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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.

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)
delGA=0.000544 (66/121350, ExAC)
delGA=0.00022 (17/78700, PAGE_STUDY)
delGA=0.00033 (9/27508, ALFA)
delGA=0.00056 (7/12518, GO-ESP)
delGA=0.0002 (1/4480, Estonian)
delGA=0.0003 (1/3854, ALSPAC)
delGA=0.0005 (2/3708, TWINSUK)
delGA=0.03 (1/40, GENOME_DK)
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.

Release Version: 20230706150541
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


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
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
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 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]
Gene: GNPTAB, N-acetylglucosamine-1-phosphate transferase subunits alpha and beta (minus strand)
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
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: delGA (allele ID: 17810 )
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
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 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
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#.

29 SubSNP, 11 Frequency, 6 ClinVar submissions
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)
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
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)
Help

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

15 citations for rs34002892
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
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