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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs118203550

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr9:132905997-132905998 (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
delCT
Variation Type
Deletion
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
TSC1 : Frameshift
Publications
4 citations
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 9 NC_000009.12:g.132905997_132905998delCT
GRCh37.p13 chr 9 NC_000009.11:g.135781384_135781385delCT
TSC1 RefSeqGene (LRG_486) NG_012386.1:g.43636_43637delAG
Gene: TSC1, tuberous sclerosis 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TSC1 transcript variant 1 NM_000368.4:c.158...

NM_000368.4:c.1580_1581delAG

Q [CAG] > R [C] Coding Sequence Variant
hamartin isoform 1 NP_000359.1:p.Gln...

NP_000359.1:p.Gln527fs

Q (Gln) > R (Arg) Frameshift
TSC1 transcript variant 3 NM_001162426.1:c....

NM_001162426.1:c.1577_1578delAG

Q [CAG] > R [C] Coding Sequence Variant
hamartin isoform 3 NP_001155898.1:p....

NP_001155898.1:p.Gln526fs

Q (Gln) > R (Arg) Frameshift
TSC1 transcript variant 4 NM_001162427.1:c....

NM_001162427.1:c.1427_1428delAG

Q [CAG] > R [C] Coding Sequence Variant
hamartin isoform 4 NP_001155899.1:p....

NP_001155899.1:p.Gln476fs

Q (Gln) > R (Arg) Frameshift
TSC1 transcript variant X1 XM_005272211.1:c....

XM_005272211.1:c.1580_1581delAG

Q [CAG] > R [C] Coding Sequence Variant
hamartin isoform X1 XP_005272268.1:p....

XP_005272268.1:p.Gln527fs

Q (Gln) > R (Arg) Frameshift
TSC1 transcript variant X2 XM_006717271.1:c....

XM_006717271.1:c.1580_1581delAG

Q [CAG] > R [C] Coding Sequence Variant
hamartin isoform X1 XP_006717334.1:p....

XP_006717334.1:p.Gln527fs

Q (Gln) > R (Arg) Frameshift
TSC1 transcript variant X3 XM_011518979.2:c....

XM_011518979.2:c.1580_1581delAG

Q [CAG] > R [C] Coding Sequence Variant
hamartin isoform X1 XP_011517281.1:p....

XP_011517281.1:p.Gln527fs

Q (Gln) > R (Arg) Frameshift
TSC1 transcript variant X4 XM_017015096.1:c....

XM_017015096.1:c.1580_1581delAG

Q [CAG] > R [C] Coding Sequence Variant
hamartin isoform X1 XP_016870585.1:p....

XP_016870585.1:p.Gln527fs

Q (Gln) > R (Arg) Frameshift
TSC1 transcript variant X5 XM_017015097.1:c....

XM_017015097.1:c.1580_1581delAG

Q [CAG] > R [C] Coding Sequence Variant
hamartin isoform X1 XP_016870586.1:p....

XP_016870586.1:p.Gln527fs

Q (Gln) > R (Arg) Frameshift
TSC1 transcript variant X6 XM_017015098.1:c....

XM_017015098.1:c.1577_1578delAG

Q [CAG] > R [C] Coding Sequence Variant
hamartin isoform X2 XP_016870587.1:p....

XP_016870587.1:p.Gln526fs

Q (Gln) > R (Arg) Frameshift
TSC1 transcript variant X7 XM_017015099.1:c....

XM_017015099.1:c.1217_1218delAG

Q [CAG] > R [C] Coding Sequence Variant
hamartin isoform X3 XP_016870588.1:p....

XP_016870588.1:p.Gln406fs

Q (Gln) > R (Arg) Frameshift
TSC1 transcript variant X8 XM_017015100.1:c....

XM_017015100.1:c.1217_1218delAG

Q [CAG] > R [C] Coding Sequence Variant
hamartin isoform X3 XP_016870589.1:p....

XP_016870589.1:p.Gln406fs

Q (Gln) > R (Arg) Frameshift
TSC1 transcript variant X9 XM_017015101.1:c....

XM_017015101.1:c.1214_1215delAG

Q [CAG] > R [C] Coding Sequence Variant
hamartin isoform X4 XP_016870590.1:p....

XP_016870590.1:p.Gln405fs

Q (Gln) > R (Arg) Frameshift
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: delCT (allele ID: 57967 )
ClinVar Accession Disease Names Clinical Significance
RCV000042052.2 Tuberous sclerosis syndrome Not-Provided
RCV000201005.1 Tuberous sclerosis 1 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 CT= delCT Note
GRCh38.p7 chr 9 NC_000009.12:g.13290599...

NC_000009.12:g.132905997_132905998CT=

NC_000009.12:g.13290599...

NC_000009.12:g.132905997_132905998delCT

GRCh37.p13 chr 9 NC_000009.11:g.13578138...

NC_000009.11:g.135781384_135781385CT=

NC_000009.11:g.13578138...

NC_000009.11:g.135781384_135781385delCT

TSC1 RefSeqGene (LRG_486) NG_012386.1:g.43636_436...

NG_012386.1:g.43636_43637AG=

NG_012386.1:g.43636_436...

NG_012386.1:g.43636_43637delAG

TSC1 transcript variant 1 NM_000368.4:c.1580_1581AG= NM_000368.4:c.1580_1581...

NM_000368.4:c.1580_1581delAG

TSC1 transcript variant 3 NM_001162426.1:c.1577_1...

NM_001162426.1:c.1577_1578AG=

NM_001162426.1:c.1577_1...

NM_001162426.1:c.1577_1578delAG

TSC1 transcript variant 4 NM_001162427.1:c.1427_1...

NM_001162427.1:c.1427_1428AG=

NM_001162427.1:c.1427_1...

NM_001162427.1:c.1427_1428delAG

TSC1 transcript variant X3 XM_011518979.2:c.1580_1...

XM_011518979.2:c.1580_1581AG=

XM_011518979.2:c.1580_1...

XM_011518979.2:c.1580_1581delAG

TSC1 transcript variant X4 XM_017015096.1:c.1580_1...

XM_017015096.1:c.1580_1581AG=

XM_017015096.1:c.1580_1...

XM_017015096.1:c.1580_1581delAG

TSC1 transcript variant X5 XM_017015097.1:c.1580_1...

XM_017015097.1:c.1580_1581AG=

XM_017015097.1:c.1580_1...

XM_017015097.1:c.1580_1581delAG

TSC1 transcript variant X7 XM_017015099.1:c.1217_1...

XM_017015099.1:c.1217_1218AG=

XM_017015099.1:c.1217_1...

XM_017015099.1:c.1217_1218delAG

TSC1 transcript variant X9 XM_017015101.1:c.1214_1...

XM_017015101.1:c.1214_1215AG=

XM_017015101.1:c.1214_1...

XM_017015101.1:c.1214_1215delAG

TSC1 transcript variant X8 XM_017015100.1:c.1217_1...

XM_017015100.1:c.1217_1218AG=

XM_017015100.1:c.1217_1...

XM_017015100.1:c.1217_1218delAG

TSC1 transcript variant X1 XM_005272211.1:c.1580_1...

XM_005272211.1:c.1580_1581AG=

XM_005272211.1:c.1580_1...

XM_005272211.1:c.1580_1581delAG

TSC1 transcript variant X6 XM_017015098.1:c.1577_1...

XM_017015098.1:c.1577_1578AG=

XM_017015098.1:c.1577_1...

XM_017015098.1:c.1577_1578delAG

TSC1 transcript variant X2 XM_006717271.1:c.1580_1...

XM_006717271.1:c.1580_1581AG=

XM_006717271.1:c.1580_1...

XM_006717271.1:c.1580_1581delAG

hamartin isoform 1 NP_000359.1:p.Gln527= NP_000359.1:p.Gln527fs
hamartin isoform 3 NP_001155898.1:p.Gln526= NP_001155898.1:p.Gln526fs
hamartin isoform 4 NP_001155899.1:p.Gln476= NP_001155899.1:p.Gln476fs
hamartin isoform X1 XP_011517281.1:p.Gln527= XP_011517281.1:p.Gln527fs
hamartin isoform X1 XP_016870585.1:p.Gln527= XP_016870585.1:p.Gln527fs
hamartin isoform X1 XP_016870586.1:p.Gln527= XP_016870586.1:p.Gln527fs
hamartin isoform X3 XP_016870588.1:p.Gln406= XP_016870588.1:p.Gln406fs
hamartin isoform X4 XP_016870590.1:p.Gln405= XP_016870590.1:p.Gln405fs
hamartin isoform X3 XP_016870589.1:p.Gln406= XP_016870589.1:p.Gln406fs
hamartin isoform X1 XP_005272268.1:p.Gln527= XP_005272268.1:p.Gln527fs
hamartin isoform X2 XP_016870587.1:p.Gln526= XP_016870587.1:p.Gln526fs
hamartin isoform X1 XP_006717334.1:p.Gln527= XP_006717334.1:p.Gln527fs
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#.

2 ClinVar, 1 SubSNP submissions
No Submitter Submission ID Date (Build)
1 TSC2DB ss252451989 Jul 23, 2010 (132)
2 ClinVar RCV000042052.2 Jul 20, 2018 (151)
3 ClinVar RCV000201005.1 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
ss252451989 NC_000009.12:132905996:CT= NC_000009.12:132905996:CT= (self)
RCV000042052.2, RCV000201005.1, ss252451989 NC_000009.12:132905996:delCT NC_000009.12:132905996:delCT (self)
Help

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

4 citations for rs118203550
PMID Title Author Year Journal
9242607 Identification of the tuberous sclerosis gene TSC1 on chromosome 9q34. van Slegtenhorst M et al. 1997 Science (New York, N.Y.)
9328481 Molecular genetic and phenotypic analysis reveals differences between TSC1 and TSC2 associated familial and sporadic tuberous sclerosis. Jones AC et al. 1997 Human molecular genetics
10363127 Comprehensive mutation analysis of TSC1 using two-dimensional DNA electrophoresis with DGGE. Dabora SL et al. 1998 Annals of human genetics
26467025 A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. Karbassi I et al. 2016 Human mutation

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