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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.

rs1488559078

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:184694527 (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
A>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000004 (1/250328, GnomAD_exome)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PRIMPOL : Missense Variant
CENPU : Non Coding Transcript Variant
Publications
0 citations
Genomic View
See rs on genome
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").

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Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 250328 A=0.999996 C=0.000004
gnomAD - Exomes European Sub 134950 A=1.000000 C=0.000000
gnomAD - Exomes Asian Sub 48950 A=1.00000 C=0.00000
gnomAD - Exomes American Sub 34414 A=1.00000 C=0.00000
gnomAD - Exomes African Sub 15906 A=1.00000 C=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10026 A=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6082 A=0.9998 C=0.0002
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 4 NC_000004.12:g.184694527A>C
GRCh37.p13 chr 4 NC_000004.11:g.185615681A>C
PRIMPOL RefSeqGene NG_051582.1:g.49915A>C
Gene: CENPU, centromere protein U (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CENPU transcript variant 1 NM_024629.4:c.*761= N/A 3 Prime UTR Variant
CENPU transcript variant 2 NR_104593.2:n.1990T>G N/A Non Coding Transcript Variant
CENPU transcript variant X1 XM_005263218.5:c.*761= N/A 3 Prime UTR Variant
CENPU transcript variant X2 XM_047416162.1:c.*761= N/A 3 Prime UTR Variant
CENPU transcript variant X3 XM_047416163.1:c. N/A Genic Downstream Transcript Variant
CENPU transcript variant X4 XR_007057963.1:n. N/A Genic Downstream Transcript Variant
Gene: PRIMPOL, primase and DNA directed polymerase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PRIMPOL transcript variant 1 NM_152683.4:c.1431A>C E [GAA] > D [GAC] Coding Sequence Variant
DNA-directed primase/polymerase protein isoform 1 NP_689896.1:p.Glu477Asp E (Glu) > D (Asp) Missense Variant
PRIMPOL transcript variant 6 NM_001345893.2:c.1467A>C E [GAA] > D [GAC] Coding Sequence Variant
DNA-directed primase/polymerase protein isoform 5 NP_001332822.1:p.Glu489Asp E (Glu) > D (Asp) Missense Variant
PRIMPOL transcript variant 4 NM_001345891.2:c.1470A>C E [GAA] > D [GAC] Coding Sequence Variant
DNA-directed primase/polymerase protein isoform 4 NP_001332820.1:p.Glu490Asp E (Glu) > D (Asp) Missense Variant
PRIMPOL transcript variant 9 NM_001345895.2:c.1431A>C E [GAA] > D [GAC] Coding Sequence Variant
DNA-directed primase/polymerase protein isoform 1 NP_001332824.1:p.Glu477Asp E (Glu) > D (Asp) Missense Variant
PRIMPOL transcript variant 8 NM_001345894.2:c.774A>C E [GAA] > D [GAC] Coding Sequence Variant
DNA-directed primase/polymerase protein isoform 6 NP_001332823.1:p.Glu258Asp E (Glu) > D (Asp) Missense Variant
PRIMPOL transcript variant 2 NM_001300767.2:c.1044A>C E [GAA] > D [GAC] Coding Sequence Variant
DNA-directed primase/polymerase protein isoform 2 NP_001287696.1:p.Glu348Asp E (Glu) > D (Asp) Missense Variant
PRIMPOL transcript variant 11 NM_001345897.2:c.735A>C E [GAA] > D [GAC] Coding Sequence Variant
DNA-directed primase/polymerase protein isoform 7 NP_001332826.1:p.Glu245Asp E (Glu) > D (Asp) Missense Variant
PRIMPOL transcript variant 10 NM_001345896.2:c.1428A>C E [GAA] > D [GAC] Coding Sequence Variant
DNA-directed primase/polymerase protein isoform 3 NP_001332825.1:p.Glu476Asp E (Glu) > D (Asp) Missense Variant
PRIMPOL transcript variant 5 NM_001345892.2:c.1467A>C E [GAA] > D [GAC] Coding Sequence Variant
DNA-directed primase/polymerase protein isoform 5 NP_001332821.1:p.Glu489Asp E (Glu) > D (Asp) Missense Variant
PRIMPOL transcript variant 17 NM_001345901.2:c.735A>C E [GAA] > D [GAC] Coding Sequence Variant
DNA-directed primase/polymerase protein isoform 7 NP_001332830.1:p.Glu245Asp E (Glu) > D (Asp) Missense Variant
PRIMPOL transcript variant 3 NM_001300768.2:c.1428A>C E [GAA] > D [GAC] Coding Sequence Variant
DNA-directed primase/polymerase protein isoform 3 NP_001287697.1:p.Glu476Asp E (Glu) > D (Asp) Missense Variant
PRIMPOL transcript variant 15 NM_001345899.2:c.1179A>C E [GAA] > D [GAC] Coding Sequence Variant
DNA-directed primase/polymerase protein isoform 9 NP_001332828.1:p.Glu393Asp E (Glu) > D (Asp) Missense Variant
PRIMPOL transcript variant 13 NM_001345898.2:c.732A>C E [GAA] > D [GAC] Coding Sequence Variant
DNA-directed primase/polymerase protein isoform 8 NP_001332827.1:p.Glu244Asp E (Glu) > D (Asp) Missense Variant
PRIMPOL transcript variant 16 NM_001345900.2:c.906A>C E [GAA] > D [GAC] Coding Sequence Variant
DNA-directed primase/polymerase protein isoform 10 NP_001332829.1:p.Glu302Asp E (Glu) > D (Asp) Missense Variant
PRIMPOL transcript variant 14 NR_144314.2:n.1573A>C N/A Non Coding Transcript Variant
PRIMPOL transcript variant 7 NR_144312.2:n.1897A>C N/A Non Coding Transcript Variant
PRIMPOL transcript variant 12 NR_144313.2:n.1647A>C N/A Non Coding Transcript Variant
PRIMPOL transcript variant X2 XM_017007867.3:c.*234= N/A 3 Prime UTR Variant
PRIMPOL transcript variant X8 XM_047449752.1:c. N/A Genic Downstream Transcript Variant
PRIMPOL transcript variant X9 XM_047449753.1:c. N/A Genic Downstream Transcript Variant
PRIMPOL transcript variant X1 XM_011531720.2:c.1470A>C E [GAA] > D [GAC] Coding Sequence Variant
DNA-directed primase/polymerase protein isoform X1 XP_011530022.1:p.Glu490Asp E (Glu) > D (Asp) Missense Variant
PRIMPOL transcript variant X4 XM_011531723.2:c.1083A>C E [GAA] > D [GAC] Coding Sequence Variant
DNA-directed primase/polymerase protein isoform X3 XP_011530025.1:p.Glu361Asp E (Glu) > D (Asp) Missense Variant
PRIMPOL transcript variant X5 XM_047449751.1:c.945A>C E [GAA] > D [GAC] Coding Sequence Variant
DNA-directed primase/polymerase protein isoform X4 XP_047305707.1:p.Glu315Asp E (Glu) > D (Asp) Missense Variant
PRIMPOL transcript variant X6 XM_011531726.4:c.945A>C E [GAA] > D [GAC] Coding Sequence Variant
DNA-directed primase/polymerase protein isoform X4 XP_011530028.1:p.Glu315Asp E (Glu) > D (Asp) Missense Variant
PRIMPOL transcript variant X7 XM_017007872.2:c.774A>C E [GAA] > D [GAC] Coding Sequence Variant
DNA-directed primase/polymerase protein isoform X5 XP_016863361.1:p.Glu258Asp E (Glu) > D (Asp) Missense Variant
PRIMPOL transcript variant X3 XR_938701.4:n.1939A>C 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.

Not Reported in ClinVar
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 A= C
GRCh38.p14 chr 4 NC_000004.12:g.184694527= NC_000004.12:g.184694527A>C
GRCh37.p13 chr 4 NC_000004.11:g.185615681= NC_000004.11:g.185615681A>C
PRIMPOL RefSeqGene NG_051582.1:g.49915= NG_051582.1:g.49915A>C
PRIMPOL transcript variant 1 NM_152683.4:c.1431= NM_152683.4:c.1431A>C
PRIMPOL transcript variant 1 NM_152683.3:c.1431= NM_152683.3:c.1431A>C
PRIMPOL transcript NM_152683.2:c.1431= NM_152683.2:c.1431A>C
PRIMPOL transcript variant 7 NR_144312.2:n.1897= NR_144312.2:n.1897A>C
PRIMPOL transcript variant 7 NR_144312.1:n.2022= NR_144312.1:n.2022A>C
PRIMPOL transcript variant 4 NM_001345891.2:c.1470= NM_001345891.2:c.1470A>C
PRIMPOL transcript variant 4 NM_001345891.1:c.1470= NM_001345891.1:c.1470A>C
PRIMPOL transcript variant 6 NM_001345893.2:c.1467= NM_001345893.2:c.1467A>C
PRIMPOL transcript variant 6 NM_001345893.1:c.1467= NM_001345893.1:c.1467A>C
PRIMPOL transcript variant 5 NM_001345892.2:c.1467= NM_001345892.2:c.1467A>C
PRIMPOL transcript variant 5 NM_001345892.1:c.1467= NM_001345892.1:c.1467A>C
PRIMPOL transcript variant 9 NM_001345895.2:c.1431= NM_001345895.2:c.1431A>C
PRIMPOL transcript variant 9 NM_001345895.1:c.1431= NM_001345895.1:c.1431A>C
PRIMPOL transcript variant 3 NM_001300768.2:c.1428= NM_001300768.2:c.1428A>C
PRIMPOL transcript variant 3 NM_001300768.1:c.1428= NM_001300768.1:c.1428A>C
PRIMPOL transcript variant 10 NM_001345896.2:c.1428= NM_001345896.2:c.1428A>C
PRIMPOL transcript variant 10 NM_001345896.1:c.1428= NM_001345896.1:c.1428A>C
PRIMPOL transcript variant 8 NM_001345894.2:c.774= NM_001345894.2:c.774A>C
PRIMPOL transcript variant 8 NM_001345894.1:c.774= NM_001345894.1:c.774A>C
PRIMPOL transcript variant 12 NR_144313.2:n.1647= NR_144313.2:n.1647A>C
PRIMPOL transcript variant 12 NR_144313.1:n.1772= NR_144313.1:n.1772A>C
PRIMPOL transcript variant 11 NM_001345897.2:c.735= NM_001345897.2:c.735A>C
PRIMPOL transcript variant 11 NM_001345897.1:c.735= NM_001345897.1:c.735A>C
PRIMPOL transcript variant 13 NM_001345898.2:c.732= NM_001345898.2:c.732A>C
PRIMPOL transcript variant 13 NM_001345898.1:c.732= NM_001345898.1:c.732A>C
PRIMPOL transcript variant 14 NR_144314.2:n.1573= NR_144314.2:n.1573A>C
PRIMPOL transcript variant 14 NR_144314.1:n.1698= NR_144314.1:n.1698A>C
PRIMPOL transcript variant 2 NM_001300767.2:c.1044= NM_001300767.2:c.1044A>C
PRIMPOL transcript variant 2 NM_001300767.1:c.1044= NM_001300767.1:c.1044A>C
PRIMPOL transcript variant 15 NM_001345899.2:c.1179= NM_001345899.2:c.1179A>C
PRIMPOL transcript variant 15 NM_001345899.1:c.1179= NM_001345899.1:c.1179A>C
PRIMPOL transcript variant 16 NM_001345900.2:c.906= NM_001345900.2:c.906A>C
PRIMPOL transcript variant 16 NM_001345900.1:c.906= NM_001345900.1:c.906A>C
PRIMPOL transcript variant 17 NM_001345901.2:c.735= NM_001345901.2:c.735A>C
PRIMPOL transcript variant 17 NM_001345901.1:c.735= NM_001345901.1:c.735A>C
CENPU transcript variant X1 XM_005263218.5:c.*761= XM_005263218.5:c.*761T>G
CENPU transcript variant X1 XM_005263218.4:c.*761= XM_005263218.4:c.*761T>G
CENPU transcript variant X1 XM_005263218.3:c.*761= XM_005263218.3:c.*761T>G
CENPU transcript variant X1 XM_005263218.2:c.*761= XM_005263218.2:c.*761T>G
CENPU transcript variant 1 NM_024629.4:c.*761= NM_024629.4:c.*761T>G
CENPU transcript variant 1 NM_024629.3:c.*761= NM_024629.3:c.*761T>G
PRIMPOL transcript variant X3 XR_938701.4:n.1939= XR_938701.4:n.1939A>C
PRIMPOL transcript variant X3 XR_938701.3:n.1952= XR_938701.3:n.1952A>C
PRIMPOL transcript variant X8 XR_938701.2:n.1941= XR_938701.2:n.1941A>C
PRIMPOL transcript variant X5 XR_938701.1:n.1941= XR_938701.1:n.1941A>C
PRIMPOL transcript variant X6 XM_011531726.4:c.945= XM_011531726.4:c.945A>C
PRIMPOL transcript variant X13 XM_011531726.3:c.945= XM_011531726.3:c.945A>C
PRIMPOL transcript variant X16 XM_011531726.2:c.945= XM_011531726.2:c.945A>C
PRIMPOL transcript variant X9 XM_011531726.1:c.945= XM_011531726.1:c.945A>C
PRIMPOL transcript variant X2 XM_017007867.3:c.*234= XM_017007867.3:c.*234A>C
PRIMPOL transcript variant X2 XM_017007867.2:c.*234= XM_017007867.2:c.*234A>C
PRIMPOL transcript variant X7 XM_017007867.1:c.*234= XM_017007867.1:c.*234A>C
CENPU transcript variant 2 NR_104593.2:n.1990= NR_104593.2:n.1990T>G
CENPU transcript variant 2 NR_104593.1:n.2026= NR_104593.1:n.2026T>G
PRIMPOL transcript variant X1 XM_011531720.2:c.1470= XM_011531720.2:c.1470A>C
PRIMPOL transcript variant X1 XM_011531720.1:c.1470= XM_011531720.1:c.1470A>C
PRIMPOL transcript variant X4 XM_011531723.2:c.1083= XM_011531723.2:c.1083A>C
PRIMPOL transcript variant X9 XM_011531723.1:c.1083= XM_011531723.1:c.1083A>C
PRIMPOL transcript variant X7 XM_017007872.2:c.774= XM_017007872.2:c.774A>C
PRIMPOL transcript variant X18 XM_017007872.1:c.774= XM_017007872.1:c.774A>C
CENPU transcript variant X2 XM_047416162.1:c.*761= XM_047416162.1:c.*761T>G
PRIMPOL transcript variant X5 XM_047449751.1:c.945= XM_047449751.1:c.945A>C
DNA-directed primase/polymerase protein isoform 1 NP_689896.1:p.Glu477= NP_689896.1:p.Glu477Asp
DNA-directed primase/polymerase protein isoform 4 NP_001332820.1:p.Glu490= NP_001332820.1:p.Glu490Asp
DNA-directed primase/polymerase protein isoform 5 NP_001332822.1:p.Glu489= NP_001332822.1:p.Glu489Asp
DNA-directed primase/polymerase protein isoform 5 NP_001332821.1:p.Glu489= NP_001332821.1:p.Glu489Asp
DNA-directed primase/polymerase protein isoform 1 NP_001332824.1:p.Glu477= NP_001332824.1:p.Glu477Asp
DNA-directed primase/polymerase protein isoform 3 NP_001287697.1:p.Glu476= NP_001287697.1:p.Glu476Asp
DNA-directed primase/polymerase protein isoform 3 NP_001332825.1:p.Glu476= NP_001332825.1:p.Glu476Asp
DNA-directed primase/polymerase protein isoform 6 NP_001332823.1:p.Glu258= NP_001332823.1:p.Glu258Asp
DNA-directed primase/polymerase protein isoform 7 NP_001332826.1:p.Glu245= NP_001332826.1:p.Glu245Asp
DNA-directed primase/polymerase protein isoform 8 NP_001332827.1:p.Glu244= NP_001332827.1:p.Glu244Asp
DNA-directed primase/polymerase protein isoform 2 NP_001287696.1:p.Glu348= NP_001287696.1:p.Glu348Asp
DNA-directed primase/polymerase protein isoform 9 NP_001332828.1:p.Glu393= NP_001332828.1:p.Glu393Asp
DNA-directed primase/polymerase protein isoform 10 NP_001332829.1:p.Glu302= NP_001332829.1:p.Glu302Asp
DNA-directed primase/polymerase protein isoform 7 NP_001332830.1:p.Glu245= NP_001332830.1:p.Glu245Asp
DNA-directed primase/polymerase protein isoform X4 XP_011530028.1:p.Glu315= XP_011530028.1:p.Glu315Asp
DNA-directed primase/polymerase protein isoform X1 XP_011530022.1:p.Glu490= XP_011530022.1:p.Glu490Asp
DNA-directed primase/polymerase protein isoform X3 XP_011530025.1:p.Glu361= XP_011530025.1:p.Glu361Asp
DNA-directed primase/polymerase protein isoform X5 XP_016863361.1:p.Glu258= XP_016863361.1:p.Glu258Asp
DNA-directed primase/polymerase protein isoform X4 XP_047305707.1:p.Glu315= XP_047305707.1:p.Glu315Asp
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#.

1 SubSNP, 1 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2734845583 Nov 08, 2017 (151)
2 gnomAD - Exomes NC_000004.11 - 185615681 Jul 13, 2019 (153)
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
3958976, ss2734845583 NC_000004.11:185615680:A:C NC_000004.12:184694526:A:C (self)
Help

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

No publications for rs1488559078

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.post820+afb47a3d