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.
rs34002892
Current Build 156
Released September 21, 2022
- Organism
- Homo sapiens
- Position
-
chr12:101753470-101753473 (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
- delGA
- Variation Type
- Indel Insertion and Deletion
- Frequency
-
delGA=0.000363 (96/264690, TOPMED)delGA=0.000513 (129/251354, GnomAD_exome)delGA=0.000349 (49/140236, GnomAD) (+ 8 more)
- Clinical Significance
- Reported in ClinVar
- Gene : Consequence
- GNPTAB : Frameshift Variant
- Publications
- 15 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.
Population | Group | Sample Size | Ref Allele | Alt Allele |
---|---|---|---|---|
Total | Global | 27508 | GAGA=0.99967 | GA=0.00033 |
European | Sub | 20214 | GAGA=0.99955 | GA=0.00045 |
African | Sub | 3492 | GAGA=1.0000 | GA=0.0000 |
African Others | Sub | 122 | GAGA=1.000 | GA=0.000 |
African American | Sub | 3370 | GAGA=1.0000 | GA=0.0000 |
Asian | Sub | 168 | GAGA=1.000 | GA=0.000 |
East Asian | Sub | 112 | GAGA=1.000 | GA=0.000 |
Other Asian | Sub | 56 | GAGA=1.00 | GA=0.00 |
Latin American 1 | Sub | 146 | GAGA=1.000 | GA=0.000 |
Latin American 2 | Sub | 610 | GAGA=1.000 | GA=0.000 |
South Asian | Sub | 98 | GAGA=1.00 | GA=0.00 |
Other | Sub | 2780 | GAGA=1.0000 | GA=0.0000 |
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").
DownloadStudy | Population | Group | Sample Size | Ref Allele | Alt Allele |
---|---|---|---|---|---|
TopMed | Global | Study-wide | 264690 | GAGA=0.999637 | delGA=0.000363 |
gnomAD - Exomes | Global | Study-wide | 251354 | GAGA=0.999487 | delGA=0.000513 |
gnomAD - Exomes | European | Sub | 135308 | GAGA=0.999416 | delGA=0.000584 |
gnomAD - Exomes | Asian | Sub | 49008 | GAGA=0.99953 | delGA=0.00047 |
gnomAD - Exomes | American | Sub | 34574 | GAGA=0.99948 | delGA=0.00052 |
gnomAD - Exomes | African | Sub | 16256 | GAGA=0.99969 | delGA=0.00031 |
gnomAD - Exomes | Ashkenazi Jewish | Sub | 10080 | GAGA=1.00000 | delGA=0.00000 |
gnomAD - Exomes | Other | Sub | 6128 | GAGA=0.9993 | delGA=0.0007 |
gnomAD - Genomes | Global | Study-wide | 140236 | GAGA=0.999651 | delGA=0.000349 |
gnomAD - Genomes | European | Sub | 75940 | GAGA=0.99950 | delGA=0.00050 |
gnomAD - Genomes | African | Sub | 42034 | GAGA=0.99988 | delGA=0.00012 |
gnomAD - Genomes | American | Sub | 13654 | GAGA=0.99971 | delGA=0.00029 |
gnomAD - Genomes | Ashkenazi Jewish | Sub | 3322 | GAGA=0.9997 | delGA=0.0003 |
gnomAD - Genomes | East Asian | Sub | 3134 | GAGA=1.0000 | delGA=0.0000 |
gnomAD - Genomes | Other | Sub | 2152 | GAGA=0.9995 | delGA=0.0005 |
ExAC | Global | Study-wide | 121350 | GAGA=0.999456 | delGA=0.000544 |
ExAC | Europe | Sub | 73338 | GAGA=0.99940 | delGA=0.00060 |
ExAC | Asian | Sub | 25164 | GAGA=0.99944 | delGA=0.00056 |
ExAC | American | Sub | 11540 | GAGA=0.99957 | delGA=0.00043 |
ExAC | African | Sub | 10400 | GAGA=0.99971 | delGA=0.00029 |
ExAC | Other | Sub | 908 | GAGA=1.000 | delGA=0.000 |
The PAGE Study | Global | Study-wide | 78700 | GAGA=0.99978 | delGA=0.00022 |
The PAGE Study | AfricanAmerican | Sub | 32516 | GAGA=0.99994 | delGA=0.00006 |
The PAGE Study | Mexican | Sub | 10810 | GAGA=0.99926 | delGA=0.00074 |
The PAGE Study | Asian | Sub | 8318 | GAGA=1.0000 | delGA=0.0000 |
The PAGE Study | PuertoRican | Sub | 7916 | GAGA=1.0000 | delGA=0.0000 |
The PAGE Study | NativeHawaiian | Sub | 4534 | GAGA=0.9996 | delGA=0.0004 |
The PAGE Study | Cuban | Sub | 4230 | GAGA=0.9998 | delGA=0.0002 |
The PAGE Study | Dominican | Sub | 3828 | GAGA=0.9995 | delGA=0.0005 |
The PAGE Study | CentralAmerican | Sub | 2450 | GAGA=1.0000 | delGA=0.0000 |
The PAGE Study | SouthAmerican | Sub | 1982 | GAGA=0.9995 | delGA=0.0005 |
The PAGE Study | NativeAmerican | Sub | 1260 | GAGA=1.0000 | delGA=0.0000 |
The PAGE Study | SouthAsian | Sub | 856 | GAGA=0.999 | delGA=0.001 |
Allele Frequency Aggregator | Total | Global | 27508 | GAGA=0.99967 | delGA=0.00033 |
Allele Frequency Aggregator | European | Sub | 20214 | GAGA=0.99955 | delGA=0.00045 |
Allele Frequency Aggregator | African | Sub | 3492 | GAGA=1.0000 | delGA=0.0000 |
Allele Frequency Aggregator | Other | Sub | 2780 | GAGA=1.0000 | delGA=0.0000 |
Allele Frequency Aggregator | Latin American 2 | Sub | 610 | GAGA=1.000 | delGA=0.000 |
Allele Frequency Aggregator | Asian | Sub | 168 | GAGA=1.000 | delGA=0.000 |
Allele Frequency Aggregator | Latin American 1 | Sub | 146 | GAGA=1.000 | delGA=0.000 |
Allele Frequency Aggregator | South Asian | Sub | 98 | GAGA=1.00 | delGA=0.00 |
GO Exome Sequencing Project | Global | Study-wide | 12518 | GAGA=0.99944 | delGA=0.00056 |
GO Exome Sequencing Project | European American | Sub | 8254 | GAGA=0.9994 | delGA=0.0006 |
GO Exome Sequencing Project | African American | Sub | 4264 | GAGA=0.9995 | delGA=0.0005 |
Genetic variation in the Estonian population | Estonian | Study-wide | 4480 | GAGA=0.9998 | delGA=0.0002 |
The Avon Longitudinal Study of Parents and Children | PARENT AND CHILD COHORT | Study-wide | 3854 | GAGA=0.9997 | delGA=0.0003 |
UK 10K study - Twins | TWIN COHORT | Study-wide | 3708 | GAGA=0.9995 | delGA=0.0005 |
The Danish reference pan genome | Danish | Study-wide | 40 | GAGA=0.97 | delGA=0.03 |
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.
Sequence name | Change |
---|---|
GRCh38.p14 chr 12 | NC_000012.12:g.101753470GA[1] |
GRCh37.p13 chr 12 | NC_000012.11:g.102147248GA[1] |
GNPTAB RefSeqGene | NG_021243.1:g.82395TC[1] |
Molecule type | Change | Amino acid[Codon] | SO Term |
---|---|---|---|
GNPTAB transcript | NM_024312.5:c.3503_3504del | L [CT] > Q [C] | Coding Sequence Variant |
N-acetylglucosamine-1-phosphotransferase subunits alpha/beta precursor | NP_077288.2:p.Leu1168fs | L (Leu) > Q (Gln) | Frameshift Variant |
GNPTAB transcript variant X2 | XM_006719593.4:c. | N/A | Genic Downstream Transcript Variant |
GNPTAB transcript variant X1 |
XM_011538731.3:c.3422_342… XM_011538731.3:c.3422_3423del |
L [CT] > Q [C] | Coding Sequence Variant |
N-acetylglucosamine-1-phosphotransferase subunits alpha/beta isoform X1 | XP_011537033.1:p.Leu1141fs | L (Leu) > Q (Gln) | Frameshift Variant |
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.
ClinVar Accession | Disease Names | Clinical Significance |
---|---|---|
RCV000002899.20 | Mucolipidosis type II | Pathogenic |
RCV000002900.11 | Pseudo-Hurler polydystrophy | Pathogenic |
RCV000082192.23 | not provided | Pathogenic |
RCV000380090.3 | GNPTAB-Related Disorders | Pathogenic |
RCV000623507.1 | Inborn genetic diseases | Pathogenic |
RCV000678389.6 | Mucolipidosis type II,Pseudo-Hurler polydystrophy | Pathogenic |
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 | GAGA= | delGA |
---|---|---|
GRCh38.p14 chr 12 | NC_000012.12:g.101753470_101753473= | NC_000012.12:g.101753470GA[1] |
GRCh37.p13 chr 12 | NC_000012.11:g.102147248_102147251= | NC_000012.11:g.102147248GA[1] |
GNPTAB RefSeqGene | NG_021243.1:g.82395_82398= | NG_021243.1:g.82395TC[1] |
GNPTAB transcript | NM_024312.5:c.3501_3504= | NM_024312.5:c.3503_3504del |
GNPTAB transcript | NM_024312.4:c.3501_3504= | NM_024312.4:c.3503_3504del |
GNPTAB transcript variant X1 | XM_011538731.3:c.3420_3423= | XM_011538731.3:c.3422_3423del |
GNPTAB transcript variant X1 | XM_011538731.2:c.3420_3423= | XM_011538731.2:c.3422_3423del |
GNPTAB transcript variant X1 | XM_011538731.1:c.3420_3423= | XM_011538731.1:c.3422_3423del |
N-acetylglucosamine-1-phosphotransferase subunits alpha/beta precursor | NP_077288.2:p.Val1167_Leu1168= | NP_077288.2:p.Leu1168fs |
N-acetylglucosamine-1-phosphotransferase subunits alpha/beta isoform X1 | XP_011537033.1:p.Val1140_Leu1141= | XP_011537033.1:p.Leu1141fs |
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#.
No | Submitter | Submission ID | Date (Build) |
---|---|---|---|
1 | GENZYME-OKC | ss49854043 | Mar 13, 2006 (126) |
2 | GENEREVIEWS | ss550827875 | Oct 31, 2012 (137) |
3 | EVA_GENOME_DK | ss1574559679 | Apr 01, 2015 (144) |
4 | EVA_UK10K_ALSPAC | ss1707599773 | Apr 01, 2015 (144) |
5 | EVA_UK10K_TWINSUK | ss1707599796 | Apr 01, 2015 (144) |
6 | EVA_EXAC | ss1712021656 | Apr 01, 2015 (144) |
7 | ILLUMINA | ss1946347814 | Feb 12, 2016 (147) |
8 | ILLUMINA | ss1959460755 | Feb 12, 2016 (147) |
9 | GNOMAD | ss2740072937 | Nov 08, 2017 (151) |
10 | GNOMAD | ss2748942385 | Nov 08, 2017 (151) |
11 | GNOMAD | ss2914468191 | Nov 08, 2017 (151) |
12 | AFFY | ss2984988850 | Nov 08, 2017 (151) |
13 | ILLUMINA | ss3021459585 | Nov 08, 2017 (151) |
14 | ILLUMINA | ss3021459586 | Nov 08, 2017 (151) |
15 | ILLUMINA | ss3625631921 | Oct 12, 2018 (152) |
16 | ILLUMINA | ss3644600819 | Oct 12, 2018 (152) |
17 | ILLUMINA | ss3651841123 | Oct 12, 2018 (152) |
18 | ILLUMINA | ss3651841124 | Oct 12, 2018 (152) |
19 | ILLUMINA | ss3653758601 | Oct 12, 2018 (152) |
20 | EGCUT_WGS | ss3677541733 | Jul 13, 2019 (153) |
21 | EVA_DECODE | ss3694340113 | Jul 13, 2019 (153) |
22 | ILLUMINA | ss3725351321 | Jul 13, 2019 (153) |
23 | ILLUMINA | ss3744104164 | Jul 13, 2019 (153) |
24 | PAGE_CC | ss3771712573 | Jul 13, 2019 (153) |
25 | EVA | ss3824762427 | Apr 27, 2020 (154) |
26 | EVA | ss3986582616 | Apr 26, 2021 (155) |
27 | TOPMED | ss4930583467 | Apr 26, 2021 (155) |
28 | HUGCELL_USP | ss5486639070 | Oct 16, 2022 (156) |
29 | EVA | ss5945232236 | Oct 16, 2022 (156) |
30 | The Avon Longitudinal Study of Parents and Children | NC_000012.11 - 102147248 | Oct 12, 2018 (152) |
31 | Genetic variation in the Estonian population | NC_000012.11 - 102147248 | Oct 12, 2018 (152) |
32 | ExAC | NC_000012.11 - 102147248 | Oct 12, 2018 (152) |
33 | The Danish reference pan genome | NC_000012.11 - 102147248 | Apr 27, 2020 (154) |
34 | gnomAD - Genomes | NC_000012.12 - 101753470 | Apr 26, 2021 (155) |
35 | gnomAD - Exomes | NC_000012.11 - 102147248 | Jul 13, 2019 (153) |
36 | GO Exome Sequencing Project | NC_000012.11 - 102147248 | Oct 12, 2018 (152) |
37 | The PAGE Study | NC_000012.12 - 101753470 | Jul 13, 2019 (153) |
38 | TopMed | NC_000012.12 - 101753470 | Apr 26, 2021 (155) |
39 | UK 10K study - Twins | NC_000012.11 - 102147248 | Oct 12, 2018 (152) |
40 | ALFA | NC_000012.12 - 101753470 | Apr 26, 2021 (155) |
41 | ClinVar | RCV000002899.20 | Oct 16, 2022 (156) |
42 | ClinVar | RCV000002900.11 | Oct 16, 2022 (156) |
43 | ClinVar | RCV000082192.23 | Oct 16, 2022 (156) |
44 | ClinVar | RCV000380090.3 | Oct 16, 2022 (156) |
45 | ClinVar | RCV000623507.1 | Oct 12, 2018 (152) |
46 | ClinVar | RCV000678389.6 | Oct 16, 2022 (156) |
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).
Submission IDs | Observation SPDI | Canonical SPDI | Source RSIDs |
---|---|---|---|
32865694, 23279981, 1380786, 375519, 9309307, 1219876, 32865694, ss1574559679, ss1707599773, ss1707599796, ss1712021656, ss1946347814, ss1959460755, ss2740072937, ss2748942385, ss2914468191, ss2984988850, ss3021459585, ss3021459586, ss3625631921, ss3644600819, ss3651841123, ss3651841124, ss3653758601, ss3677541733, ss3744104164, ss3824762427, ss3986582616, ss5945232236 | NC_000012.11:102147247:GA: | NC_000012.12:101753469:GAGA:GA | (self) |
417512824, 934042, 146129124, ss550827875, ss3694340113, ss3725351321, ss3771712573, ss4930583467, ss5486639070 | NC_000012.12:101753469:GA: | NC_000012.12:101753469:GAGA:GA | (self) |
RCV000002899.20, RCV000002900.11, RCV000082192.23, RCV000380090.3, RCV000623507.1, RCV000678389.6, 11097955849 | NC_000012.12:101753469:GAGA:GA | NC_000012.12:101753469:GAGA:GA | (self) |
ss49854043 | NT_029419.12:64290553:GA: | NC_000012.12:101753469:GAGA:GA | (self) |
Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.
PMID | Title | Author | Year | Journal |
---|---|---|---|---|
16465621 | Mucolipidosis II (I-cell disease) and mucolipidosis IIIA (classical pseudo-hurler polydystrophy) are caused by mutations in the GlcNAc-phosphotransferase alpha / beta -subunits precursor gene. | Kudo M et al. | 2006 | American journal of human genetics |
16630736 | When Mucolipidosis III meets Mucolipidosis II: GNPTA gene mutations in 24 patients. | Bargal R et al. | 2006 | Molecular genetics and metabolism |
18190596 | Mucolipidosis II: a single causal mutation in the N-acetylglucosamine-1-phosphotransferase gene (GNPTAB) in a French Canadian founder population. | Plante M et al. | 2008 | Clinical genetics |
19617216 | Phenotype and genotype in mucolipidoses II and III alpha/beta: a study of 61 probands. | Cathey SS et al. | 2010 | Journal of medical genetics |
19659762 | Molecular analysis of the GNPTAB and GNPTG genes in 13 patients with mucolipidosis type II or type III - identification of eight novel mutations. | Encarnação M et al. | 2009 | Clinical genetics |
20301728 | GNPTAB-Related Disorders. | Leroy JG et al. | 1993 | GeneReviews(®) |
20301730 | Mucolipidosis III Alpha/Beta – RETIRED CHAPTER, FOR HISTORICAL REFERENCE ONLY. | Leroy JG et al. | 1993 | GeneReviews(®) |
20880125 | Origin and spread of a common deletion causing mucolipidosis type II: insights from patterns of haplotypic diversity. | Coutinho MF et al. | 2011 | Clinical genetics |
23566849 | Mucolipidosis II and III alpha/beta in Brazil: analysis of the GNPTAB gene. | Cury GK et al. | 2013 | Gene |
23757202 | Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data. | Bean LJ et al. | 2013 | Human mutation |
24033266 | A systematic approach to assessing the clinical significance of genetic variants. | Duzkale H et al. | 2013 | Clinical genetics |
24375680 | Mucolipidosis II-related mutations inhibit the exit from the endoplasmic reticulum and proteolytic cleavage of GlcNAc-1-phosphotransferase precursor protein (GNPTAB). | De Pace R et al. | 2014 | Human mutation |
24685522 | Prenatal skeletal dysplasia phenotype in severe MLII alpha/beta with novel GNPTAB mutation. | Aggarwal S et al. | 2014 | Gene |
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 |
25788519 | Analyses of disease-related GNPTAB mutations define a novel GlcNAc-1-phosphotransferase interaction domain and an alternative site-1 protease cleavage site. | Velho RV et al. | 2015 | Human molecular genetics |
The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.
Genomic regions, transcripts, and products
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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.
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.