VCV000714382.14 - ClinVar

NM_001352702.2(PTK2):c.2907C>T (p.Tyr969=)

Germline

Classification

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.

(3)

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.

Benign

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001352702.2(PTK2):c.2907C>T (p.Tyr969=)

Variation ID: 714382 Accession: VCV000714382.14

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 8q24.3 8: 140668359 (GRCh38) [ NCBI UCSC ] 8: 141678458 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	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	Oct 20, 2024	Sep 1, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NM_001352702.2:c.2907C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001339631.1:p.Tyr969=	synonymous
NM_001199649.2:c.2814C>T	NP_001186578.1:p.Tyr938=	synonymous
NM_001316342.2:c.2484C>T	NP_001303271.1:p.Tyr828=	synonymous
NM_001352694.2:c.2775C>T	NP_001339623.1:p.Tyr925=	synonymous
NM_001352695.2:c.2814C>T	NP_001339624.1:p.Tyr938=	synonymous
NM_001352696.2:c.2484C>T	NP_001339625.1:p.Tyr828=	synonymous
NM_001352697.2:c.2967C>T	NP_001339626.1:p.Tyr989=	synonymous
NM_001352698.2:c.2946C>T	NP_001339627.1:p.Tyr982=	synonymous
NM_001352699.2:c.2907C>T	NP_001339628.1:p.Tyr969=	synonymous
NM_001352700.2:c.2907C>T	NP_001339629.1:p.Tyr969=	synonymous
NM_001352701.2:c.2907C>T	NP_001339630.1:p.Tyr969=	synonymous
NM_001352703.2:c.2907C>T	NP_001339632.1:p.Tyr969=	synonymous
NM_001352704.2:c.2886C>T	NP_001339633.1:p.Tyr962=	synonymous
NM_001352705.2:c.2862C>T	NP_001339634.1:p.Tyr954=	synonymous
NM_001352706.2:c.2823C>T	NP_001339635.1:p.Tyr941=	synonymous
NM_001352707.2:c.2823C>T	NP_001339636.1:p.Tyr941=	synonymous
NM_001352708.2:c.2823C>T	NP_001339637.1:p.Tyr941=	synonymous
NM_001352709.2:c.2823C>T	NP_001339638.1:p.Tyr941=	synonymous
NM_001352710.2:c.2823C>T	NP_001339639.1:p.Tyr941=	synonymous
NM_001352711.2:c.2820C>T	NP_001339640.1:p.Tyr940=	synonymous
NM_001352712.2:c.2898C>T	NP_001339641.1:p.Tyr966=	synonymous
NM_001352713.2:c.2805C>T	NP_001339642.1:p.Tyr935=	synonymous
NM_001352714.2:c.2805C>T	NP_001339643.1:p.Tyr935=	synonymous
NM_001352715.2:c.2802C>T	NP_001339644.1:p.Tyr934=	synonymous
NM_001352716.2:c.2799C>T	NP_001339645.1:p.Tyr933=	synonymous
NM_001352717.2:c.2793C>T	NP_001339646.1:p.Tyr931=	synonymous
NM_001352718.2:c.2784C>T	NP_001339647.1:p.Tyr928=	synonymous
NM_001352719.2:c.2784C>T	NP_001339648.1:p.Tyr928=	synonymous
NM_001352720.2:c.2784C>T	NP_001339649.1:p.Tyr928=	synonymous
NM_001352721.2:c.2760C>T	NP_001339650.1:p.Tyr920=	synonymous
NM_001352722.2:c.2760C>T	NP_001339651.1:p.Tyr920=	synonymous
NM_001352723.2:c.2760C>T	NP_001339652.1:p.Tyr920=	synonymous
NM_001352724.2:c.2823C>T	NP_001339653.1:p.Tyr941=	synonymous
NM_001352725.2:c.2721C>T	NP_001339654.1:p.Tyr907=	synonymous
NM_001352726.2:c.2715C>T	NP_001339655.1:p.Tyr905=	synonymous
NM_001352727.2:c.2760C>T	NP_001339656.1:p.Tyr920=	synonymous
NM_001352728.2:c.2667C>T	NP_001339657.1:p.Tyr889=	synonymous
NM_001352729.2:c.2652C>T	NP_001339658.1:p.Tyr884=	synonymous
NM_001352730.2:c.2568C>T	NP_001339659.1:p.Tyr856=	synonymous
NM_001352731.2:c.2562C>T	NP_001339660.1:p.Tyr854=	synonymous
NM_001352732.2:c.2559C>T	NP_001339661.1:p.Tyr853=	synonymous
NM_001352733.2:c.2547C>T	NP_001339662.1:p.Tyr849=	synonymous
NM_001352734.2:c.2505C>T	NP_001339663.1:p.Tyr835=	synonymous
NM_001352735.2:c.2505C>T	NP_001339664.1:p.Tyr835=	synonymous
NM_001352736.2:c.2499C>T	NP_001339665.1:p.Tyr833=	synonymous
NM_001352737.2:c.2538C>T	NP_001339666.1:p.Tyr846=	synonymous
NM_001352738.2:c.2478C>T	NP_001339667.1:p.Tyr826=	synonymous
NM_001352739.2:c.2466C>T	NP_001339668.1:p.Tyr822=	synonymous
NM_001352740.2:c.2463C>T	NP_001339669.1:p.Tyr821=	synonymous
NM_001352741.2:c.2445C>T	NP_001339670.1:p.Tyr815=	synonymous
NM_001352742.2:c.2421C>T	NP_001339671.1:p.Tyr807=	synonymous
NM_001352743.2:c.2421C>T	NP_001339672.1:p.Tyr807=	synonymous
NM_001352744.2:c.2376C>T	NP_001339673.1:p.Tyr792=	synonymous
NM_001352745.2:c.2358C>T	NP_001339674.1:p.Tyr786=	synonymous
NM_001352746.2:c.2313C>T	NP_001339675.1:p.Tyr771=	synonymous
NM_001352747.2:c.1362C>T	NP_001339676.1:p.Tyr454=	synonymous
NM_001352749.2:c.714C>T	NP_001339678.1:p.Tyr238=	synonymous
NM_001352750.2:c.705C>T	NP_001339679.1:p.Tyr235=	synonymous
NM_001352751.2:c.651C>T	NP_001339680.1:p.Tyr217=	synonymous
NM_001352752.2:c.642C>T	NP_001339681.1:p.Tyr214=	synonymous
NM_005607.5:c.2841C>T	NP_005598.3:p.Tyr947=	synonymous
NM_153831.4:c.2775C>T	NP_722560.1:p.Tyr925=	synonymous
NR_148036.2:n.3074C>T		non-coding transcript variant
NR_148037.2:n.3105C>T		non-coding transcript variant
NR_148038.2:n.2823C>T		non-coding transcript variant
NR_148039.2:n.2715C>T		non-coding transcript variant
NC_000008.11:g.140668359G>A
NC_000008.10:g.141678458G>A
NG_029467.2:g.337955C>T

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000008.11:140668358:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The 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.

0.00180 (A)

Allele frequency Help The frequency of the allele represented by this VCV record.

Exome Aggregation Consortium (ExAC) 0.00044

Trans-Omics for Precision Medicine (TOPMed) 0.00159

1000 Genomes Project 30x 0.00187

The Genome Aggregation Database (gnomAD), exomes 0.00040

1000 Genomes Project 0.00180

The Genome Aggregation Database (gnomAD) 0.00151

NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00169

Links

dbSNP: rs56114800 VarSome

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
Gene	OMIM	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.
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.
not provided	Benign (3)	criteria provided, multiple submitters, no conflicts	Sep 1, 2022	RCV000886681.14

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.
Benign (Aug 16, 2018)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV001030201.1 First in ClinVar: Dec 17, 2019 Last updated: Dec 17, 2019
Benign (Sep 01, 2022)	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2) Method: clinical testing	not provided Affected status: yes Allele origin: germline	CeGaT Center for Human Genetics Tuebingen Accession: SCV004163320.10 First in ClinVar: Nov 20, 2023 Last updated: Oct 20, 2024	Comment: PTK2: BS1, BS2 Number of individuals with the variant: 1
Benign (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: not provided	not provided (Unknown mechanism) Affected status: yes Allele origin: germline	Breakthrough Genomics, Breakthrough Genomics Accession: SCV005271570.1 First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024

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

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 rs56114800 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 20, 2024

ClinVar Genomic variation as it relates to human health

NM_001352702.2(PTK2):c.2907C>T (p.Tyr969=)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs56114800 ...