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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.

rs267608058

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr2:47800130-47800136 (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
delTCAG
Variation Type
Indel Insertion and Deletion
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
MSH6 : Frameshift
Publications
7 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 2 NC_000002.12:g.47800133_47800136delTCAG
GRCh37.p13 chr 2 NC_000002.11:g.48027272_48027275delTCAG
MSH6 RefSeqGene (LRG_219) NG_007111.1:g.21987_21990delTCAG
Gene: MSH6, mutS homolog 6 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MSH6 transcript variant 1 NM_000179.2:c.215...

NM_000179.2:c.2150_2153delTCAG

V [GTCAGC] > A [GC] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform 1 NP_000170.1:p.Val...

NP_000170.1:p.Val717fs

V (Val) > A (Ala) Frameshift
MSH6 transcript variant 2 NM_001281492.1:c....

NM_001281492.1:c.1760_1763delTCAG

V [GTCAGC] > A [GC] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform 2 NP_001268421.1:p....

NP_001268421.1:p.Val587fs

V (Val) > A (Ala) Frameshift
MSH6 transcript variant 3 NM_001281493.1:c....

NM_001281493.1:c.1244_1247delTCAG

V [GTCAGC] > A [GC] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform 3 NP_001268422.1:p....

NP_001268422.1:p.Val415fs

V (Val) > A (Ala) Frameshift
MSH6 transcript variant 4 NM_001281494.1:c....

NM_001281494.1:c.1244_1247delTCAG

V [GTCAGC] > A [GC] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform 3 NP_001268423.1:p....

NP_001268423.1:p.Val415fs

V (Val) > A (Ala) Frameshift
MSH6 transcript variant X1 XM_011532798.1:c....

XM_011532798.1:c.1967_1970delTCAG

V [GTCAGC] > A [GC] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform X1 XP_011531100.1:p....

XP_011531100.1:p.Val656fs

V (Val) > A (Ala) Frameshift
MSH6 transcript variant X2 XM_011532799.1:c....

XM_011532799.1:c.1853_1856delTCAG

V [GTCAGC] > A [GC] Coding Sequence Variant
DNA mismatch repair protein Msh6 isoform X2 XP_011531101.1:p....

XP_011531101.1:p.Val618fs

V (Val) > A (Ala) 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: delTCAG (allele ID: 94730 )
ClinVar Accession Disease Names Clinical Significance
RCV000074720.3 Lynch syndrome Pathogenic
RCV000162408.4 Hereditary cancer-predisposing syndrome Pathogenic
RCV000202111.3 not provided Pathogenic
RCV000411212.1 Hereditary nonpolyposis colorectal cancer type 5 Pathogenic
RCV000524132.2 Hereditary nonpolyposis colon cancer 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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
The Exome Aggregation Consortium Global Study-wide 121168 -

No frequency provided

delTCAG=0.00001
The Exome Aggregation Consortium Europe Sub 73216 -

No frequency provided

delTCAG=0.0000
The Exome Aggregation Consortium Asian Sub 25146 -

No frequency provided

delTCAG=0.0000
The Exome Aggregation Consortium American Sub 11558 -

No frequency provided

delTCAG=0.0000
The Exome Aggregation Consortium African Sub 10344 -

No frequency provided

delTCAG=0.0000
The Exome Aggregation Consortium Other Sub 904 -

No frequency provided

delTCAG=0.00
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 CAGTCAG= delTCAG Note
GRCh38.p7 chr 2 NC_000002.12:g.47800130...

NC_000002.12:g.47800130_47800136CAGTCAG=

NC_000002.12:g.47800133...

NC_000002.12:g.47800133_47800136delTCAG

GRCh37.p13 chr 2 NC_000002.11:g.48027269...

NC_000002.11:g.48027269_48027275CAGTCAG=

NC_000002.11:g.48027272...

NC_000002.11:g.48027272_48027275delTCAG

MSH6 RefSeqGene (LRG_219) NG_007111.1:g.21984_219...

NG_007111.1:g.21984_21990CAGTCAG=

NG_007111.1:g.21987_219...

NG_007111.1:g.21987_21990delTCAG

MSH6 transcript variant 1 NM_000179.2:c.2147_2153...

NM_000179.2:c.2147_2153CAGTCAG=

NM_000179.2:c.2150_2153...

NM_000179.2:c.2150_2153delTCAG

MSH6 transcript variant 3 NM_001281493.1:c.1241_1...

NM_001281493.1:c.1241_1247CAGTCAG=

NM_001281493.1:c.1244_1...

NM_001281493.1:c.1244_1247delTCAG

MSH6 transcript variant 4 NM_001281494.1:c.1241_1...

NM_001281494.1:c.1241_1247CAGTCAG=

NM_001281494.1:c.1244_1...

NM_001281494.1:c.1244_1247delTCAG

MSH6 transcript variant 2 NM_001281492.1:c.1757_1...

NM_001281492.1:c.1757_1763CAGTCAG=

NM_001281492.1:c.1760_1...

NM_001281492.1:c.1760_1763delTCAG

MSH6 transcript variant X2 XM_011532799.1:c.1850_1...

XM_011532799.1:c.1850_1856CAGTCAG=

XM_011532799.1:c.1853_1...

XM_011532799.1:c.1853_1856delTCAG

MSH6 transcript variant X1 XM_011532798.1:c.1964_1...

XM_011532798.1:c.1964_1970CAGTCAG=

XM_011532798.1:c.1967_1...

XM_011532798.1:c.1967_1970delTCAG

DNA mismatch repair protein Msh6 isoform 1 NP_000170.1:p.Thr716_Se...

NP_000170.1:p.Thr716_Ser718=

NP_000170.1:p.Val717fs
DNA mismatch repair protein Msh6 isoform 3 NP_001268422.1:p.Thr414...

NP_001268422.1:p.Thr414_Ser416=

NP_001268422.1:p.Val415fs
DNA mismatch repair protein Msh6 isoform 3 NP_001268423.1:p.Thr414...

NP_001268423.1:p.Thr414_Ser416=

NP_001268423.1:p.Val415fs
DNA mismatch repair protein Msh6 isoform 2 NP_001268421.1:p.Thr586...

NP_001268421.1:p.Thr586_Ser588=

NP_001268421.1:p.Val587fs
DNA mismatch repair protein Msh6 isoform X2 XP_011531101.1:p.Thr617...

XP_011531101.1:p.Thr617_Ser619=

XP_011531101.1:p.Val618fs
DNA mismatch repair protein Msh6 isoform X1 XP_011531100.1:p.Thr655...

XP_011531100.1:p.Thr655_Ser657=

XP_011531100.1:p.Val656fs
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#.

5 ClinVar, 1 Frequency, 3 SubSNP submissions
No Submitter Submission ID Date (Build)
1 MMR_WOODS ss538294669 Jul 31, 2012 (137)
2 CLINVAR ss1457621024 Nov 23, 2014 (136)
3 EVA_EXAC ss1711672750 Apr 01, 2015 (136)
4 The Exome Aggregation Consortium NC_000002.11 - 48027269 Jul 19, 2018 (151)
5 ClinVar RCV000074720.3 Jul 19, 2018 (151)
6 ClinVar RCV000162408.4 Jul 19, 2018 (151)
7 ClinVar RCV000202111.3 Jul 19, 2018 (151)
8 ClinVar RCV000411212.1 Jul 19, 2018 (151)
9 ClinVar RCV000524132.2 Jul 19, 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).

Associated ID History Updated (Build)
rs587782275 May 11, 2017 (136)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
6170670, ss1711672750 NC_000002.11:48027268:delCAGT NC_000002.12:47800129:delTCAG (self)
ss1457621024 NC_000002.12:47800129:delCAGT NC_000002.12:47800129:delTCAG (self)
RCV000074720.3, RCV000162408.4, RCV000202111.3, RCV000411212.1, RCV000524132.2, ss538294669 NC_000002.12:47800132:delTCAG NC_000002.12:47800129:delTCAG (self)
Help

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

7 citations for rs267608058
PMID Title Author Year Journal
10537275 Germ-line msh6 mutations in colorectal cancer families. Kolodner RD et al. 1999 Cancer research
18566915 Major contribution from recurrent alterations and MSH6 mutations in the Danish Lynch syndrome population. Nilbert M et al. 2009 Familial cancer
20487569 MSH6 and PMS2 mutation positive Australian Lynch syndrome families: novel mutations, cancer risk and age of diagnosis of colorectal cancer. Talseth-Palmer BA et al. 2010 Hereditary cancer in clinical practice
22006311 Mutations in 12 genes for inherited ovarian, fallopian tube, and peritoneal carcinoma identified by massively parallel sequencing. Walsh T et al. 2011 Proceedings of the National Academy of Sciences of the United States of America
23047549 Frequency of mutations in mismatch repair genes in a population-based study of women with ovarian cancer. Pal T et al. 2012 British journal of cancer
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
26845104 Improving performance of multigene panels for genomic analysis of cancer predisposition. Shirts BH et al. 2016 Genetics in medicine

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