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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.

rs868984000

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:41768991 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
None
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
JUP : Missense Variant
Publications
0 citations
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 17 NC_000017.11:g.41768991G>A
GRCh37.p13 chr 17 NC_000017.10:g.39925243G>A
JUP RefSeqGene (LRG_401) NG_009090.2:g.22722C>T
GRCh37.p13 chr 17 fix patch HG185_PATCH NW_003571052.1:g.55633G>A
Gene: JUP, junction plakoglobin (minus strand)
Molecule type Change Amino acid[Codon] SO Term
JUP transcript variant 1 NM_002230.4:c.685C>T P [CCT] > S [TCT] Coding Sequence Variant
junction plakoglobin NP_002221.1:p.Pro229Ser P (Pro) > S (Ser) Missense Variant
JUP transcript variant 6 NM_001352776.2:c.685C>T P [CCT] > S [TCT] Coding Sequence Variant
junction plakoglobin NP_001339705.1:p.Pro229Ser P (Pro) > S (Ser) Missense Variant
JUP transcript variant 3 NM_001352773.2:c.685C>T P [CCT] > S [TCT] Coding Sequence Variant
junction plakoglobin NP_001339702.1:p.Pro229Ser P (Pro) > S (Ser) Missense Variant
JUP transcript variant 2 NM_021991.4:c.685C>T P [CCT] > S [TCT] Coding Sequence Variant
junction plakoglobin NP_068831.1:p.Pro229Ser P (Pro) > S (Ser) Missense Variant
JUP transcript variant 5 NM_001352775.2:c.685C>T P [CCT] > S [TCT] Coding Sequence Variant
junction plakoglobin NP_001339704.1:p.Pro229Ser P (Pro) > S (Ser) Missense Variant
JUP transcript variant 4 NM_001352774.2:c.685C>T P [CCT] > S [TCT] Coding Sequence Variant
junction plakoglobin NP_001339703.1:p.Pro229Ser P (Pro) > S (Ser) Missense Variant
JUP transcript variant 7 NM_001352777.2:c.685C>T P [CCT] > S [TCT] Coding Sequence Variant
junction plakoglobin NP_001339706.1:p.Pro229Ser P (Pro) > S (Ser) Missense Variant
JUP transcript variant X1 XM_047435934.1:c.736C>T P [CCT] > S [TCT] Coding Sequence Variant
junction plakoglobin isoform X1 XP_047291890.1:p.Pro246Ser P (Pro) > S (Ser) Missense Variant
JUP transcript variant X8 XM_047435935.1:c.736C>T P [CCT] > S [TCT] Coding Sequence Variant
junction plakoglobin isoform X1 XP_047291891.1:p.Pro246Ser P (Pro) > S (Ser) Missense Variant
JUP transcript variant X2 XM_047435937.1:c.736C>T P [CCT] > S [TCT] Coding Sequence Variant
junction plakoglobin isoform X1 XP_047291893.1:p.Pro246Ser P (Pro) > S (Ser) Missense Variant
JUP transcript variant X3 XM_006721874.4:c.685C>T P [CCT] > S [TCT] Coding Sequence Variant
junction plakoglobin isoform X2 XP_006721937.1:p.Pro229Ser P (Pro) > S (Ser) Missense Variant
JUP transcript variant X6 XM_006721875.2:c.685C>T P [CCT] > S [TCT] Coding Sequence Variant
junction plakoglobin isoform X2 XP_006721938.1:p.Pro229Ser P (Pro) > S (Ser) Missense Variant
JUP transcript variant X4 XM_011524758.2:c.685C>T P [CCT] > S [TCT] Coding Sequence Variant
junction plakoglobin isoform X2 XP_011523060.1:p.Pro229Ser P (Pro) > S (Ser) Missense Variant
JUP transcript variant X9 XM_047435938.1:c.685C>T P [CCT] > S [TCT] Coding Sequence Variant
junction plakoglobin isoform X2 XP_047291894.1:p.Pro229Ser P (Pro) > S (Ser) Missense Variant
JUP transcript variant X10 XM_047435939.1:c.685C>T P [CCT] > S [TCT] Coding Sequence Variant
junction plakoglobin isoform X2 XP_047291895.1:p.Pro229Ser P (Pro) > S (Ser) Missense Variant
JUP transcript variant X7 XM_047435940.1:c.685C>T P [CCT] > S [TCT] Coding Sequence Variant
junction plakoglobin isoform X2 XP_047291896.1:p.Pro229Ser P (Pro) > S (Ser) Missense Variant
JUP transcript variant X11 XM_047435941.1:c.685C>T P [CCT] > S [TCT] Coding Sequence Variant
junction plakoglobin isoform X2 XP_047291897.1:p.Pro229Ser P (Pro) > S (Ser) Missense Variant
JUP transcript variant X12 XM_047435942.1:c.685C>T P [CCT] > S [TCT] Coding Sequence Variant
junction plakoglobin isoform X2 XP_047291898.1:p.Pro229Ser P (Pro) > S (Ser) Missense Variant
JUP transcript variant X5 XM_017024590.2:c.685C>T P [CCT] > S [TCT] Coding Sequence Variant
junction plakoglobin isoform X2 XP_016880079.1:p.Pro229Ser P (Pro) > S (Ser) Missense 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.

Not Reported in ClinVar
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= A
GRCh38.p14 chr 17 NC_000017.11:g.41768991= NC_000017.11:g.41768991G>A
GRCh37.p13 chr 17 NC_000017.10:g.39925243= NC_000017.10:g.39925243G>A
JUP RefSeqGene (LRG_401) NG_009090.2:g.22722= NG_009090.2:g.22722C>T
JUP transcript variant 1 NM_002230.4:c.685= NM_002230.4:c.685C>T
JUP transcript variant 1 NM_002230.3:c.685= NM_002230.3:c.685C>T
JUP transcript variant 1 NM_002230.2:c.685= NM_002230.2:c.685C>T
JUP transcript variant 2 NM_021991.4:c.685= NM_021991.4:c.685C>T
JUP transcript variant 2 NM_021991.3:c.685= NM_021991.3:c.685C>T
JUP transcript variant 2 NM_021991.2:c.685= NM_021991.2:c.685C>T
JUP transcript variant 3 NM_001352773.2:c.685= NM_001352773.2:c.685C>T
JUP transcript variant 3 NM_001352773.1:c.685= NM_001352773.1:c.685C>T
JUP transcript variant 6 NM_001352776.2:c.685= NM_001352776.2:c.685C>T
JUP transcript variant 6 NM_001352776.1:c.685= NM_001352776.1:c.685C>T
JUP transcript variant 5 NM_001352775.2:c.685= NM_001352775.2:c.685C>T
JUP transcript variant 5 NM_001352775.1:c.685= NM_001352775.1:c.685C>T
JUP transcript variant 4 NM_001352774.2:c.685= NM_001352774.2:c.685C>T
JUP transcript variant 4 NM_001352774.1:c.685= NM_001352774.1:c.685C>T
JUP transcript variant 7 NM_001352777.2:c.685= NM_001352777.2:c.685C>T
JUP transcript variant 7 NM_001352777.1:c.685= NM_001352777.1:c.685C>T
GRCh37.p13 chr 17 fix patch HG185_PATCH NW_003571052.1:g.55633= NW_003571052.1:g.55633G>A
JUP transcript variant X3 XM_006721874.4:c.685= XM_006721874.4:c.685C>T
JUP transcript variant X2 XM_006721874.3:c.685= XM_006721874.3:c.685C>T
JUP transcript variant X3 XM_006721874.2:c.685= XM_006721874.2:c.685C>T
JUP transcript variant X1 XM_006721874.1:c.685= XM_006721874.1:c.685C>T
JUP transcript variant X6 XM_006721875.2:c.685= XM_006721875.2:c.685C>T
JUP transcript variant X5 XM_006721875.1:c.685= XM_006721875.1:c.685C>T
JUP transcript variant X5 XM_017024590.2:c.685= XM_017024590.2:c.685C>T
JUP transcript variant X7 XM_017024590.1:c.685= XM_017024590.1:c.685C>T
JUP transcript variant X4 XM_011524758.2:c.685= XM_011524758.2:c.685C>T
JUP transcript variant X6 XM_011524758.1:c.685= XM_011524758.1:c.685C>T
JUP transcript variant X11 XM_047435941.1:c.685= XM_047435941.1:c.685C>T
JUP transcript variant X8 XM_047435935.1:c.736= XM_047435935.1:c.736C>T
JUP transcript variant X1 XM_047435934.1:c.736= XM_047435934.1:c.736C>T
JUP transcript variant X2 XM_047435937.1:c.736= XM_047435937.1:c.736C>T
JUP transcript variant X10 XM_047435939.1:c.685= XM_047435939.1:c.685C>T
JUP transcript variant X7 XM_047435940.1:c.685= XM_047435940.1:c.685C>T
JUP transcript variant X12 XM_047435942.1:c.685= XM_047435942.1:c.685C>T
JUP transcript variant X9 XM_047435938.1:c.685= XM_047435938.1:c.685C>T
junction plakoglobin NP_002221.1:p.Pro229= NP_002221.1:p.Pro229Ser
junction plakoglobin NP_068831.1:p.Pro229= NP_068831.1:p.Pro229Ser
junction plakoglobin NP_001339702.1:p.Pro229= NP_001339702.1:p.Pro229Ser
junction plakoglobin NP_001339705.1:p.Pro229= NP_001339705.1:p.Pro229Ser
junction plakoglobin NP_001339704.1:p.Pro229= NP_001339704.1:p.Pro229Ser
junction plakoglobin NP_001339703.1:p.Pro229= NP_001339703.1:p.Pro229Ser
junction plakoglobin NP_001339706.1:p.Pro229= NP_001339706.1:p.Pro229Ser
junction plakoglobin isoform X2 XP_006721937.1:p.Pro229= XP_006721937.1:p.Pro229Ser
junction plakoglobin isoform X2 XP_006721938.1:p.Pro229= XP_006721938.1:p.Pro229Ser
junction plakoglobin isoform X2 XP_016880079.1:p.Pro229= XP_016880079.1:p.Pro229Ser
junction plakoglobin isoform X2 XP_011523060.1:p.Pro229= XP_011523060.1:p.Pro229Ser
junction plakoglobin isoform X2 XP_047291897.1:p.Pro229= XP_047291897.1:p.Pro229Ser
junction plakoglobin isoform X1 XP_047291891.1:p.Pro246= XP_047291891.1:p.Pro246Ser
junction plakoglobin isoform X1 XP_047291890.1:p.Pro246= XP_047291890.1:p.Pro246Ser
junction plakoglobin isoform X1 XP_047291893.1:p.Pro246= XP_047291893.1:p.Pro246Ser
junction plakoglobin isoform X2 XP_047291895.1:p.Pro229= XP_047291895.1:p.Pro229Ser
junction plakoglobin isoform X2 XP_047291896.1:p.Pro229= XP_047291896.1:p.Pro229Ser
junction plakoglobin isoform X2 XP_047291898.1:p.Pro229= XP_047291898.1:p.Pro229Ser
junction plakoglobin isoform X2 XP_047291894.1:p.Pro229= XP_047291894.1:p.Pro229Ser
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 submission
No Submitter Submission ID Date (Build)
1 YSAMUELS ss1849914403 Feb 17, 2016 (147)
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
ss1849914403 NC_000017.10:39925242:G:A NC_000017.11:41768990:G:A (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 rs868984000

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