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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.

rs781901019

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:41769517 (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 / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000008 (2/245880, GnomAD_exome)
A=0.000010 (1/101074, ExAC)
C=0.0003 (1/2918, KOREAN)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
JUP : Synonymous 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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 245880 G=0.999992 A=0.000008
gnomAD - Exomes European Sub 132030 G=1.000000 A=0.000000
gnomAD - Exomes Asian Sub 48118 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 34128 G=0.99994 A=0.00006
gnomAD - Exomes African Sub 15672 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 9948 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 5984 G=1.0000 A=0.0000
ExAC Global Study-wide 101074 G=0.999990 A=0.000010
ExAC Europe Sub 61414 G=1.00000 A=0.00000
ExAC Asian Sub 21344 G=1.00000 A=0.00000
ExAC American Sub 8924 G=0.9999 A=0.0001
ExAC African Sub 8678 G=1.0000 A=0.0000
ExAC Other Sub 714 G=1.000 A=0.000
KOREAN population from KRGDB KOREAN Study-wide 2918 G=0.9997 C=0.0003
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.41769517G>A
GRCh38.p14 chr 17 NC_000017.11:g.41769517G>C
GRCh37.p13 chr 17 NC_000017.10:g.39925769G>A
GRCh37.p13 chr 17 NC_000017.10:g.39925769G>C
JUP RefSeqGene (LRG_401) NG_009090.2:g.22196C>T
JUP RefSeqGene (LRG_401) NG_009090.2:g.22196C>G
GRCh37.p13 chr 17 fix patch HG185_PATCH NW_003571052.1:g.56159G>A
GRCh37.p13 chr 17 fix patch HG185_PATCH NW_003571052.1:g.56159G>C
Gene: JUP, junction plakoglobin (minus strand)
Molecule type Change Amino acid[Codon] SO Term
JUP transcript variant 1 NM_002230.4:c.369C>T L [CTC] > L [CTT] Coding Sequence Variant
junction plakoglobin NP_002221.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant 1 NM_002230.4:c.369C>G L [CTC] > L [CTG] Coding Sequence Variant
junction plakoglobin NP_002221.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant 6 NM_001352776.2:c.369C>T L [CTC] > L [CTT] Coding Sequence Variant
junction plakoglobin NP_001339705.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant 6 NM_001352776.2:c.369C>G L [CTC] > L [CTG] Coding Sequence Variant
junction plakoglobin NP_001339705.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant 3 NM_001352773.2:c.369C>T L [CTC] > L [CTT] Coding Sequence Variant
junction plakoglobin NP_001339702.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant 3 NM_001352773.2:c.369C>G L [CTC] > L [CTG] Coding Sequence Variant
junction plakoglobin NP_001339702.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant 2 NM_021991.4:c.369C>T L [CTC] > L [CTT] Coding Sequence Variant
junction plakoglobin NP_068831.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant 2 NM_021991.4:c.369C>G L [CTC] > L [CTG] Coding Sequence Variant
junction plakoglobin NP_068831.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant 5 NM_001352775.2:c.369C>T L [CTC] > L [CTT] Coding Sequence Variant
junction plakoglobin NP_001339704.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant 5 NM_001352775.2:c.369C>G L [CTC] > L [CTG] Coding Sequence Variant
junction plakoglobin NP_001339704.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant 4 NM_001352774.2:c.369C>T L [CTC] > L [CTT] Coding Sequence Variant
junction plakoglobin NP_001339703.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant 4 NM_001352774.2:c.369C>G L [CTC] > L [CTG] Coding Sequence Variant
junction plakoglobin NP_001339703.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant 7 NM_001352777.2:c.369C>T L [CTC] > L [CTT] Coding Sequence Variant
junction plakoglobin NP_001339706.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant 7 NM_001352777.2:c.369C>G L [CTC] > L [CTG] Coding Sequence Variant
junction plakoglobin NP_001339706.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X1 XM_047435934.1:c.420C>T L [CTC] > L [CTT] Coding Sequence Variant
junction plakoglobin isoform X1 XP_047291890.1:p.Leu140= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X1 XM_047435934.1:c.420C>G L [CTC] > L [CTG] Coding Sequence Variant
junction plakoglobin isoform X1 XP_047291890.1:p.Leu140= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X8 XM_047435935.1:c.420C>T L [CTC] > L [CTT] Coding Sequence Variant
junction plakoglobin isoform X1 XP_047291891.1:p.Leu140= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X8 XM_047435935.1:c.420C>G L [CTC] > L [CTG] Coding Sequence Variant
junction plakoglobin isoform X1 XP_047291891.1:p.Leu140= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X2 XM_047435937.1:c.420C>T L [CTC] > L [CTT] Coding Sequence Variant
junction plakoglobin isoform X1 XP_047291893.1:p.Leu140= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X2 XM_047435937.1:c.420C>G L [CTC] > L [CTG] Coding Sequence Variant
junction plakoglobin isoform X1 XP_047291893.1:p.Leu140= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X3 XM_006721874.4:c.369C>T L [CTC] > L [CTT] Coding Sequence Variant
junction plakoglobin isoform X2 XP_006721937.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X3 XM_006721874.4:c.369C>G L [CTC] > L [CTG] Coding Sequence Variant
junction plakoglobin isoform X2 XP_006721937.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X6 XM_006721875.2:c.369C>T L [CTC] > L [CTT] Coding Sequence Variant
junction plakoglobin isoform X2 XP_006721938.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X6 XM_006721875.2:c.369C>G L [CTC] > L [CTG] Coding Sequence Variant
junction plakoglobin isoform X2 XP_006721938.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X4 XM_011524758.2:c.369C>T L [CTC] > L [CTT] Coding Sequence Variant
junction plakoglobin isoform X2 XP_011523060.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X4 XM_011524758.2:c.369C>G L [CTC] > L [CTG] Coding Sequence Variant
junction plakoglobin isoform X2 XP_011523060.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X9 XM_047435938.1:c.369C>T L [CTC] > L [CTT] Coding Sequence Variant
junction plakoglobin isoform X2 XP_047291894.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X9 XM_047435938.1:c.369C>G L [CTC] > L [CTG] Coding Sequence Variant
junction plakoglobin isoform X2 XP_047291894.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X10 XM_047435939.1:c.369C>T L [CTC] > L [CTT] Coding Sequence Variant
junction plakoglobin isoform X2 XP_047291895.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X10 XM_047435939.1:c.369C>G L [CTC] > L [CTG] Coding Sequence Variant
junction plakoglobin isoform X2 XP_047291895.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X7 XM_047435940.1:c.369C>T L [CTC] > L [CTT] Coding Sequence Variant
junction plakoglobin isoform X2 XP_047291896.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X7 XM_047435940.1:c.369C>G L [CTC] > L [CTG] Coding Sequence Variant
junction plakoglobin isoform X2 XP_047291896.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X11 XM_047435941.1:c.369C>T L [CTC] > L [CTT] Coding Sequence Variant
junction plakoglobin isoform X2 XP_047291897.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X11 XM_047435941.1:c.369C>G L [CTC] > L [CTG] Coding Sequence Variant
junction plakoglobin isoform X2 XP_047291897.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X12 XM_047435942.1:c.369C>T L [CTC] > L [CTT] Coding Sequence Variant
junction plakoglobin isoform X2 XP_047291898.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X12 XM_047435942.1:c.369C>G L [CTC] > L [CTG] Coding Sequence Variant
junction plakoglobin isoform X2 XP_047291898.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X5 XM_017024590.2:c.369C>T L [CTC] > L [CTT] Coding Sequence Variant
junction plakoglobin isoform X2 XP_016880079.1:p.Leu123= L (Leu) > L (Leu) Synonymous Variant
JUP transcript variant X5 XM_017024590.2:c.369C>G L [CTC] > L [CTG] Coding Sequence Variant
junction plakoglobin isoform X2 XP_016880079.1:p.Leu123= L (Leu) > L (Leu) Synonymous 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 C
GRCh38.p14 chr 17 NC_000017.11:g.41769517= NC_000017.11:g.41769517G>A NC_000017.11:g.41769517G>C
GRCh37.p13 chr 17 NC_000017.10:g.39925769= NC_000017.10:g.39925769G>A NC_000017.10:g.39925769G>C
JUP RefSeqGene (LRG_401) NG_009090.2:g.22196= NG_009090.2:g.22196C>T NG_009090.2:g.22196C>G
JUP transcript variant 1 NM_002230.4:c.369= NM_002230.4:c.369C>T NM_002230.4:c.369C>G
JUP transcript variant 1 NM_002230.3:c.369= NM_002230.3:c.369C>T NM_002230.3:c.369C>G
JUP transcript variant 1 NM_002230.2:c.369= NM_002230.2:c.369C>T NM_002230.2:c.369C>G
JUP transcript variant 2 NM_021991.4:c.369= NM_021991.4:c.369C>T NM_021991.4:c.369C>G
JUP transcript variant 2 NM_021991.3:c.369= NM_021991.3:c.369C>T NM_021991.3:c.369C>G
JUP transcript variant 2 NM_021991.2:c.369= NM_021991.2:c.369C>T NM_021991.2:c.369C>G
JUP transcript variant 3 NM_001352773.2:c.369= NM_001352773.2:c.369C>T NM_001352773.2:c.369C>G
JUP transcript variant 3 NM_001352773.1:c.369= NM_001352773.1:c.369C>T NM_001352773.1:c.369C>G
JUP transcript variant 6 NM_001352776.2:c.369= NM_001352776.2:c.369C>T NM_001352776.2:c.369C>G
JUP transcript variant 6 NM_001352776.1:c.369= NM_001352776.1:c.369C>T NM_001352776.1:c.369C>G
JUP transcript variant 5 NM_001352775.2:c.369= NM_001352775.2:c.369C>T NM_001352775.2:c.369C>G
JUP transcript variant 5 NM_001352775.1:c.369= NM_001352775.1:c.369C>T NM_001352775.1:c.369C>G
JUP transcript variant 4 NM_001352774.2:c.369= NM_001352774.2:c.369C>T NM_001352774.2:c.369C>G
JUP transcript variant 4 NM_001352774.1:c.369= NM_001352774.1:c.369C>T NM_001352774.1:c.369C>G
JUP transcript variant 7 NM_001352777.2:c.369= NM_001352777.2:c.369C>T NM_001352777.2:c.369C>G
JUP transcript variant 7 NM_001352777.1:c.369= NM_001352777.1:c.369C>T NM_001352777.1:c.369C>G
GRCh37.p13 chr 17 fix patch HG185_PATCH NW_003571052.1:g.56159= NW_003571052.1:g.56159G>A NW_003571052.1:g.56159G>C
JUP transcript variant X3 XM_006721874.4:c.369= XM_006721874.4:c.369C>T XM_006721874.4:c.369C>G
JUP transcript variant X2 XM_006721874.3:c.369= XM_006721874.3:c.369C>T XM_006721874.3:c.369C>G
JUP transcript variant X3 XM_006721874.2:c.369= XM_006721874.2:c.369C>T XM_006721874.2:c.369C>G
JUP transcript variant X1 XM_006721874.1:c.369= XM_006721874.1:c.369C>T XM_006721874.1:c.369C>G
JUP transcript variant X6 XM_006721875.2:c.369= XM_006721875.2:c.369C>T XM_006721875.2:c.369C>G
JUP transcript variant X5 XM_006721875.1:c.369= XM_006721875.1:c.369C>T XM_006721875.1:c.369C>G
JUP transcript variant X5 XM_017024590.2:c.369= XM_017024590.2:c.369C>T XM_017024590.2:c.369C>G
JUP transcript variant X7 XM_017024590.1:c.369= XM_017024590.1:c.369C>T XM_017024590.1:c.369C>G
JUP transcript variant X4 XM_011524758.2:c.369= XM_011524758.2:c.369C>T XM_011524758.2:c.369C>G
JUP transcript variant X6 XM_011524758.1:c.369= XM_011524758.1:c.369C>T XM_011524758.1:c.369C>G
JUP transcript variant X11 XM_047435941.1:c.369= XM_047435941.1:c.369C>T XM_047435941.1:c.369C>G
JUP transcript variant X8 XM_047435935.1:c.420= XM_047435935.1:c.420C>T XM_047435935.1:c.420C>G
JUP transcript variant X1 XM_047435934.1:c.420= XM_047435934.1:c.420C>T XM_047435934.1:c.420C>G
JUP transcript variant X2 XM_047435937.1:c.420= XM_047435937.1:c.420C>T XM_047435937.1:c.420C>G
JUP transcript variant X10 XM_047435939.1:c.369= XM_047435939.1:c.369C>T XM_047435939.1:c.369C>G
JUP transcript variant X7 XM_047435940.1:c.369= XM_047435940.1:c.369C>T XM_047435940.1:c.369C>G
JUP transcript variant X12 XM_047435942.1:c.369= XM_047435942.1:c.369C>T XM_047435942.1:c.369C>G
JUP transcript variant X9 XM_047435938.1:c.369= XM_047435938.1:c.369C>T XM_047435938.1:c.369C>G
junction plakoglobin NP_002221.1:p.Leu123= NP_002221.1:p.Leu123= NP_002221.1:p.Leu123=
junction plakoglobin NP_068831.1:p.Leu123= NP_068831.1:p.Leu123= NP_068831.1:p.Leu123=
junction plakoglobin NP_001339702.1:p.Leu123= NP_001339702.1:p.Leu123= NP_001339702.1:p.Leu123=
junction plakoglobin NP_001339705.1:p.Leu123= NP_001339705.1:p.Leu123= NP_001339705.1:p.Leu123=
junction plakoglobin NP_001339704.1:p.Leu123= NP_001339704.1:p.Leu123= NP_001339704.1:p.Leu123=
junction plakoglobin NP_001339703.1:p.Leu123= NP_001339703.1:p.Leu123= NP_001339703.1:p.Leu123=
junction plakoglobin NP_001339706.1:p.Leu123= NP_001339706.1:p.Leu123= NP_001339706.1:p.Leu123=
junction plakoglobin isoform X2 XP_006721937.1:p.Leu123= XP_006721937.1:p.Leu123= XP_006721937.1:p.Leu123=
junction plakoglobin isoform X2 XP_006721938.1:p.Leu123= XP_006721938.1:p.Leu123= XP_006721938.1:p.Leu123=
junction plakoglobin isoform X2 XP_016880079.1:p.Leu123= XP_016880079.1:p.Leu123= XP_016880079.1:p.Leu123=
junction plakoglobin isoform X2 XP_011523060.1:p.Leu123= XP_011523060.1:p.Leu123= XP_011523060.1:p.Leu123=
junction plakoglobin isoform X2 XP_047291897.1:p.Leu123= XP_047291897.1:p.Leu123= XP_047291897.1:p.Leu123=
junction plakoglobin isoform X1 XP_047291891.1:p.Leu140= XP_047291891.1:p.Leu140= XP_047291891.1:p.Leu140=
junction plakoglobin isoform X1 XP_047291890.1:p.Leu140= XP_047291890.1:p.Leu140= XP_047291890.1:p.Leu140=
junction plakoglobin isoform X1 XP_047291893.1:p.Leu140= XP_047291893.1:p.Leu140= XP_047291893.1:p.Leu140=
junction plakoglobin isoform X2 XP_047291895.1:p.Leu123= XP_047291895.1:p.Leu123= XP_047291895.1:p.Leu123=
junction plakoglobin isoform X2 XP_047291896.1:p.Leu123= XP_047291896.1:p.Leu123= XP_047291896.1:p.Leu123=
junction plakoglobin isoform X2 XP_047291898.1:p.Leu123= XP_047291898.1:p.Leu123= XP_047291898.1:p.Leu123=
junction plakoglobin isoform X2 XP_047291894.1:p.Leu123= XP_047291894.1:p.Leu123= XP_047291894.1:p.Leu123=
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#.

3 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1692778168 Apr 09, 2015 (144)
2 GNOMAD ss2742715235 Oct 12, 2018 (152)
3 KRGDB ss3935422887 Apr 27, 2020 (154)
4 ExAC NC_000017.10 - 39925769 Oct 12, 2018 (152)
5 gnomAD - Exomes NC_000017.10 - 39925769 Jul 13, 2019 (153)
6 KOREAN population from KRGDB NC_000017.10 - 39925769 Apr 27, 2020 (154)
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
3221527, 12019622, ss1692778168, ss2742715235 NC_000017.10:39925768:G:A NC_000017.11:41769516:G:A (self)
42600281, ss3935422887 NC_000017.10:39925768:G:C NC_000017.11:41769516:G:C (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 rs781901019

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