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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.

rs137852912

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:55057454 (GRCh38.p13) 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 / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000023 (6/264690, TOPMED)
A=0.000072 (18/251144, GnomAD_exome)
A=0.000036 (5/140266, GnomAD) (+ 4 more)
A=0.000084 (10/119070, ExAC)
A=0.00000 (0/14050, ALFA)
G=0.5 (1/2, Siberian)
A=0.5 (1/2, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PCSK9 : Missense Variant
Publications
7 citations
Genomic View
See rs on genome
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.p13 chr 1 NC_000001.11:g.55057454G>A
GRCh38.p13 chr 1 NC_000001.11:g.55057454G>C
GRCh38.p13 chr 1 NC_000001.11:g.55057454G>T
GRCh37.p13 chr 1 NC_000001.10:g.55523127G>A
GRCh37.p13 chr 1 NC_000001.10:g.55523127G>C
GRCh37.p13 chr 1 NC_000001.10:g.55523127G>T
PCSK9 RefSeqGene (LRG_275) NG_009061.1:g.22908G>A
PCSK9 RefSeqGene (LRG_275) NG_009061.1:g.22908G>C
PCSK9 RefSeqGene (LRG_275) NG_009061.1:g.22908G>T
Gene: PCSK9, proprotein convertase subtilisin/kexin type 9 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PCSK9 transcript variant 1 NM_174936.4:c.1120G>A D [GAC] > N [AAC] Coding Sequence Variant
proprotein convertase subtilisin/kexin type 9 preproprotein NP_777596.2:p.Asp374Asn D (Asp) > N (Asn) Missense Variant
PCSK9 transcript variant 1 NM_174936.4:c.1120G>C D [GAC] > H [CAC] Coding Sequence Variant
proprotein convertase subtilisin/kexin type 9 preproprotein NP_777596.2:p.Asp374His D (Asp) > H (His) Missense Variant
PCSK9 transcript variant 1 NM_174936.4:c.1120G>T D [GAC] > Y [TAC] Coding Sequence Variant
proprotein convertase subtilisin/kexin type 9 preproprotein NP_777596.2:p.Asp374Tyr D (Asp) > Y (Tyr) Missense Variant
PCSK9 transcript variant 2 NR_110451.2:n.779G>A N/A Non Coding Transcript Variant
PCSK9 transcript variant 2 NR_110451.2:n.779G>C N/A Non Coding Transcript Variant
PCSK9 transcript variant 2 NR_110451.2:n.779G>T N/A Non Coding Transcript 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: A (allele ID: 907408 )
ClinVar Accession Disease Names Clinical Significance
RCV001182496.1 Familial hypercholesterolemia Uncertain-Significance
Allele: C (allele ID: 260615 )
ClinVar Accession Disease Names Clinical Significance
RCV000256334.1 Familial hypercholesterolemia 1 Pathogenic
Allele: T (allele ID: 17914 )
ClinVar Accession Disease Names Clinical Significance
RCV000003009.5 Familial hypercholesterolemia 3 Pathogenic
RCV000505195.3 Familial hypercholesterolemia 1 Pathogenic-Likely-Pathogenic

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 14050 G=1.00000 A=0.00000
European Sub 9690 G=1.0000 A=0.0000
African Sub 2898 G=1.0000 A=0.0000
African Others Sub 114 G=1.000 A=0.000
African American Sub 2784 G=1.0000 A=0.0000
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 496 G=1.000 A=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
TopMed Global Study-wide 264690 G=0.999977 A=0.000023
gnomAD - Exomes Global Study-wide 251144 G=0.999928 A=0.000072
gnomAD - Exomes European Sub 135144 G=0.999941 A=0.000059
gnomAD - Exomes Asian Sub 48996 G=0.99988 A=0.00012
gnomAD - Exomes American Sub 34562 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 16238 G=0.99988 A=0.00012
gnomAD - Exomes Ashkenazi Jewish Sub 10072 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6132 G=0.9997 A=0.0003
gnomAD - Genomes Global Study-wide 140266 G=0.999964 A=0.000036
gnomAD - Genomes European Sub 75948 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 42048 G=0.99990 A=0.00010
gnomAD - Genomes American Sub 13664 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=0.9997 A=0.0003
gnomAD - Genomes Other Sub 2152 G=1.0000 A=0.0000
ExAC Global Study-wide 119070 G=0.999916 A=0.000084
ExAC Europe Sub 71908 G=0.99990 A=0.00010
ExAC Asian Sub 24710 G=0.99992 A=0.00008
ExAC American Sub 11380 G=1.00000 A=0.00000
ExAC African Sub 10184 G=0.99990 A=0.00010
ExAC Other Sub 888 G=1.000 A=0.000
Siberian Global Study-wide 2 G=0.5 A=0.5
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 T
GRCh38.p13 chr 1 NC_000001.11:g.55057454= NC_000001.11:g.55057454G>A NC_000001.11:g.55057454G>C NC_000001.11:g.55057454G>T
GRCh37.p13 chr 1 NC_000001.10:g.55523127= NC_000001.10:g.55523127G>A NC_000001.10:g.55523127G>C NC_000001.10:g.55523127G>T
PCSK9 RefSeqGene (LRG_275) NG_009061.1:g.22908= NG_009061.1:g.22908G>A NG_009061.1:g.22908G>C NG_009061.1:g.22908G>T
PCSK9 transcript variant 1 NM_174936.4:c.1120= NM_174936.4:c.1120G>A NM_174936.4:c.1120G>C NM_174936.4:c.1120G>T
PCSK9 transcript variant 1 NM_174936.3:c.1120= NM_174936.3:c.1120G>A NM_174936.3:c.1120G>C NM_174936.3:c.1120G>T
PCSK9 transcript variant 2 NR_110451.2:n.779= NR_110451.2:n.779G>A NR_110451.2:n.779G>C NR_110451.2:n.779G>T
PCSK9 transcript variant 2 NR_110451.1:n.779= NR_110451.1:n.779G>A NR_110451.1:n.779G>C NR_110451.1:n.779G>T
proprotein convertase subtilisin/kexin type 9 preproprotein NP_777596.2:p.Asp374= NP_777596.2:p.Asp374Asn NP_777596.2:p.Asp374His NP_777596.2:p.Asp374Tyr
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#.

16 SubSNP, 6 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss290490005 Jan 19, 2011 (133)
2 NHLBI-ESP ss341966526 May 09, 2011 (134)
3 EVA_EXAC ss1685565295 Apr 01, 2015 (144)
4 ILLUMINA ss1958273572 Feb 12, 2016 (147)
5 CLINVAR ss2137496136 Feb 23, 2017 (149)
6 USC_VALOUEV ss2147714892 Dec 20, 2016 (150)
7 HUMAN_LONGEVITY ss2162511486 Dec 20, 2016 (150)
8 GNOMAD ss2731525341 Nov 08, 2017 (151)
9 GNOMAD ss2746339899 Nov 08, 2017 (151)
10 GNOMAD ss2755161880 Nov 08, 2017 (151)
11 SWEGEN ss2986819098 Nov 08, 2017 (151)
12 ILLUMINA ss3021088351 Nov 08, 2017 (151)
13 TOPMED ss3076675998 Nov 08, 2017 (151)
14 ILLUMINA ss3651414807 Oct 11, 2018 (152)
15 EVA ss3823615351 Apr 25, 2020 (154)
16 TOPMED ss4449769439 Apr 25, 2021 (155)
17 ExAC NC_000001.10 - 55523127 Oct 11, 2018 (152)
18 gnomAD - Genomes NC_000001.11 - 55057454 Apr 25, 2021 (155)
19 gnomAD - Exomes NC_000001.10 - 55523127 Jul 12, 2019 (153)
20 Siberian NC_000001.10 - 55523127 Apr 25, 2020 (154)
21 TopMed NC_000001.11 - 55057454 Apr 25, 2021 (155)
22 ALFA NC_000001.11 - 55057454 Apr 25, 2021 (155)
23 ClinVar RCV000003009.5 Apr 25, 2021 (155)
24 ClinVar RCV000256334.1 Oct 11, 2018 (152)
25 ClinVar RCV000505195.3 Oct 11, 2018 (152)
26 ClinVar RCV001182496.1 Apr 25, 2021 (155)
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
4763364, 543887, 231246, ss341966526, ss1685565295, ss2147714892, ss2731525341, ss2746339899, ss2755161880, ss2986819098, ss3823615351 NC_000001.10:55523126:G:A NC_000001.11:55057453:G:A (self)
RCV001182496.1, 11423990, 8418425, 13375774, 6646718719, ss2162511486, ss3076675998, ss4449769439 NC_000001.11:55057453:G:A NC_000001.11:55057453:G:A (self)
RCV000256334.1, ss2137496136 NC_000001.11:55057453:G:C NC_000001.11:55057453:G:C (self)
ss1958273572, ss3021088351, ss3651414807 NC_000001.10:55523126:G:T NC_000001.11:55057453:G:T (self)
RCV000003009.5, RCV000505195.3, ss290490005 NC_000001.11:55057453:G:T NC_000001.11:55057453:G:T (self)
Help

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

7 citations for rs137852912
PMID Title Author Year Journal
10205269 A third major locus for autosomal dominant hypercholesterolemia maps to 1p34.1-p32. Varret M et al. 1999 American journal of human genetics
10764678 Genetic localization to chromosome 1p32 of the third locus for familial hypercholesterolemia in a Utah kindred. Hunt SC et al. 2000 Arteriosclerosis, thrombosis, and vascular biology
14727179 A mutation in PCSK9 causing autosomal-dominant hypercholesterolemia in a Utah pedigree. Timms KM et al. 2004 Human genetics
15772090 Evidence for effect of mutant PCSK9 on apolipoprotein B secretion as the cause of unusually severe dominant hypercholesterolaemia. Sun XM et al. 2005 Human molecular genetics
18250299 Molecular basis for LDL receptor recognition by PCSK9. Kwon HJ et al. 2008 Proceedings of the National Academy of Sciences of the United States of America
19081568 Degradation of LDLR protein mediated by 'gain of function' PCSK9 mutants in normal and ARH cells. Fasano T et al. 2009 Atherosclerosis
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
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.post596+ae089ad