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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.

rs75462234

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr10:100749772-100749778 (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
delG / dupG / dupGG
Variation Type
Indel Insertion and Deletion
Frequency
dupG=0.000157 (18/114532, ExAC)
dupG=0.00000 (0/10680, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PAX2 : Frameshift Variant
Publications
4 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20231103111315
Population Group Sample Size Ref Allele Alt Allele
Total Global 10680 GGGGGGG=1.00000 GGGGGGGG=0.00000
European Sub 6962 GGGGGGG=1.0000 GGGGGGGG=0.0000
African Sub 2294 GGGGGGG=1.0000 GGGGGGGG=0.0000
African Others Sub 84 GGGGGGG=1.00 GGGGGGGG=0.00
African American Sub 2210 GGGGGGG=1.0000 GGGGGGGG=0.0000
Asian Sub 108 GGGGGGG=1.000 GGGGGGGG=0.000
East Asian Sub 84 GGGGGGG=1.00 GGGGGGGG=0.00
Other Asian Sub 24 GGGGGGG=1.00 GGGGGGGG=0.00
Latin American 1 Sub 146 GGGGGGG=1.000 GGGGGGGG=0.000
Latin American 2 Sub 610 GGGGGGG=1.000 GGGGGGGG=0.000
South Asian Sub 94 GGGGGGG=1.00 GGGGGGGG=0.00
Other Sub 466 GGGGGGG=1.000 GGGGGGGG=0.000


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
ExAC Global Study-wide 114532 -

No frequency provided

dupG=0.000157
ExAC Europe Sub 69278 -

No frequency provided

dupG=0.00019
ExAC Asian Sub 23714 -

No frequency provided

dupG=0.00000
ExAC American Sub 11468 -

No frequency provided

dupG=0.00009
ExAC African Sub 9232 -

No frequency provided

dupG=0.0003
ExAC Other Sub 840 -

No frequency provided

dupG=0.001
Allele Frequency Aggregator Total Global 10680 (G)7=1.00000 dupG=0.00000
Allele Frequency Aggregator European Sub 6962 (G)7=1.0000 dupG=0.0000
Allele Frequency Aggregator African Sub 2294 (G)7=1.0000 dupG=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 (G)7=1.000 dupG=0.000
Allele Frequency Aggregator Other Sub 466 (G)7=1.000 dupG=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 (G)7=1.000 dupG=0.000
Allele Frequency Aggregator Asian Sub 108 (G)7=1.000 dupG=0.000
Allele Frequency Aggregator South Asian Sub 94 (G)7=1.00 dupG=0.00
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 10 NC_000010.11:g.100749778del
GRCh38.p14 chr 10 NC_000010.11:g.100749778dup
GRCh38.p14 chr 10 NC_000010.11:g.100749777_100749778dup
GRCh37.p13 chr 10 NC_000010.10:g.102509535del
GRCh37.p13 chr 10 NC_000010.10:g.102509535dup
GRCh37.p13 chr 10 NC_000010.10:g.102509534_102509535dup
PAX2 RefSeqGene NG_008680.2:g.19070del
PAX2 RefSeqGene NG_008680.2:g.19070dup
PAX2 RefSeqGene NG_008680.2:g.19069_19070dup
Gene: PAX2, paired box 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PAX2 transcript variant g NM_001374303.1:c. N/A Genic Downstream Transcript Variant
PAX2 transcript variant e NM_003990.5:c.76del V [GTG] > C [TG] Coding Sequence Variant
paired box protein Pax-2 isoform e NP_003981.3:p.Val26fs V (Val) > C (Cys) Frameshift Variant
PAX2 transcript variant e NM_003990.5:c.76dup V [GTG] > G [GGTG] Coding Sequence Variant
paired box protein Pax-2 isoform e NP_003981.3:p.Val26fs V (Val) > G (Gly) Frameshift Variant
PAX2 transcript variant e NM_003990.5:c.75_76dup V [GTG] > G [GGGTG] Coding Sequence Variant
paired box protein Pax-2 isoform e NP_003981.3:p.Val26fs V (Val) > G (Gly) Frameshift Variant
PAX2 transcript variant c NM_003988.5:c.76del V [GTG] > C [TG] Coding Sequence Variant
paired box protein Pax-2 isoform c NP_003979.2:p.Val26fs V (Val) > C (Cys) Frameshift Variant
PAX2 transcript variant c NM_003988.5:c.76dup V [GTG] > G [GGTG] Coding Sequence Variant
paired box protein Pax-2 isoform c NP_003979.2:p.Val26fs V (Val) > G (Gly) Frameshift Variant
PAX2 transcript variant c NM_003988.5:c.75_76dup V [GTG] > G [GGGTG] Coding Sequence Variant
paired box protein Pax-2 isoform c NP_003979.2:p.Val26fs V (Val) > G (Gly) Frameshift Variant
PAX2 transcript variant d NM_003989.5:c.76del V [GTG] > C [TG] Coding Sequence Variant
paired box protein Pax-2 isoform d NP_003980.3:p.Val26fs V (Val) > C (Cys) Frameshift Variant
PAX2 transcript variant d NM_003989.5:c.76dup V [GTG] > G [GGTG] Coding Sequence Variant
paired box protein Pax-2 isoform d NP_003980.3:p.Val26fs V (Val) > G (Gly) Frameshift Variant
PAX2 transcript variant d NM_003989.5:c.75_76dup V [GTG] > G [GGGTG] Coding Sequence Variant
paired box protein Pax-2 isoform d NP_003980.3:p.Val26fs V (Val) > G (Gly) Frameshift Variant
PAX2 transcript variant f NM_001304569.2:c.169del V [GTG] > C [TG] Coding Sequence Variant
paired box protein Pax-2 isoform f precursor NP_001291498.1:p.Val57fs V (Val) > C (Cys) Frameshift Variant
PAX2 transcript variant f NM_001304569.2:c.169dup V [GTG] > G [GGTG] Coding Sequence Variant
paired box protein Pax-2 isoform f precursor NP_001291498.1:p.Val57fs V (Val) > G (Gly) Frameshift Variant
PAX2 transcript variant f NM_001304569.2:c.168_169d…

NM_001304569.2:c.168_169dup

V [GTG] > G [GGGTG] Coding Sequence Variant
paired box protein Pax-2 isoform f precursor NP_001291498.1:p.Val57fs V (Val) > G (Gly) Frameshift Variant
PAX2 transcript variant b NM_000278.5:c.76del V [GTG] > C [TG] Coding Sequence Variant
paired box protein Pax-2 isoform b NP_000269.3:p.Val26fs V (Val) > C (Cys) Frameshift Variant
PAX2 transcript variant b NM_000278.5:c.76dup V [GTG] > G [GGTG] Coding Sequence Variant
paired box protein Pax-2 isoform b NP_000269.3:p.Val26fs V (Val) > G (Gly) Frameshift Variant
PAX2 transcript variant b NM_000278.5:c.75_76dup V [GTG] > G [GGGTG] Coding Sequence Variant
paired box protein Pax-2 isoform b NP_000269.3:p.Val26fs V (Val) > G (Gly) Frameshift Variant
PAX2 transcript variant a NM_003987.5:c.76del V [GTG] > C [TG] Coding Sequence Variant
paired box protein Pax-2 isoform a NP_003978.3:p.Val26fs V (Val) > C (Cys) Frameshift Variant
PAX2 transcript variant a NM_003987.5:c.76dup V [GTG] > G [GGTG] Coding Sequence Variant
paired box protein Pax-2 isoform a NP_003978.3:p.Val26fs V (Val) > G (Gly) Frameshift Variant
PAX2 transcript variant a NM_003987.5:c.75_76dup V [GTG] > G [GGGTG] Coding Sequence Variant
paired box protein Pax-2 isoform a NP_003978.3:p.Val26fs V (Val) > G (Gly) Frameshift 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.

Allele: delG (allele ID: 28840 )
ClinVar Accession Disease Names Clinical Significance
RCV000014812.27 Renal coloboma syndrome Pathogenic
Allele: dupG (allele ID: 166077 )
ClinVar Accession Disease Names Clinical Significance
RCV000014806.25 Renal coloboma syndrome Pathogenic
RCV000144381.15 not provided Pathogenic
RCV000587907.3 Focal segmental glomerulosclerosis 7 Pathogenic
RCV001068182.3 Focal segmental glomerulosclerosis 7,Renal coloboma syndrome Pathogenic
RCV001328165.1 Congenital anomaly of kidney and urinary tract Pathogenic
RCV001849315.1 Focal segmental glomerulosclerosis,Steroid-resistant nephrotic syndrome Likely-Pathogenic
Allele: dupGG (allele ID: 28841 )
ClinVar Accession Disease Names Clinical Significance
RCV000014813.26 Renal coloboma syndrome Pathogenic
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)7= delG dupG dupGG
GRCh38.p14 chr 10 NC_000010.11:g.100749772_100749778= NC_000010.11:g.100749778del NC_000010.11:g.100749778dup NC_000010.11:g.100749777_100749778dup
GRCh37.p13 chr 10 NC_000010.10:g.102509529_102509535= NC_000010.10:g.102509535del NC_000010.10:g.102509535dup NC_000010.10:g.102509534_102509535dup
PAX2 RefSeqGene NG_008680.2:g.19064_19070= NG_008680.2:g.19070del NG_008680.2:g.19070dup NG_008680.2:g.19069_19070dup
PAX2 transcript variant c NM_003988.5:c.70_76= NM_003988.5:c.76del NM_003988.5:c.76dup NM_003988.5:c.75_76dup
PAX2 transcript variant c NM_003988.4:c.70_76= NM_003988.4:c.76del NM_003988.4:c.76dup NM_003988.4:c.75_76dup
PAX2 transcript variant c NM_003988.3:c.70_76= NM_003988.3:c.76del NM_003988.3:c.76dup NM_003988.3:c.75_76dup
PAX2 transcript variant a NM_003987.5:c.70_76= NM_003987.5:c.76del NM_003987.5:c.76dup NM_003987.5:c.75_76dup
PAX2 transcript variant a NM_003987.4:c.70_76= NM_003987.4:c.76del NM_003987.4:c.76dup NM_003987.4:c.75_76dup
PAX2 transcript variant a NM_003987.3:c.70_76= NM_003987.3:c.76del NM_003987.3:c.76dup NM_003987.3:c.75_76dup
PAX2 transcript variant e NM_003990.5:c.70_76= NM_003990.5:c.76del NM_003990.5:c.76dup NM_003990.5:c.75_76dup
PAX2 transcript variant e NM_003990.4:c.70_76= NM_003990.4:c.76del NM_003990.4:c.76dup NM_003990.4:c.75_76dup
PAX2 transcript variant e NM_003990.3:c.70_76= NM_003990.3:c.76del NM_003990.3:c.76dup NM_003990.3:c.75_76dup
PAX2 transcript variant b NM_000278.5:c.70_76= NM_000278.5:c.76del NM_000278.5:c.76dup NM_000278.5:c.75_76dup
PAX2 transcript variant b NM_000278.4:c.70_76= NM_000278.4:c.76del NM_000278.4:c.76dup NM_000278.4:c.75_76dup
PAX2 transcript variant b NM_000278.3:c.70_76= NM_000278.3:c.76del NM_000278.3:c.76dup NM_000278.3:c.75_76dup
PAX2 transcript variant d NM_003989.5:c.70_76= NM_003989.5:c.76del NM_003989.5:c.76dup NM_003989.5:c.75_76dup
PAX2 transcript variant d NM_003989.4:c.70_76= NM_003989.4:c.76del NM_003989.4:c.76dup NM_003989.4:c.75_76dup
PAX2 transcript variant d NM_003989.3:c.70_76= NM_003989.3:c.76del NM_003989.3:c.76dup NM_003989.3:c.75_76dup
PAX2 transcript variant f NM_001304569.2:c.163_169= NM_001304569.2:c.169del NM_001304569.2:c.169dup NM_001304569.2:c.168_169dup
PAX2 transcript variant f NM_001304569.1:c.163_169= NM_001304569.1:c.169del NM_001304569.1:c.169dup NM_001304569.1:c.168_169dup
paired box protein Pax-2 isoform c NP_003979.2:p.Gly24_Val26= NP_003979.2:p.Val26fs NP_003979.2:p.Val26fs NP_003979.2:p.Val26fs
paired box protein Pax-2 isoform a NP_003978.3:p.Gly24_Val26= NP_003978.3:p.Val26fs NP_003978.3:p.Val26fs NP_003978.3:p.Val26fs
paired box protein Pax-2 isoform e NP_003981.3:p.Gly24_Val26= NP_003981.3:p.Val26fs NP_003981.3:p.Val26fs NP_003981.3:p.Val26fs
paired box protein Pax-2 isoform b NP_000269.3:p.Gly24_Val26= NP_000269.3:p.Val26fs NP_000269.3:p.Val26fs NP_000269.3:p.Val26fs
paired box protein Pax-2 isoform d NP_003980.3:p.Gly24_Val26= NP_003980.3:p.Val26fs NP_003980.3:p.Val26fs NP_003980.3:p.Val26fs
paired box protein Pax-2 isoform f precursor NP_001291498.1:p.Gly55_Val57= NP_001291498.1:p.Val57fs NP_001291498.1:p.Val57fs NP_001291498.1:p.Val57fs
paired box protein Pax-2 isoform b NP_000269.2:p.Gly24_Val26= NP_000269.2:p.Val26fs NP_000269.2:p.Val26fs NP_000269.2:p.Val26fs
paired box protein Pax-2 isoform a NP_003978.2:p.Gly24_Val26= NP_003978.2:p.Val26fs NP_003978.2:p.Val26fs NP_003978.2:p.Val26fs
paired box protein Pax-2 isoform d NP_003980.2:p.Gly24_Val26= NP_003980.2:p.Val26fs NP_003980.2:p.Val26fs NP_003980.2:p.Val26fs
paired box protein Pax-2 isoform e NP_003981.2:p.Gly24_Val26= NP_003981.2:p.Val26fs NP_003981.2:p.Val26fs NP_003981.2:p.Val26fs
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#.

8 SubSNP, 2 Frequency, 8 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NCBI-CURATED-RECORDS ss140406771 Dec 01, 2009 (131)
2 NCBI-CURATED-RECORDS ss140406793 Dec 01, 2009 (131)
3 NCBI-CURATED-RECORDS ss140406795 Dec 01, 2009 (131)
4 OMIM-CURATED-RECORDS ss1505810928 Dec 08, 2014 (142)
5 OMIM-CURATED-RECORDS ss1505810929 Dec 08, 2014 (136)
6 EVA_EXAC ss1711947903 Apr 01, 2015 (144)
7 GNOMAD ss2738470053 Nov 08, 2017 (151)
8 EVA ss5236886685 Apr 26, 2021 (155)
9 ExAC NC_000010.10 - 102509529 Oct 12, 2018 (152)
10 ALFA NC_000010.11 - 100749772 Apr 26, 2021 (155)
11 ClinVar RCV000014806.25 Oct 16, 2022 (156)
12 ClinVar RCV000014812.27 Oct 16, 2022 (156)
13 ClinVar RCV000014813.26 Jul 13, 2019 (153)
14 ClinVar RCV000144381.15 Oct 16, 2022 (156)
15 ClinVar RCV000587907.3 Oct 16, 2022 (156)
16 ClinVar RCV001068182.3 Oct 16, 2022 (156)
17 ClinVar RCV001328165.1 Apr 26, 2021 (155)
18 ClinVar RCV001849315.1 Oct 16, 2022 (156)
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)
rs80159664 Oct 26, 2010 (133)
rs606231211 Feb 13, 2015 (136)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
RCV000014812.27 NC_000010.11:100749771:GGGGGGG:GGG…

NC_000010.11:100749771:GGGGGGG:GGGGGG

NC_000010.11:100749771:GGGGGGG:GGG…

NC_000010.11:100749771:GGGGGGG:GGGGGG

(self)
ss140406795 NC_000010.11:100749777:G: NC_000010.11:100749771:GGGGGGG:GGG…

NC_000010.11:100749771:GGGGGGG:GGGGGG

(self)
275844, ss1711947903, ss2738470053 NC_000010.10:102509528::G NC_000010.11:100749771:GGGGGGG:GGG…

NC_000010.11:100749771:GGGGGGG:GGGGGGGG

(self)
ss5236886685 NC_000010.11:100749771::G NC_000010.11:100749771:GGGGGGG:GGG…

NC_000010.11:100749771:GGGGGGG:GGGGGGGG

(self)
RCV000014806.25, RCV000144381.15, RCV000587907.3, RCV001068182.3, RCV001328165.1, RCV001849315.1, 11439171236 NC_000010.11:100749771:GGGGGGG:GGG…

NC_000010.11:100749771:GGGGGGG:GGGGGGGG

NC_000010.11:100749771:GGGGGGG:GGG…

NC_000010.11:100749771:GGGGGGG:GGGGGGGG

(self)
ss140406771, ss1505810928 NC_000010.11:100749778::G NC_000010.11:100749771:GGGGGGG:GGG…

NC_000010.11:100749771:GGGGGGG:GGGGGGGG

(self)
RCV000014813.26 NC_000010.11:100749771:GGGGGGG:GGG…

NC_000010.11:100749771:GGGGGGG:GGGGGGGGG

NC_000010.11:100749771:GGGGGGG:GGG…

NC_000010.11:100749771:GGGGGGG:GGGGGGGGG

(self)
ss140406793, ss1505810929 NC_000010.11:100749778::GG NC_000010.11:100749771:GGGGGGG:GGG…

NC_000010.11:100749771:GGGGGGG:GGGGGGGGG

(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 rs75462234
PMID Title Author Year Journal
10533062 Homonucleotide expansion and contraction mutations of PAX2 and inclusion of Chiari 1 malformation as part of renal-coloboma syndrome. Schimmenti LA et al. 1999 Human mutation
22213154 Update of PAX2 mutations in renal coloboma syndrome and establishment of a locus-specific database. Bower M et al. 2012 Human mutation
27657687 Whole-exome sequencing in the molecular diagnosis of individuals with congenital anomalies of the kidney and urinary tract and identification of a new causative gene. Bekheirnia MR et al. 2017 Genetics in medicine
31689173 Genetic Variations of Ultraconserved Elements in the Human Genome. Habic A et al. 2019 Omics
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.post774+babeb33