NP_001374586.1:p.Arg814Ter nonsense NM_001387658.1:c.2440C>T NP_001374587.1:p.Arg814Ter nonsense NM_001387659.1:c.2440C>T NP_001374588.1:p.Arg814Ter nonsense NM_001387660.1:c.2572C>T NP_001374589.1:p.Arg858Ter nonsense NM_001387661.1:c.2572C>T NP_001374590.1:p.Arg858Ter nonsense NM_001387662.1:c.2572C>T NP_001374591.1:p.Arg858Ter nonsense NM_005607.5:c.2506C>T NP_005598.3:p.Arg836Ter nonsense NM_153831.4:c.2440C>T NP_722560.1:p.Arg814Ter nonsense NR_148036.2:n.2730C>T non-coding transcript variant NR_148037.2:n.2761C>T non-coding transcript variant NR_148038.2:n.2479C>T non-coding transcript variant NR_148039.2:n.2371C>T non-coding transcript variant NR_170671.1:n.2351C>T non-coding transcript variant NR_170672.1:n.2518C>T non-coding transcript variant NR_170673.1:n.2630C>T non-coding transcript variant NC_000008.11:g.140700950G>A NC_000008.10:g.141711049G>A NG_029467.2:g.305364C>T - Protein change
- R124*, R340*, R500*, R506*, R640*, R657*, R665*, R672*, R678*, R693*, R701*, R707*, R708*, R714*, R719*, R721*, R735*, R742*, R778*, R791*, R814*, R819*, R820*, R821*, R826*, R827*, R836*, R840*, R848*, R855*, R858*, R861*, R868*, R871*, R899*
- Other names
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- Canonical SPDI
- NC_000008.11:140700949: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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Allele frequency
Help
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
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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PTK2 | - | - |
GRCh38 GRCh37 |
55 | 111 |
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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Uncertain significance (1) |
criteria provided, single submitter
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Mar 24, 2023 | RCV003313338.2 |
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
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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Uncertain significance
(Mar 24, 2023)
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criteria provided, single submitter
Method: research
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Hypertonia
Autism Epicanthus Deeply set eye Bulbous nose High palate Dental crowding Mandibular prognathia Hypotonia Failure to thrive Shallow orbits
Explanation for multiple conditions: Novel disease.
The variant classification is for a novel disease that is unnamed and only defined by a set of clinical features.
Affected status: unknown
Allele origin:
unknown
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HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology
Study: HudsonAlpha-AGHI-WGS
Accession: SCV004012100.1 First in ClinVar: Jul 16, 2023 Last updated: Jul 16, 2023 |
Number of individuals with the variant: 1
Clinical Features:
Hypertonia (present) , Autism (present) , Epicanthus (present) , Deeply set eye (present) , Bulbous nose (present) , High palate (present) , Dental crowding (present) … (more)
Hypertonia (present) , Autism (present) , Epicanthus (present) , Deeply set eye (present) , Bulbous nose (present) , High palate (present) , Dental crowding (present) , Mandibular prognathia (present) , Hypotonia (present) , Failure to thrive (present) , Shallow orbits (present) (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 Jan 26, 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.