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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.

rs786204821

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr2:144399007-144399011 (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
delAAGA
Variation Type
Indel Insertion and Deletion
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
ZEB2 : Frameshift
Publications
0 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.144399008_144399011delAAGA
GRCh37.p13 chr 2 NC_000002.11:g.145156575_145156578delAAGA
ZEB2 RefSeqGene NG_016431.1:g.126382_126385delCTTT
Gene: ZEB2, zinc finger E-box binding homeobox 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ZEB2 transcript variant 1 NM_014795.3:c.217...

NM_014795.3:c.2177_2180delCTTT

S [TCTTTA] > Y [TA] Coding Sequence Variant
zinc finger E-box-binding homeobox 2 isoform 1 NP_055610.1:p.Ser...

NP_055610.1:p.Ser726fs

S (Ser) > Y (Tyr) Frameshift
ZEB2 transcript variant 2 NM_001171653.1:c....

NM_001171653.1:c.2105_2108delCTTT

S [TCTTTA] > Y [TA] Coding Sequence Variant
zinc finger E-box-binding homeobox 2 isoform 2 NP_001165124.1:p....

NP_001165124.1:p.Ser702fs

S (Ser) > Y (Tyr) Frameshift
ZEB2 transcript variant 3 NR_033258.1:n. N/A Genic Downstream Transcript Variant
ZEB2 transcript variant X1 XM_006712882.3:c....

XM_006712882.3:c.2177_2180delCTTT

S [TCTTTA] > Y [TA] Coding Sequence Variant
zinc finger E-box-binding homeobox 2 isoform X1 XP_006712945.1:p....

XP_006712945.1:p.Ser726fs

S (Ser) > Y (Tyr) Frameshift
ZEB2 transcript variant X2 XM_006712881.3:c....

XM_006712881.3:c.2177_2180delCTTT

S [TCTTTA] > Y [TA] Coding Sequence Variant
zinc finger E-box-binding homeobox 2 isoform X1 XP_006712944.1:p....

XP_006712944.1:p.Ser726fs

S (Ser) > Y (Tyr) Frameshift
ZEB2 transcript variant X3 XM_017005414.1:c....

XM_017005414.1:c.1841_1844delCTTT

S [TCTTTA] > Y [TA] Coding Sequence Variant
zinc finger E-box-binding homeobox 2 isoform X2 XP_016860903.1:p....

XP_016860903.1:p.Ser614fs

S (Ser) > Y (Tyr) Frameshift
ZEB2 transcript variant X4 XM_017005415.1:c....

XM_017005415.1:c.1841_1844delCTTT

S [TCTTTA] > Y [TA] Coding Sequence Variant
zinc finger E-box-binding homeobox 2 isoform X2 XP_016860904.1:p....

XP_016860904.1:p.Ser614fs

S (Ser) > Y (Tyr) Frameshift
ZEB2 transcript variant X5 XM_011512232.2:c....

XM_011512232.2:c.2156_2159delCTTT

S [TCTTTA] > Y [TA] Coding Sequence Variant
zinc finger E-box-binding homeobox 2 isoform X3 XP_011510534.1:p....

XP_011510534.1:p.Ser719fs

S (Ser) > Y (Tyr) 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: delAAGA (allele ID: 187153 )
ClinVar Accession Disease Names Clinical Significance
RCV000169722.1 Mowat-Wilson syndrome 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 AAAGA= delAAGA Note
GRCh38.p7 chr 2 NC_000002.12:g.14439900...

NC_000002.12:g.144399007_144399011AAAGA=

NC_000002.12:g.14439900...

NC_000002.12:g.144399008_144399011delAAGA

GRCh37.p13 chr 2 NC_000002.11:g.14515657...

NC_000002.11:g.145156574_145156578AAAGA=

NC_000002.11:g.14515657...

NC_000002.11:g.145156575_145156578delAAGA

ZEB2 RefSeqGene NG_016431.1:g.126381_12...

NG_016431.1:g.126381_126385TCTTT=

NG_016431.1:g.126382_12...

NG_016431.1:g.126382_126385delCTTT

ZEB2 transcript variant 1 NM_014795.3:c.2176_2180...

NM_014795.3:c.2176_2180TCTTT=

NM_014795.3:c.2177_2180...

NM_014795.3:c.2177_2180delCTTT

ZEB2 transcript variant 2 NM_001171653.1:c.2104_2...

NM_001171653.1:c.2104_2108TCTTT=

NM_001171653.1:c.2105_2...

NM_001171653.1:c.2105_2108delCTTT

ZEB2 transcript variant X1 XM_006712882.3:c.2176_2...

XM_006712882.3:c.2176_2180TCTTT=

XM_006712882.3:c.2177_2...

XM_006712882.3:c.2177_2180delCTTT

ZEB2 transcript variant X2 XM_006712881.3:c.2176_2...

XM_006712881.3:c.2176_2180TCTTT=

XM_006712881.3:c.2177_2...

XM_006712881.3:c.2177_2180delCTTT

ZEB2 transcript variant X5 XM_011512232.2:c.2155_2...

XM_011512232.2:c.2155_2159TCTTT=

XM_011512232.2:c.2156_2...

XM_011512232.2:c.2156_2159delCTTT

ZEB2 transcript variant X4 XM_017005415.1:c.1840_1...

XM_017005415.1:c.1840_1844TCTTT=

XM_017005415.1:c.1841_1...

XM_017005415.1:c.1841_1844delCTTT

ZEB2 transcript variant X3 XM_017005414.1:c.1840_1...

XM_017005414.1:c.1840_1844TCTTT=

XM_017005414.1:c.1841_1...

XM_017005414.1:c.1841_1844delCTTT

zinc finger E-box-binding homeobox 2 isoform 1 NP_055610.1:p.Ser726_Le...

NP_055610.1:p.Ser726_Leu727=

NP_055610.1:p.Ser726fs
zinc finger E-box-binding homeobox 2 isoform 2 NP_001165124.1:p.Ser702...

NP_001165124.1:p.Ser702_Leu703=

NP_001165124.1:p.Ser702fs
zinc finger E-box-binding homeobox 2 isoform X1 XP_006712945.1:p.Ser726...

XP_006712945.1:p.Ser726_Leu727=

XP_006712945.1:p.Ser726fs
zinc finger E-box-binding homeobox 2 isoform X1 XP_006712944.1:p.Ser726...

XP_006712944.1:p.Ser726_Leu727=

XP_006712944.1:p.Ser726fs
zinc finger E-box-binding homeobox 2 isoform X3 XP_011510534.1:p.Ser719...

XP_011510534.1:p.Ser719_Leu720=

XP_011510534.1:p.Ser719fs
zinc finger E-box-binding homeobox 2 isoform X2 XP_016860904.1:p.Ser614...

XP_016860904.1:p.Ser614_Leu615=

XP_016860904.1:p.Ser614fs
zinc finger E-box-binding homeobox 2 isoform X2 XP_016860903.1:p.Ser614...

XP_016860903.1:p.Ser614_Leu615=

XP_016860903.1:p.Ser614fs
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 CLINVAR ss1751114226 May 21, 2015 (144)
2 ClinVar RCV000169722.1 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).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
RCV000169722.1, ss1751114226 NC_000002.12:144399006:delAAAG NC_000002.12:144399006:delAAGA (self)
Help

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

No publications for rs786204821

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