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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.

rs137852327

Current Build 157

Released September 3, 2024

Organism
Homo sapiens
Position
chrX:154533122 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000113 (30/264690, TOPMED)
T=0.000136 (15/110642, GnomAD_genomes)
T=0.00025 (22/86541, ExAC) (+ 5 more)
T=0.00002 (1/66161, 38KJPN)
T=0.00010 (3/29902, ALFA)
T=0.0012 (6/4805, 1000G_30X)
T=0.0016 (6/3775, 1000G)
T=0.01 (1/100, Vietnamese)
Clinical Significance
Reported in ClinVar
Gene : Consequence
G6PD : Missense 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 29902 C=0.99990 T=0.00010 0.999799 0.0 0.000201 0
European Sub 21890 C=1.00000 T=0.00000 1.0 0.0 0.0 N/A
African Sub 3916 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 122 C=1.000 T=0.000 1.0 0.0 0.0 N/A
African American Sub 3794 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 168 C=0.982 T=0.018 0.964286 0.0 0.035714 0
East Asian Sub 112 C=1.000 T=0.000 1.0 0.0 0.0 N/A
Other Asian Sub 56 C=0.95 T=0.05 0.892857 0.0 0.107143 0
Latin American 1 Sub 146 C=1.000 T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 C=1.000 T=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Sub 3074 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A


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 C=0.999887 T=0.000113
gnomAD v4 - Genomes Global Study-wide 110642 C=0.999864 T=0.000136
gnomAD v4 - Genomes European Sub 59530 C=1.00000 T=0.00000
gnomAD v4 - Genomes African Sub 31148 C=1.00000 T=0.00000
gnomAD v4 - Genomes American Sub 10792 C=0.99991 T=0.00009
gnomAD v4 - Genomes East Asian Sub 3550 C=0.9961 T=0.0039
gnomAD v4 - Genomes South Asian Sub 2752 C=1.0000 T=0.0000
gnomAD v4 - Genomes Ashkenazi Jewish Sub 2651 C=1.0000 T=0.0000
gnomAD v4 - Genomes Middle Eastern sub 219 C=1.000 T=0.000
ExAC Global Study-wide 86541 C=0.99975 T=0.00025
ExAC Europe Sub 51669 C=1.00000 T=0.00000
ExAC Asian Sub 16613 C=0.99868 T=0.00132
ExAC American Sub 9281 C=1.0000 T=0.0000
ExAC African Sub 8356 C=1.0000 T=0.0000
ExAC Other Sub 622 C=1.000 T=0.000
38KJPN JAPANESE Study-wide 66161 C=0.99998 T=0.00002
Allele Frequency Aggregator Total Global 29902 C=0.99990 T=0.00010
Allele Frequency Aggregator European Sub 21890 C=1.00000 T=0.00000
Allele Frequency Aggregator African Sub 3916 C=1.0000 T=0.0000
Allele Frequency Aggregator Other Sub 3074 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 168 C=0.982 T=0.018
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
1000Genomes_30X Global Study-wide 4805 C=0.9988 T=0.0012
1000Genomes_30X African Sub 1328 C=1.0000 T=0.0000
1000Genomes_30X Europe Sub 961 C=1.000 T=0.000
1000Genomes_30X South Asian Sub 883 C=1.000 T=0.000
1000Genomes_30X East Asian Sub 878 C=0.993 T=0.007
1000Genomes_30X American Sub 755 C=1.000 T=0.000
1000Genomes Global Study-wide 3775 C=0.9984 T=0.0016
1000Genomes African Sub 1003 C=1.0000 T=0.0000
1000Genomes Europe Sub 766 C=1.000 T=0.000
1000Genomes East Asian Sub 764 C=0.992 T=0.008
1000Genomes South Asian Sub 718 C=1.000 T=0.000
1000Genomes American Sub 524 C=1.000 T=0.000
A Vietnamese Genetic Variation Database Global Study-wide 100 C=0.99 T=0.01
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 X NC_000023.11:g.154533122C>A
GRCh38.p14 chr X NC_000023.11:g.154533122C>T
GRCh37.p13 chr X fix patch HG1497_PATCH NW_003871103.3:g.1967101C>A
GRCh37.p13 chr X fix patch HG1497_PATCH NW_003871103.3:g.1967101C>T
G6PD RefSeqGene NG_009015.2:g.19451G>T
G6PD RefSeqGene NG_009015.2:g.19451G>A
GRCh37.p13 chr X NC_000023.10:g.153761337C>A
GRCh37.p13 chr X NC_000023.10:g.153761337C>T
Gene: G6PD, glucose-6-phosphate dehydrogenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
G6PD transcript variant 1 NM_000402.4:c.961G>T V [GTG] > L [TTG] Coding Sequence Variant
glucose-6-phosphate 1-dehydrogenase isoform a NP_000393.4:p.Val321Leu V (Val) > L (Leu) Missense Variant
G6PD transcript variant 1 NM_000402.4:c.961G>A V [GTG] > M [ATG] Coding Sequence Variant
glucose-6-phosphate 1-dehydrogenase isoform a NP_000393.4:p.Val321Met V (Val) > M (Met) Missense Variant
G6PD transcript variant 3 NM_001360016.2:c.871G>T V [GTG] > L [TTG] Coding Sequence Variant
glucose-6-phosphate 1-dehydrogenase isoform b NP_001346945.1:p.Val291Leu V (Val) > L (Leu) Missense Variant
G6PD transcript variant 3 NM_001360016.2:c.871G>A V [GTG] > M [ATG] Coding Sequence Variant
glucose-6-phosphate 1-dehydrogenase isoform b NP_001346945.1:p.Val291Met V (Val) > M (Met) Missense Variant
G6PD transcript variant 2 NM_001042351.3:c.871G>T V [GTG] > L [TTG] Coding Sequence Variant
glucose-6-phosphate 1-dehydrogenase isoform b NP_001035810.1:p.Val291Leu V (Val) > L (Leu) Missense Variant
G6PD transcript variant 2 NM_001042351.3:c.871G>A V [GTG] > M [ATG] Coding Sequence Variant
glucose-6-phosphate 1-dehydrogenase isoform b NP_001035810.1:p.Val291Met V (Val) > M (Met) 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.

Allele: T (allele ID: 25425 )
ClinVar Accession Disease Names Clinical Significance
RCV000011116.12 G6PD VIANGCHAN Other
RCV000011117.12 G6PD JAMMU Other
RCV000180545.37 Anemia, nonspherocytic hemolytic, due to G6PD deficiency Pathogenic-Likely-Pathogenic
RCV000405688.14 G6PD deficiency Pathogenic
RCV000757320.33 not provided Pathogenic
RCV000763203.11 Anemia, nonspherocytic hemolytic, due to G6PD deficiency,Malaria, susceptibility to Pathogenic
RCV001250220.9 G6PD deficient hemolytic anemia Pathogenic
RCV001266092.10 Inborn genetic diseases Pathogenic
RCV002305706.10 Anemia, nonspherocytic hemolytic, due to G6PD deficiency Likely-Pathogenic
RCV002305707.10 Anemia, nonspherocytic hemolytic, due to G6PD deficiency Likely-Pathogenic
RCV003460452.2 Malaria, susceptibility to 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 C= A T
GRCh38.p14 chr X NC_000023.11:g.154533122= NC_000023.11:g.154533122C>A NC_000023.11:g.154533122C>T
GRCh37.p13 chr X fix patch HG1497_PATCH NW_003871103.3:g.1967101= NW_003871103.3:g.1967101C>A NW_003871103.3:g.1967101C>T
G6PD RefSeqGene NG_009015.2:g.19451= NG_009015.2:g.19451G>T NG_009015.2:g.19451G>A
G6PD transcript variant 1 NM_000402.4:c.961= NM_000402.4:c.961G>T NM_000402.4:c.961G>A
G6PD transcript variant 1 NM_000402.3:c.961= NM_000402.3:c.961G>T NM_000402.3:c.961G>A
G6PD transcript variant 2 NM_001042351.3:c.871= NM_001042351.3:c.871G>T NM_001042351.3:c.871G>A
G6PD transcript variant 2 NM_001042351.2:c.871= NM_001042351.2:c.871G>T NM_001042351.2:c.871G>A
G6PD transcript variant 2 NM_001042351.1:c.871= NM_001042351.1:c.871G>T NM_001042351.1:c.871G>A
G6PD transcript variant 3 NM_001360016.2:c.871= NM_001360016.2:c.871G>T NM_001360016.2:c.871G>A
G6PD transcript variant 1 NM_001360016.1:c.871= NM_001360016.1:c.871G>T NM_001360016.1:c.871G>A
GRCh37.p13 chr X NC_000023.10:g.153761337= NC_000023.10:g.153761337C>A NC_000023.10:g.153761337C>T
glucose-6-phosphate 1-dehydrogenase isoform a NP_000393.4:p.Val321= NP_000393.4:p.Val321Leu NP_000393.4:p.Val321Met
glucose-6-phosphate 1-dehydrogenase isoform b NP_001035810.1:p.Val291= NP_001035810.1:p.Val291Leu NP_001035810.1:p.Val291Met
glucose-6-phosphate 1-dehydrogenase isoform b NP_001346945.1:p.Val291= NP_001346945.1:p.Val291Leu NP_001346945.1:p.Val291Met
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#.

30 SubSNP, 10 Frequency, 11 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss289479854 Jan 06, 2011 (133)
2 SSMP ss663088378 Apr 25, 2013 (138)
3 1000GENOMES ss1556698346 Apr 09, 2015 (144)
4 EVA_EXAC ss1694662661 Apr 09, 2015 (144)
5 ILLUMINA ss1958229217 Feb 17, 2016 (147)
6 HUMAN_LONGEVITY ss2321325297 Dec 20, 2016 (150)
7 GNOMAD ss2745624828 Oct 13, 2018 (152)
8 GNOMAD ss2746166171 Oct 13, 2018 (152)
9 GNOMAD ss2984756049 Oct 13, 2018 (152)
10 AFFY ss2985493617 Oct 13, 2018 (152)
11 ILLUMINA ss3023047851 Oct 13, 2018 (152)
12 ILLUMINA ss3653606119 Oct 13, 2018 (152)
13 ILLUMINA ss3654261367 Oct 13, 2018 (152)
14 ILLUMINA ss3726710847 Jul 14, 2019 (153)
15 EVA ss3770770109 Jul 14, 2019 (153)
16 KHV_HUMAN_GENOMES ss3823525337 Jul 14, 2019 (153)
17 TOMMO_GENOMICS ss6205662039 Nov 02, 2024 (157)
18 GNOMAD ss6473686115 Nov 02, 2024 (157)
19 GNOMAD ss6473686116 Nov 02, 2024 (157)
20 TOPMED ss8141612850 Nov 02, 2024 (157)
21 TOMMO_GENOMICS ss8236816514 Nov 02, 2024 (157)
22 1000G_HIGH_COVERAGE ss8314364492 Nov 02, 2024 (157)
23 TRAN_CS_UWATERLOO ss8314460915 Nov 02, 2024 (157)
24 1000G_HIGH_COVERAGE ss8623703341 Nov 02, 2024 (157)
25 TOMMO_GENOMICS ss8799353924 Nov 02, 2024 (157)
26 EVA ss8848241658 Nov 02, 2024 (157)
27 EVA ss8857242452 Nov 02, 2024 (157)
28 EVA ss8979924766 Nov 02, 2024 (157)
29 GNOMAD ss10110230171 Nov 02, 2024 (157)
30 SHFJ ss10111240837 Nov 02, 2024 (157)
31 1000Genomes NC_000023.10 - 153761337 Oct 13, 2018 (152)
32 1000Genomes_30X NC_000023.11 - 154533122 Nov 02, 2024 (157)
33 ExAC NC_000023.10 - 153761337 Oct 13, 2018 (152)
34 gnomAD v4 - Exomes

Submission ignored due to conflicting rows:
Row 69039653 (NC_000023.11:154533121:C:A 1/1051731)
Row 69039654 (NC_000023.11:154533121:C:T 70/1051731)

- Nov 02, 2024 (157)
35 gnomAD v4 - Exomes

Submission ignored due to conflicting rows:
Row 69039653 (NC_000023.11:154533121:C:A 1/1051731)
Row 69039654 (NC_000023.11:154533121:C:T 70/1051731)

- Nov 02, 2024 (157)
36 gnomAD v4 - Genomes NC_000023.11 - 154533122 Nov 02, 2024 (157)
37 38KJPN NC_000023.11 - 154533122 Nov 02, 2024 (157)
38 TopMed NC_000023.11 - 154533122 Apr 27, 2021 (155)
39 A Vietnamese Genetic Variation Database NC_000023.10 - 153761337 Jul 14, 2019 (153)
40 ALFA NC_000023.11 - 154533122 Nov 02, 2024 (157)
41 ClinVar RCV000011116.12 Nov 02, 2024 (157)
42 ClinVar RCV000011117.12 Nov 02, 2024 (157)
43 ClinVar RCV000180545.37 Nov 02, 2024 (157)
44 ClinVar RCV000405688.14 Nov 02, 2024 (157)
45 ClinVar RCV000757320.33 Nov 02, 2024 (157)
46 ClinVar RCV000763203.11 Nov 02, 2024 (157)
47 ClinVar RCV001250220.9 Nov 02, 2024 (157)
48 ClinVar RCV001266092.10 Nov 02, 2024 (157)
49 ClinVar RCV002305706.10 Nov 02, 2024 (157)
50 ClinVar RCV002305707.10 Nov 02, 2024 (157)
51 ClinVar RCV003460452.2 Nov 02, 2024 (157)
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
ss6473686115 NC_000023.11:154533121:C:A NC_000023.11:154533121:C:A
84651563, 10174502, 10240011, ss663088378, ss1556698346, ss1694662661, ss1958229217, ss2745624828, ss2746166171, ss2984756049, ss2985493617, ss3023047851, ss3653606119, ss3654261367, ss3770770109, ss8236816514, ss8848241658, ss8979924766, ss10111240837 NC_000023.10:153761336:C:T NC_000023.11:154533121:C:T (self)
RCV000011116.12, RCV000011117.12, RCV000180545.37, RCV000405688.14, RCV000757320.33, RCV000763203.11, RCV001250220.9, RCV001266092.10, RCV002305706.10, RCV002305707.10, RCV003460452.2, 111229276, 638030697, 223037859, 705219207, 9122208557, ss289479854, ss2321325297, ss3726710847, ss3823525337, ss6205662039, ss6473686116, ss8141612850, ss8314364492, ss8314460915, ss8623703341, ss8799353924, ss8857242452, ss10110230171 NC_000023.11:154533121:C:T NC_000023.11:154533121:C:T (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 rs137852327
PMID Title Author Year Journal
1805484 Definition of the mutations of G6PD Wayne, G6PD Viangchan, G6PD Jammu, and G6PD 'LeJeune'. Beutler E et al. 1991 Acta haematologica
1984194 Glucose-6-phosphate dehydrogenase deficiency. Beutler E et al. 1991 The New England journal of medicine
3338798 G6PD Viangchan: a new glucose 6-phosphate dehydrogenase variant from Laos. Poon MC et al. 1988 Human genetics
7949118 G6PD deficiency. Beutler E et al. 1994 Blood
10502785 Glucose-6-phosphate dehydrogenase (G6PD) variants in Malaysian Chinese. Ainoon O et al. 1999 Human mutation
11499668 Distribution of glucose-6-phosphate dehydrogenase mutations in Southeast Asia. Iwai K et al. 2001 Human genetics
11793482 Glucose-6-phosphate dehydrogenase (G6PD) mutations in Thailand: G6PD Viangchan (871G>A) is the most common deficiency variant in the Thai population. Nuchprayoon I et al. 2002 Human mutation
12850494 Glucose-6-phosphate dehydrogenase (G-6-PD) mutations in Mexico: four new G-6-PD variants. Vaca G et al. 2003 Blood cells, molecules & diseases
16136268 Glucose-6-phosphate dehydrogenase (G6PD) mutations in Cambodia: G6PD Viangchan (871G>A) is the most common variant in the Cambodian population. Matsuoka H et al. 2005 Journal of human genetics
16155737 G6PD Viangchan (871G>A) is the most common G6PD-deficient variant in the Cambodian population. Louicharoen C et al. 2005 Journal of human genetics
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
25536053 Characterization of G6PD genotypes and phenotypes on the northwestern Thailand-Myanmar border. Bancone G et al. 2014 PloS one
25775246 Large cohort screening of G6PD deficiency and the mutational spectrum in the Dongguan District in Southern China. Peng Q et al. 2015 PloS one
26226515 Prevalence and Molecular Characterization of Glucose-6-Phosphate Dehydrogenase Deficiency at the China-Myanmar Border. Li Q et al. 2015 PloS one
27053284 Detailed functional analysis of two clinical glucose-6-phosphate dehydrogenase (G6PD) variants, G6PDViangchan and G6PDViangchan+Mahidol: Decreased stability and catalytic efficiency contribute to the clinical phenotype. Boonyuen U et al. 2016 Molecular genetics and metabolism
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.post825+45319f0