This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
ClinVar Genomic variation as it relates to human health
NM_001352702.2(PTK2):c.3128A>G (p.Asn1043Ser)
Germline
Classification
Help
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.
(1)
Help
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.
Likely benign
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_001352702.2(PTK2):c.3128A>G (p.Asn1043Ser)
Variation ID: 2512796 Accession: VCV002512796.2
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 8q24.3 8: 140659629 (GRCh38) [ NCBI UCSC ] 8: 141669728 (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 8, 2023 May 1, 2024 Jun 6, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001352702.2:c.3128A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001339631.1:p.Asn1043Ser missense NM_001199649.2:c.3035A>G NP_001186578.1:p.Asn1012Ser missense NM_001316342.2:c.2705A>G NP_001303271.1:p.Asn902Ser missense NM_001352694.2:c.2996A>G NP_001339623.1:p.Asn999Ser missense NM_001352695.2:c.3035A>G NP_001339624.1:p.Asn1012Ser missense NM_001352696.2:c.2705A>G NP_001339625.1:p.Asn902Ser missense NM_001352697.2:c.3188A>G NP_001339626.1:p.Asn1063Ser missense NM_001352698.2:c.3167A>G NP_001339627.1:p.Asn1056Ser missense NM_001352699.2:c.3128A>G NP_001339628.1:p.Asn1043Ser missense NM_001352700.2:c.3128A>G NP_001339629.1:p.Asn1043Ser missense NM_001352701.2:c.3128A>G NP_001339630.1:p.Asn1043Ser missense NM_001352703.2:c.3128A>G NP_001339632.1:p.Asn1043Ser missense NM_001352704.2:c.3107A>G NP_001339633.1:p.Asn1036Ser missense NM_001352705.2:c.3083A>G NP_001339634.1:p.Asn1028Ser missense NM_001352706.2:c.3044A>G NP_001339635.1:p.Asn1015Ser missense NM_001352707.2:c.3044A>G NP_001339636.1:p.Asn1015Ser missense NM_001352708.2:c.3044A>G NP_001339637.1:p.Asn1015Ser missense NM_001352709.2:c.3044A>G NP_001339638.1:p.Asn1015Ser missense NM_001352710.2:c.3044A>G NP_001339639.1:p.Asn1015Ser missense NM_001352711.2:c.3041A>G NP_001339640.1:p.Asn1014Ser missense NM_001352712.2:c.3119A>G NP_001339641.1:p.Asn1040Ser missense NM_001352713.2:c.3026A>G NP_001339642.1:p.Asn1009Ser missense NM_001352714.2:c.3026A>G NP_001339643.1:p.Asn1009Ser missense NM_001352715.2:c.3023A>G NP_001339644.1:p.Asn1008Ser missense NM_001352716.2:c.3020A>G NP_001339645.1:p.Asn1007Ser missense NM_001352717.2:c.3014A>G NP_001339646.1:p.Asn1005Ser missense NM_001352718.2:c.3005A>G NP_001339647.1:p.Asn1002Ser missense NM_001352719.2:c.3005A>G NP_001339648.1:p.Asn1002Ser missense NM_001352720.2:c.3005A>G NP_001339649.1:p.Asn1002Ser missense NM_001352721.2:c.2981A>G NP_001339650.1:p.Asn994Ser missense NM_001352722.2:c.2981A>G NP_001339651.1:p.Asn994Ser missense NM_001352723.2:c.2981A>G NP_001339652.1:p.Asn994Ser missense NM_001352724.2:c.2963A>G NP_001339653.1:p.Asn988Ser missense NM_001352725.2:c.2942A>G NP_001339654.1:p.Asn981Ser missense NM_001352726.2:c.2936A>G NP_001339655.1:p.Asn979Ser missense NM_001352727.2:c.2900A>G NP_001339656.1:p.Asn967Ser missense NM_001352728.2:c.2888A>G NP_001339657.1:p.Asn963Ser missense NM_001352729.2:c.2873A>G NP_001339658.1:p.Asn958Ser missense NM_001352730.2:c.2789A>G NP_001339659.1:p.Asn930Ser missense NM_001352731.2:c.2783A>G NP_001339660.1:p.Asn928Ser missense NM_001352732.2:c.2780A>G NP_001339661.1:p.Asn927Ser missense NM_001352733.2:c.2768A>G NP_001339662.1:p.Asn923Ser missense NM_001352734.2:c.2726A>G NP_001339663.1:p.Asn909Ser missense NM_001352735.2:c.2726A>G NP_001339664.1:p.Asn909Ser missense NM_001352736.2:c.2720A>G NP_001339665.1:p.Asn907Ser missense NM_001352737.2:c.2759A>G NP_001339666.1:p.Asn920Ser missense NM_001352738.2:c.2699A>G NP_001339667.1:p.Asn900Ser missense NM_001352739.2:c.2687A>G NP_001339668.1:p.Asn896Ser missense NM_001352740.2:c.2684A>G NP_001339669.1:p.Asn895Ser missense NM_001352741.2:c.2666A>G NP_001339670.1:p.Asn889Ser missense NM_001352742.2:c.2642A>G NP_001339671.1:p.Asn881Ser missense NM_001352743.2:c.2642A>G NP_001339672.1:p.Asn881Ser missense NM_001352744.2:c.2597A>G NP_001339673.1:p.Asn866Ser missense NM_001352745.2:c.2579A>G NP_001339674.1:p.Asn860Ser missense NM_001352746.2:c.2534A>G NP_001339675.1:p.Asn845Ser missense NM_001352747.2:c.1583A>G NP_001339676.1:p.Asn528Ser missense NM_001352749.2:c.935A>G NP_001339678.1:p.Asn312Ser missense NM_001352750.2:c.926A>G NP_001339679.1:p.Asn309Ser missense NM_001352751.2:c.872A>G NP_001339680.1:p.Asn291Ser missense NM_001352752.2:c.863A>G NP_001339681.1:p.Asn288Ser missense NM_001387584.1:c.2657A>G NP_001374513.1:p.Asn886Ser missense NM_001387585.1:c.2933A>G NP_001374514.1:p.Asn978Ser missense NM_001387586.1:c.2996A>G NP_001374515.1:p.Asn999Ser missense NM_001387587.1:c.2996A>G NP_001374516.1:p.Asn999Ser missense NM_001387590.1:c.2549A>G NP_001374519.1:p.Asn850Ser missense NM_001387591.1:c.2594A>G NP_001374520.1:p.Asn865Ser missense NM_001387592.1:c.2054A>G NP_001374521.1:p.Asn685Ser missense NM_001387603.1:c.2603A>G NP_001374532.1:p.Asn868Ser missense NM_001387604.1:c.2063A>G NP_001374533.1:p.Asn688Ser missense NM_001387605.1:c.2657A>G NP_001374534.1:p.Asn886Ser missense NM_001387606.1:c.2687A>G NP_001374535.1:p.Asn896Ser missense NM_001387607.1:c.2696A>G NP_001374536.1:p.Asn899Ser missense NM_001387608.1:c.2657A>G NP_001374537.1:p.Asn886Ser missense NM_001387609.1:c.2666A>G NP_001374538.1:p.Asn889Ser missense NM_001387610.1:c.2474A>G NP_001374539.1:p.Asn825Ser missense NM_001387611.1:c.2675A>G NP_001374540.1:p.Asn892Ser missense NM_001387612.1:c.2657A>G NP_001374541.1:p.Asn886Ser missense NM_001387613.1:c.2666A>G NP_001374542.1:p.Asn889Ser missense NM_001387614.1:c.2933A>G NP_001374543.1:p.Asn978Ser missense NM_001387615.1:c.2936A>G NP_001374544.1:p.Asn979Ser missense NM_001387616.1:c.2054A>G NP_001374545.1:p.Asn685Ser missense NM_001387617.1:c.2054A>G NP_001374546.1:p.Asn685Ser missense NM_001387618.1:c.2657A>G NP_001374547.1:p.Asn886Ser missense NM_001387619.1:c.2888A>G NP_001374548.1:p.Asn963Ser missense NM_001387620.1:c.2705A>G NP_001374549.1:p.Asn902Ser missense NM_001387621.1:c.2054A>G NP_001374550.1:p.Asn685Ser missense NM_001387622.1:c.3014A>G NP_001374551.1:p.Asn1005Ser missense NM_001387623.1:c.2657A>G NP_001374552.1:p.Asn886Ser missense NM_001387624.1:c.3020A>G NP_001374553.1:p.Asn1007Ser missense NM_001387625.1:c.2942A>G NP_001374554.1:p.Asn981Ser missense NM_001387627.1:c.2951A>G NP_001374556.1:p.Asn984Ser missense NM_001387628.1:c.2996A>G NP_001374557.1:p.Asn999Ser missense NM_001387629.1:c.2081A>G NP_001374558.1:p.Asn694Ser missense NM_001387630.1:c.2474A>G NP_001374559.1:p.Asn825Ser missense NM_001387631.1:c.3020A>G NP_001374560.1:p.Asn1007Ser missense NM_001387632.1:c.2933A>G NP_001374561.1:p.Asn978Ser missense NM_001387633.1:c.2963A>G NP_001374562.1:p.Asn988Ser missense NM_001387634.1:c.3023A>G NP_001374563.1:p.Asn1008Ser missense NM_001387635.1:c.2549A>G NP_001374564.1:p.Asn850Ser missense NM_001387636.1:c.2996A>G NP_001374565.1:p.Asn999Ser missense NM_001387637.1:c.2996A>G NP_001374566.1:p.Asn999Ser missense NM_001387638.1:c.3005A>G NP_001374567.1:p.Asn1002Ser missense NM_001387639.1:c.3044A>G NP_001374568.1:p.Asn1015Ser missense NM_001387640.1:c.3065A>G NP_001374569.1:p.Asn1022Ser missense NM_001387641.1:c.3035A>G NP_001374570.1:p.Asn1012Ser missense NM_001387642.1:c.2996A>G NP_001374571.1:p.Asn999Ser missense NM_001387643.1:c.3128A>G NP_001374572.1:p.Asn1043Ser missense NM_001387644.1:c.3146A>G NP_001374573.1:p.Asn1049Ser missense NM_001387645.1:c.2996A>G NP_001374574.1:p.Asn999Ser missense NM_001387646.1:c.3128A>G NP_001374575.1:p.Asn1043Ser missense NM_001387647.1:c.2996A>G NP_001374576.1:p.Asn999Ser missense NM_001387648.1:c.3128A>G NP_001374577.1:p.Asn1043Ser missense NM_001387649.1:c.3176A>G NP_001374578.1:p.Asn1059Ser missense NM_001387650.1:c.3128A>G NP_001374579.1:p.Asn1043Ser missense NM_001387652.1:c.2657A>G NP_001374581.1:p.Asn886Ser missense NM_001387653.1:c.2888A>G NP_001374582.1:p.Asn963Ser missense NM_001387654.1:c.2657A>G NP_001374583.1:p.Asn886Ser missense NM_001387655.1:c.2996A>G NP_001374584.1:p.Asn999Ser missense NM_001387656.1:c.2942A>G NP_001374585.1:p.Asn981Ser missense NM_001387657.1:c.2996A>G NP_001374586.1:p.Asn999Ser missense NM_001387658.1:c.2996A>G NP_001374587.1:p.Asn999Ser missense NM_001387659.1:c.3005A>G NP_001374588.1:p.Asn1002Ser missense NM_001387660.1:c.3128A>G NP_001374589.1:p.Asn1043Ser missense NM_001387661.1:c.3128A>G NP_001374590.1:p.Asn1043Ser missense NM_001387662.1:c.3137A>G NP_001374591.1:p.Asn1046Ser missense NM_005607.5:c.3062A>G NP_005598.3:p.Asn1021Ser missense NM_153831.4:c.2996A>G NP_722560.1:p.Asn999Ser missense NR_148036.2:n.3295A>G non-coding transcript variant NR_148037.2:n.3326A>G non-coding transcript variant NR_148038.2:n.3044A>G non-coding transcript variant NR_148039.2:n.2936A>G non-coding transcript variant NR_170671.1:n.2907A>G non-coding transcript variant NR_170672.1:n.3074A>G non-coding transcript variant NR_170673.1:n.3284A>G non-coding transcript variant NC_000008.11:g.140659629T>C NC_000008.10:g.141669728T>C NG_029467.2:g.346685A>G - Protein change
- N889S, N896S, N907S, N909S, N930S, N967S, N999S, N1015S, N1028S, N1049S, N291S, N309S, N528S, N860S, N900S, N902S, N927S, N978S, N988S, N994S, N1005S, N1007S, N1012S, N1021S, N1040S, N1056S, N1059S, N1063S, N685S, N845S, N866S, N868S, N928S, N963S, N979S, N984S, N1002S, N1008S, N1009S, N1014S, N1022S, N1036S, N1043S, N312S, N688S, N825S, N850S, N1046S, N288S, N694S, N865S, N881S, N886S, N892S, N895S, N899S, N920S, N923S, N958S, N981S
- Other names
- -
- Canonical SPDI
- NC_000008.11:140659628:T: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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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 | ||
|---|---|---|---|---|---|---|
| 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. |
|---|---|---|---|---|
| Likely benign (1) |
criteria provided, single submitter
|
Jun 6, 2023 | RCV004293207.1 |
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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Likely benign
(Jun 06, 2023)
|
criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
|
Ambry Genetics
Accession: SCV003943474.2
First in ClinVar: Jul 08, 2023 Last updated: May 01, 2024 |
Comment:
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of … (more)
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. (less)
|
Comment:
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. |
Comment:
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
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 this variant ...
HelpRecord last updated Nov 03, 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.