Skip to main page content
Accesskeys

dbSNP Short Genetic Variations

Reference SNP (rs) Report

Alpha

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs121909655

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr5:180614142 (GRCh38.p7) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
FLT4 : Missense Variant
Publications
1 citation
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p7 chr 5 NC_000005.10:g.180614142A>G
GRCh37.p13 chr 5 NC_000005.9:g.180041142A>G
FLT4 RefSeqGene NG_011536.1:g.40483T>C
Gene: FLT4, fms related tyrosine kinase 4 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
FLT4 transcript variant 2 NM_002020.4:c.325...

NM_002020.4:c.3257T>C

I [ATC] > T [ACC] Coding Sequence Variant
vascular endothelial growth factor receptor 3 isoform 2 precursor NP_002011.2:p.Ile...

NP_002011.2:p.Ile1086Thr

I (Ile) > T (Thr) Missense Variant
FLT4 transcript variant 1 NM_182925.4:c.325...

NM_182925.4:c.3257T>C

I [ATC] > T [ACC] Coding Sequence Variant
vascular endothelial growth factor receptor 3 isoform 1 precursor NP_891555.2:p.Ile...

NP_891555.2:p.Ile1086Thr

I (Ile) > T (Thr) Missense Variant
FLT4 transcript variant X1 XM_011534478.2:c....

XM_011534478.2:c.3488T>C

I [ATC] > T [ACC] Coding Sequence Variant
vascular endothelial growth factor receptor 3 isoform X1 XP_011532780.1:p....

XP_011532780.1:p.Ile1163Thr

I (Ile) > T (Thr) Missense Variant
FLT4 transcript variant X2 XM_017009263.1:c....

XM_017009263.1:c.3488T>C

I [ATC] > T [ACC] Coding Sequence Variant
vascular endothelial growth factor receptor 3 isoform X2 XP_016864752.1:p....

XP_016864752.1:p.Ile1163Thr

I (Ile) > T (Thr) Missense Variant
FLT4 transcript variant X3 XM_017009264.1:c....

XM_017009264.1:c.3488T>C

I [ATC] > T [ACC] Coding Sequence Variant
vascular endothelial growth factor receptor 3 isoform X2 XP_016864753.1:p....

XP_016864753.1:p.Ile1163Thr

I (Ile) > T (Thr) Missense Variant
FLT4 transcript variant X4 XM_017009265.1:c....

XM_017009265.1:c.3488T>C

I [ATC] > T [ACC] Coding Sequence Variant
vascular endothelial growth factor receptor 3 isoform X2 XP_016864754.1:p....

XP_016864754.1:p.Ile1163Thr

I (Ile) > T (Thr) Missense Variant
FLT4 transcript variant X5 XM_017009266.1:c....

XM_017009266.1:c.3488T>C

I [ATC] > T [ACC] Coding Sequence Variant
vascular endothelial growth factor receptor 3 isoform X3 XP_016864755.1:p....

XP_016864755.1:p.Ile1163Thr

I (Ile) > T (Thr) Missense Variant
FLT4 transcript variant X6 XM_017009267.1:c....

XM_017009267.1:c.3488T>C

I [ATC] > T [ACC] Coding Sequence Variant
vascular endothelial growth factor receptor 3 isoform X4 XP_016864756.1:p....

XP_016864756.1:p.Ile1163Thr

I (Ile) > T (Thr) Missense Variant
FLT4 transcript variant X7 XM_017009268.1:c....

XM_017009268.1:c.3179T>C

I [ATC] > T [ACC] Coding Sequence Variant
vascular endothelial growth factor receptor 3 isoform X5 XP_016864757.1:p....

XP_016864757.1:p.Ile1060Thr

I (Ile) > T (Thr) Missense Variant
FLT4 transcript variant X9 XM_011534484.2:c....

XM_011534484.2:c.2798T>C

I [ATC] > T [ACC] Coding Sequence Variant
vascular endothelial growth factor receptor 3 isoform X6 XP_011532786.1:p....

XP_011532786.1:p.Ile933Thr

I (Ile) > T (Thr) Missense Variant
FLT4 transcript variant X8 XR_001742050.1:n....

XR_001742050.1:n.3721T>C

N/A Non Coding Transcript Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: G (allele ID: 31305 )
ClinVar Accession Disease Names Clinical Significance
RCV000017654.29 Hereditary lymphedema type I Pathogenic
Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

None
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement A= G Note
GRCh38.p7 chr 5 NC_000005.10:g.180614142A= NC_000005.10:g.18061414...

NC_000005.10:g.180614142A>G

GRCh37.p13 chr 5 NC_000005.9:g.180041142A= NC_000005.9:g.180041142A>G
FLT4 RefSeqGene NG_011536.1:g.40483T= NG_011536.1:g.40483T>C
FLT4 transcript variant 1 NM_182925.4:c.3257T= NM_182925.4:c.3257T>C
FLT4 transcript variant 2 NM_002020.4:c.3257T= NM_002020.4:c.3257T>C
FLT4 transcript variant X1 XM_011534478.2:c.3488T= XM_011534478.2:c.3488T>C
FLT4 transcript variant X9 XM_011534484.2:c.2798T= XM_011534484.2:c.2798T>C
FLT4 transcript variant X2 XM_017009263.1:c.3488T= XM_017009263.1:c.3488T>C
FLT4 transcript variant X8 XR_001742050.1:n.3721T= XR_001742050.1:n.3721T>C
FLT4 transcript variant X7 XM_017009268.1:c.3179T= XM_017009268.1:c.3179T>C
FLT4 transcript variant X4 XM_017009265.1:c.3488T= XM_017009265.1:c.3488T>C
FLT4 transcript variant X6 XM_017009267.1:c.3488T= XM_017009267.1:c.3488T>C
FLT4 transcript variant X5 XM_017009266.1:c.3488T= XM_017009266.1:c.3488T>C
FLT4 transcript variant X3 XM_017009264.1:c.3488T= XM_017009264.1:c.3488T>C
vascular endothelial growth factor receptor 3 isoform 1 precursor NP_891555.2:p.Ile1086= NP_891555.2:p.Ile1086Thr
vascular endothelial growth factor receptor 3 isoform 2 precursor NP_002011.2:p.Ile1086= NP_002011.2:p.Ile1086Thr
vascular endothelial growth factor receptor 3 isoform X1 XP_011532780.1:p.Ile1163= XP_011532780.1:p.Ile116...

XP_011532780.1:p.Ile1163Thr

vascular endothelial growth factor receptor 3 isoform X6 XP_011532786.1:p.Ile933= XP_011532786.1:p.Ile933Thr
vascular endothelial growth factor receptor 3 isoform X2 XP_016864752.1:p.Ile1163= XP_016864752.1:p.Ile116...

XP_016864752.1:p.Ile1163Thr

vascular endothelial growth factor receptor 3 isoform X5 XP_016864757.1:p.Ile1060= XP_016864757.1:p.Ile106...

XP_016864757.1:p.Ile1060Thr

vascular endothelial growth factor receptor 3 isoform X2 XP_016864754.1:p.Ile1163= XP_016864754.1:p.Ile116...

XP_016864754.1:p.Ile1163Thr

vascular endothelial growth factor receptor 3 isoform X4 XP_016864756.1:p.Ile1163= XP_016864756.1:p.Ile116...

XP_016864756.1:p.Ile1163Thr

vascular endothelial growth factor receptor 3 isoform X3 XP_016864755.1:p.Ile1163= XP_016864755.1:p.Ile116...

XP_016864755.1:p.Ile1163Thr

vascular endothelial growth factor receptor 3 isoform X2 XP_016864753.1:p.Ile1163= XP_016864753.1:p.Ile116...

XP_016864753.1:p.Ile1163Thr

Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

1 ClinVar, 1 SubSNP submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss263197898 Nov 04, 2010 (133)
2 ClinVar RCV000017654.29 Jul 20, 2018 (151)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss263197898 NC_000005.10:180614141:A= NC_000005.10:180614141:A= (self)
RCV000017654.29, ss263197898 NC_000005.10:180614141:A>G NC_000005.10:180614141:A>G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs121909655
PMID Title Author Year Journal
16965327 Hereditary lymphedema type I associated with VEGFR3 mutation: the first de novo case and atypical presentations. Ghalamkarpour A et al. 2006 Clinical genetics

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 0.1.4.post833+d3ba21e