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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

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.

rs80358307

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:68363862-68363873 (GRCh38.p14) 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
del(G)4AAGAGG
Variation Type
Indel Insertion and Deletion
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
LRP5 : Frameshift Variant
Publications
1 citation
Genomic View
See rs on genome
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

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.p14 chr 11 NC_000011.10:g.68363864_68363873del
GRCh37.p13 chr 11 NC_000011.9:g.68131332_68131341del
LRP5 RefSeqGene NG_015835.2:g.56225_56234del
Gene: LRP5, LDL receptor related protein 5 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LRP5 transcript variant 2 NM_001291902.2:c.-964_-95…

NM_001291902.2:c.-964_-953=

N/A 5 Prime UTR Variant
LRP5 transcript variant 1 NM_002335.4:c.804_813del G [GGG] > G [GG] Coding Sequence Variant
low-density lipoprotein receptor-related protein 5 isoform 1 precursor NP_002326.2:p.Gly269fs G (Gly) > G (Gly) Frameshift Variant
LRP5 transcript variant X8 XM_017017735.2:c. N/A Genic Upstream Transcript Variant
LRP5 transcript variant X10 XM_017017736.2:c. N/A Genic Upstream Transcript Variant
LRP5 transcript variant X1 XM_011545029.2:c.831_840d…

XM_011545029.2:c.831_840del

G [GGG] > G [GG] Coding Sequence Variant
low-density lipoprotein receptor-related protein 5 isoform X1 XP_011543331.1:p.Gly278fs G (Gly) > G (Gly) Frameshift Variant
LRP5 transcript variant X2 XM_005273994.3:c.804_813d…

XM_005273994.3:c.804_813del

G [GGG] > G [GG] Coding Sequence Variant
low-density lipoprotein receptor-related protein 5 isoform X2 XP_005274051.1:p.Gly269fs G (Gly) > G (Gly) Frameshift Variant
LRP5 transcript variant X3 XM_011545030.2:c.831_840d…

XM_011545030.2:c.831_840del

G [GGG] > G [GG] Coding Sequence Variant
low-density lipoprotein receptor-related protein 5 isoform X3 XP_011543332.1:p.Gly278fs G (Gly) > G (Gly) Frameshift Variant
LRP5 transcript variant X4 XM_011545031.2:c.831_840d…

XM_011545031.2:c.831_840del

G [GGG] > G [GG] Coding Sequence Variant
low-density lipoprotein receptor-related protein 5 isoform X4 XP_011543333.1:p.Gly278fs G (Gly) > G (Gly) Frameshift Variant
LRP5 transcript variant X5 XM_047426948.1:c.831_840d…

XM_047426948.1:c.831_840del

G [GGG] > G [GG] Coding Sequence Variant
low-density lipoprotein receptor-related protein 5 isoform X5 XP_047282904.1:p.Gly278fs G (Gly) > G (Gly) Frameshift Variant
LRP5 transcript variant X6 XM_047426949.1:c.831_840d…

XM_047426949.1:c.831_840del

G [GGG] > G [GG] Coding Sequence Variant
low-density lipoprotein receptor-related protein 5 isoform X6 XP_047282905.1:p.Gly278fs G (Gly) > G (Gly) Frameshift Variant
LRP5 transcript variant X7 XM_047426950.1:c.831_840d…

XM_047426950.1:c.831_840del

G [GGG] > G [GG] Coding Sequence Variant
low-density lipoprotein receptor-related protein 5 isoform X7 XP_047282906.1:p.Gly278fs G (Gly) > G (Gly) Frameshift Variant
LRP5 transcript variant X9 XR_001747874.2:n.1300_130…

XR_001747874.2:n.1300_1309del

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: del(G)4AAGAGG (allele ID: 21334 )
ClinVar Accession Disease Names Clinical Significance
RCV000006675.3 Exudative vitreoretinopathy 4, autosomal recessive Pathogenic
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 (G)6AAGAGG= del(G)4AAGAGG
GRCh38.p14 chr 11 NC_000011.10:g.68363862_68363873= NC_000011.10:g.68363864_68363873del
GRCh37.p13 chr 11 NC_000011.9:g.68131330_68131341= NC_000011.9:g.68131332_68131341del
LRP5 RefSeqGene NG_015835.2:g.56223_56234= NG_015835.2:g.56225_56234del
LRP5 transcript variant 1 NM_002335.4:c.802_813= NM_002335.4:c.804_813del
LRP5 transcript variant 1 NM_002335.3:c.802_813= NM_002335.3:c.804_813del
LRP5 transcript NM_002335.2:c.802_813= NM_002335.2:c.804_813del
LRP5 transcript variant 2 NM_001291902.2:c.-964_-953= NM_001291902.2:c.-962_-953del
LRP5 transcript variant 2 NM_001291902.1:c.-964_-953= NM_001291902.1:c.-962_-953del
LRP5 transcript variant X2 XM_005273994.3:c.802_813= XM_005273994.3:c.804_813del
LRP5 transcript variant X2 XM_005273994.2:c.802_813= XM_005273994.2:c.804_813del
LRP5 transcript variant X1 XM_005273994.1:c.802_813= XM_005273994.1:c.804_813del
LRP5 transcript variant X4 XM_011545031.2:c.829_840= XM_011545031.2:c.831_840del
LRP5 transcript variant X4 XM_011545031.1:c.829_840= XM_011545031.1:c.831_840del
LRP5 transcript variant X1 XM_011545029.2:c.829_840= XM_011545029.2:c.831_840del
LRP5 transcript variant X1 XM_011545029.1:c.829_840= XM_011545029.1:c.831_840del
LRP5 transcript variant X3 XM_011545030.2:c.829_840= XM_011545030.2:c.831_840del
LRP5 transcript variant X3 XM_011545030.1:c.829_840= XM_011545030.1:c.831_840del
LRP5 transcript variant X9 XR_001747874.2:n.1298_1309= XR_001747874.2:n.1300_1309del
LRP5 transcript variant X8 XR_001747874.1:n.844_855= XR_001747874.1:n.846_855del
LRP5 transcript variant X6 XM_047426949.1:c.829_840= XM_047426949.1:c.831_840del
LRP5 transcript variant X5 XM_047426948.1:c.829_840= XM_047426948.1:c.831_840del
LRP5 transcript variant X7 XM_047426950.1:c.829_840= XM_047426950.1:c.831_840del
low-density lipoprotein receptor-related protein 5 isoform 1 precursor NP_002326.2:p.Gly268_Arg271= NP_002326.2:p.Gly269fs
low-density lipoprotein receptor-related protein 5 isoform X2 XP_005274051.1:p.Gly268_Arg271= XP_005274051.1:p.Gly269fs
low-density lipoprotein receptor-related protein 5 isoform X4 XP_011543333.1:p.Gly277_Arg280= XP_011543333.1:p.Gly278fs
low-density lipoprotein receptor-related protein 5 isoform X1 XP_011543331.1:p.Gly277_Arg280= XP_011543331.1:p.Gly278fs
low-density lipoprotein receptor-related protein 5 isoform X3 XP_011543332.1:p.Gly277_Arg280= XP_011543332.1:p.Gly278fs
low-density lipoprotein receptor-related protein 5 isoform X6 XP_047282905.1:p.Gly277_Arg280= XP_047282905.1:p.Gly278fs
low-density lipoprotein receptor-related protein 5 isoform X5 XP_047282904.1:p.Gly277_Arg280= XP_047282904.1:p.Gly278fs
low-density lipoprotein receptor-related protein 5 isoform X7 XP_047282906.1:p.Gly277_Arg280= XP_047282906.1:p.Gly278fs
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 SubSNP, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 GENEREVIEWS ss187636990 Feb 04, 2010 (132)
2 ClinVar RCV000006675.3 Oct 12, 2018 (152)
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
RCV000006675.3 NC_000011.10:68363861:GGGGGGAAGAGG…

NC_000011.10:68363861:GGGGGGAAGAGG:GG

NC_000011.10:68363861:GGGGGGAAGAGG…

NC_000011.10:68363861:GGGGGGAAGAGG:GG

(self)
ss187636990 NC_000011.10:68363862:GGGGGAAGAG: NC_000011.10:68363861:GGGGGGAAGAGG…

NC_000011.10:68363861:GGGGGGAAGAGG:GG

(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 rs80358307
PMID Title Author Year Journal
15981244 Complexity of the genotype-phenotype correlation in familial exudative vitreoretinopathy with mutations in the LRP5 and/or FZD4 genes. Qin M et al. 2005 Human mutation
Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

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: 2.0.1.post761+d5e8e07