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.
rs1491018513
Current Build 156
Released September 21, 2022
- Organism
- Homo sapiens
- Position
-
chr9:8858695-8858696 (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
- delTG
- Variation Type
- Deletion
- Frequency
- delTG=0.00023 (6/26360, GnomAD)
- Clinical Significance
- Not Reported in ClinVar
- Gene : Consequence
-
PTPRD : Intron VariantPTPRD-AS1 : Intron Variant
- Publications
- 0 citations
- Genomic View
- See rs on genome
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").
Download| Study | Population | Group | Sample Size | Ref Allele | Alt Allele |
|---|---|---|---|---|---|
| gnomAD - Genomes | Global | Study-wide | 26360 | TG=0.99977 | delTG=0.00023 |
| gnomAD - Genomes | European | Sub | 13060 | TG=1.00000 | delTG=0.00000 |
| gnomAD - Genomes | African | Sub | 10010 | TG=0.99940 | delTG=0.00060 |
| gnomAD - Genomes | American | Sub | 2364 | TG=1.0000 | delTG=0.0000 |
| gnomAD - Genomes | Ashkenazi Jewish | Sub | 424 | TG=1.000 | delTG=0.000 |
| gnomAD - Genomes | Other | Sub | 312 | TG=1.000 | delTG=0.000 |
| gnomAD - Genomes | East Asian | Sub | 190 | TG=1.000 | delTG=0.000 |
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.
| Sequence name | Change |
|---|---|
| GRCh38.p14 chr 9 | NC_000009.12:g.8858695_8858696del |
| GRCh37.p13 chr 9 | NC_000009.11:g.8858695_8858696del |
| PTPRD RefSeqGene | NG_033963.1:g.1759028_1759029del |
| Molecule type | Change | Amino acid[Codon] | SO Term |
|---|---|---|---|
| PTPRD transcript variant 1 |
NM_002839.4:c.-103-124750… NM_002839.4:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant 5 | NM_001040712.2:c. | N/A | Genic Upstream Transcript Variant |
| PTPRD transcript variant 6 | NM_001171025.2:c. | N/A | Genic Upstream Transcript Variant |
| PTPRD transcript variant 7 | NM_001377946.1:c. | N/A | Genic Upstream Transcript Variant |
| PTPRD transcript variant 8 | NM_001377947.1:c. | N/A | Genic Upstream Transcript Variant |
| PTPRD transcript variant 9 | NM_001377958.1:c. | N/A | Genic Upstream Transcript Variant |
| PTPRD transcript variant 10 | NM_001378058.1:c. | N/A | Genic Upstream Transcript Variant |
| PTPRD transcript variant 2 | NM_130391.4:c. | N/A | Genic Upstream Transcript Variant |
| PTPRD transcript variant 3 | NM_130392.3:c. | N/A | Genic Upstream Transcript Variant |
| PTPRD transcript variant 4 | NM_130393.3:c. | N/A | Genic Upstream Transcript Variant |
| PTPRD transcript variant X7 |
XM_006716817.5:c.-103-124… XM_006716817.5:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X24 |
XM_006716823.4:c.-103-124… XM_006716823.4:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X27 |
XM_006716825.5:c.-103-124… XM_006716825.5:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X40 |
XM_006716827.5:c.-103-124… XM_006716827.5:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X1 |
XM_017014958.3:c.-103-124… XM_017014958.3:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X2 |
XM_017014961.3:c.-103-124… XM_017014961.3:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X5 |
XM_017014963.3:c.-103-124… XM_017014963.3:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X4 |
XM_017014964.3:c.-103-124… XM_017014964.3:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X6 |
XM_017014965.3:c.-103-124… XM_017014965.3:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X8 |
XM_017014966.3:c.-103-124… XM_017014966.3:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X9 |
XM_017014967.3:c.-103-124… XM_017014967.3:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X10 |
XM_017014968.3:c.-103-124… XM_017014968.3:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X13 |
XM_017014969.3:c.-103-124… XM_017014969.3:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X12 |
XM_017014970.3:c.-103-124… XM_017014970.3:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X15 |
XM_017014971.3:c.-103-124… XM_017014971.3:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X16 |
XM_017014972.3:c.-103-124… XM_017014972.3:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X17 |
XM_017014974.3:c.-103-124… XM_017014974.3:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X20 |
XM_017014976.3:c.-103-124… XM_017014976.3:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X19 |
XM_017014977.3:c.-103-124… XM_017014977.3:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X22 |
XM_017014978.3:c.-103-124… XM_017014978.3:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X23 |
XM_017014979.3:c.-103-124… XM_017014979.3:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X33 |
XM_017014980.3:c.-103-124… XM_017014980.3:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X44 |
XM_017014982.3:c.-103-124… XM_017014982.3:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X45 |
XM_017014983.3:c.-103-124… XM_017014983.3:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X14 |
XM_024447625.2:c.-103-124… XM_024447625.2:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X3 |
XM_047423641.1:c.-103-124… XM_047423641.1:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X11 |
XM_047423642.1:c.-103-124… XM_047423642.1:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X21 |
XM_047423644.1:c.-103-124… XM_047423644.1:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X25 |
XM_047423645.1:c.-103-124… XM_047423645.1:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X28 |
XM_047423647.1:c.-103-124… XM_047423647.1:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X30 |
XM_047423649.1:c.-103-124… XM_047423649.1:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X31 |
XM_047423650.1:c.-103-124… XM_047423650.1:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X32 |
XM_047423651.1:c.-103-124… XM_047423651.1:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X34 |
XM_047423652.1:c.-103-124… XM_047423652.1:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X35 |
XM_047423653.1:c.-103-124… XM_047423653.1:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X36 |
XM_047423654.1:c.-103-124… XM_047423654.1:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X39 |
XM_047423657.1:c.-103-124… XM_047423657.1:c.-103-124750_-103-124749del |
N/A | Intron Variant |
| PTPRD transcript variant X18 | XM_047423643.1:c. | N/A | Genic Upstream Transcript Variant |
| PTPRD transcript variant X26 | XM_047423646.1:c. | N/A | Genic Upstream Transcript Variant |
| PTPRD transcript variant X29 | XM_047423648.1:c. | N/A | Genic Upstream Transcript Variant |
| PTPRD transcript variant X37 | XM_047423655.1:c. | N/A | Genic Upstream Transcript Variant |
| PTPRD transcript variant X38 | XM_047423656.1:c. | N/A | Genic Upstream Transcript Variant |
| PTPRD transcript variant X41 | XM_047423658.1:c. | N/A | Genic Upstream Transcript Variant |
| PTPRD transcript variant X42 | XM_047423659.1:c. | N/A | Genic Upstream Transcript Variant |
| PTPRD transcript variant X43 | XM_047423660.1:c. | N/A | Genic Upstream Transcript Variant |
| Molecule type | Change | Amino acid[Codon] | SO Term |
|---|---|---|---|
| PTPRD-AS1 transcript variant 1 | NR_121599.1:n. | N/A | Intron Variant |
| PTPRD-AS1 transcript variant 2 | NR_121600.1:n. | N/A | Intron Variant |
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.
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 | TG= | delTG |
|---|---|---|
| GRCh38.p14 chr 9 | NC_000009.12:g.8858695_8858696= | NC_000009.12:g.8858695_8858696del |
| GRCh37.p13 chr 9 | NC_000009.11:g.8858695_8858696= | NC_000009.11:g.8858695_8858696del |
| PTPRD RefSeqGene | NG_033963.1:g.1759028_1759029= | NG_033963.1:g.1759028_1759029del |
| PTPRD transcript variant 1 | NM_002839.3:c.-103-124749= | NM_002839.3:c.-103-124750_-103-124749del |
| PTPRD transcript variant 1 | NM_002839.4:c.-103-124749= | NM_002839.4:c.-103-124750_-103-124749del |
| PTPRD transcript variant X1 | XM_005251529.1:c.-103-124749= | XM_005251529.1:c.-103-124750_-103-124749del |
| PTPRD transcript variant X5 | XM_005251533.1:c.-103-124749= | XM_005251533.1:c.-103-124750_-103-124749del |
| PTPRD transcript variant X7 | XM_006716817.5:c.-103-124749= | XM_006716817.5:c.-103-124750_-103-124749del |
| PTPRD transcript variant X24 | XM_006716823.4:c.-103-124749= | XM_006716823.4:c.-103-124750_-103-124749del |
| PTPRD transcript variant X27 | XM_006716825.5:c.-103-124749= | XM_006716825.5:c.-103-124750_-103-124749del |
| PTPRD transcript variant X40 | XM_006716827.5:c.-103-124749= | XM_006716827.5:c.-103-124750_-103-124749del |
| PTPRD transcript variant X1 | XM_017014958.3:c.-103-124749= | XM_017014958.3:c.-103-124750_-103-124749del |
| PTPRD transcript variant X2 | XM_017014961.3:c.-103-124749= | XM_017014961.3:c.-103-124750_-103-124749del |
| PTPRD transcript variant X5 | XM_017014963.3:c.-103-124749= | XM_017014963.3:c.-103-124750_-103-124749del |
| PTPRD transcript variant X4 | XM_017014964.3:c.-103-124749= | XM_017014964.3:c.-103-124750_-103-124749del |
| PTPRD transcript variant X6 | XM_017014965.3:c.-103-124749= | XM_017014965.3:c.-103-124750_-103-124749del |
| PTPRD transcript variant X8 | XM_017014966.3:c.-103-124749= | XM_017014966.3:c.-103-124750_-103-124749del |
| PTPRD transcript variant X9 | XM_017014967.3:c.-103-124749= | XM_017014967.3:c.-103-124750_-103-124749del |
| PTPRD transcript variant X10 | XM_017014968.3:c.-103-124749= | XM_017014968.3:c.-103-124750_-103-124749del |
| PTPRD transcript variant X13 | XM_017014969.3:c.-103-124749= | XM_017014969.3:c.-103-124750_-103-124749del |
| PTPRD transcript variant X12 | XM_017014970.3:c.-103-124749= | XM_017014970.3:c.-103-124750_-103-124749del |
| PTPRD transcript variant X15 | XM_017014971.3:c.-103-124749= | XM_017014971.3:c.-103-124750_-103-124749del |
| PTPRD transcript variant X16 | XM_017014972.3:c.-103-124749= | XM_017014972.3:c.-103-124750_-103-124749del |
| PTPRD transcript variant X17 | XM_017014974.3:c.-103-124749= | XM_017014974.3:c.-103-124750_-103-124749del |
| PTPRD transcript variant X20 | XM_017014976.3:c.-103-124749= | XM_017014976.3:c.-103-124750_-103-124749del |
| PTPRD transcript variant X19 | XM_017014977.3:c.-103-124749= | XM_017014977.3:c.-103-124750_-103-124749del |
| PTPRD transcript variant X22 | XM_017014978.3:c.-103-124749= | XM_017014978.3:c.-103-124750_-103-124749del |
| PTPRD transcript variant X23 | XM_017014979.3:c.-103-124749= | XM_017014979.3:c.-103-124750_-103-124749del |
| PTPRD transcript variant X33 | XM_017014980.3:c.-103-124749= | XM_017014980.3:c.-103-124750_-103-124749del |
| PTPRD transcript variant X44 | XM_017014982.3:c.-103-124749= | XM_017014982.3:c.-103-124750_-103-124749del |
| PTPRD transcript variant X45 | XM_017014983.3:c.-103-124749= | XM_017014983.3:c.-103-124750_-103-124749del |
| PTPRD transcript variant X14 | XM_024447625.2:c.-103-124749= | XM_024447625.2:c.-103-124750_-103-124749del |
| PTPRD transcript variant X3 | XM_047423641.1:c.-103-124749= | XM_047423641.1:c.-103-124750_-103-124749del |
| PTPRD transcript variant X11 | XM_047423642.1:c.-103-124749= | XM_047423642.1:c.-103-124750_-103-124749del |
| PTPRD transcript variant X21 | XM_047423644.1:c.-103-124749= | XM_047423644.1:c.-103-124750_-103-124749del |
| PTPRD transcript variant X25 | XM_047423645.1:c.-103-124749= | XM_047423645.1:c.-103-124750_-103-124749del |
| PTPRD transcript variant X28 | XM_047423647.1:c.-103-124749= | XM_047423647.1:c.-103-124750_-103-124749del |
| PTPRD transcript variant X30 | XM_047423649.1:c.-103-124749= | XM_047423649.1:c.-103-124750_-103-124749del |
| PTPRD transcript variant X31 | XM_047423650.1:c.-103-124749= | XM_047423650.1:c.-103-124750_-103-124749del |
| PTPRD transcript variant X32 | XM_047423651.1:c.-103-124749= | XM_047423651.1:c.-103-124750_-103-124749del |
| PTPRD transcript variant X34 | XM_047423652.1:c.-103-124749= | XM_047423652.1:c.-103-124750_-103-124749del |
| PTPRD transcript variant X35 | XM_047423653.1:c.-103-124749= | XM_047423653.1:c.-103-124750_-103-124749del |
| PTPRD transcript variant X36 | XM_047423654.1:c.-103-124749= | XM_047423654.1:c.-103-124750_-103-124749del |
| PTPRD transcript variant X39 | XM_047423657.1:c.-103-124749= | XM_047423657.1:c.-103-124750_-103-124749del |
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#.
| No | Submitter | Submission ID | Date (Build) |
|---|---|---|---|
| 1 | GNOMAD | ss2875193093 | Nov 17, 2017 (151) |
| 2 | gnomAD - Genomes | NC_000009.12 - 8858695 | Apr 27, 2021 (155) |
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).
Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.
No publications for rs1491018513
The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.
Genomic regions, transcripts, and products
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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.
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.