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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.

rs1460753925

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:220631035 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000011 (3/264690, TOPMED)
A=0.000004 (1/249610, GnomAD_exome)
A=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MARK1 : Missense Variant
Publications
0 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 29982 C=0.99997 A=0.00003 0.999933 0.0 6.7e-05 0
European Sub 19404 C=1.00000 A=0.00000 1.0 0.0 0.0 N/A
African Sub 7706 C=0.9999 A=0.0001 0.99974 0.0 0.00026 0
African Others Sub 298 C=1.000 A=0.000 1.0 0.0 0.0 N/A
African American Sub 7408 C=0.9999 A=0.0001 0.99973 0.0 0.00027 0
Asian Sub 112 C=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 C=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 C=1.00 A=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 C=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 C=1.000 A=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 C=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 1906 C=1.0000 A=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=0.999989 A=0.000011
gnomAD - Exomes Global Study-wide 249610 C=0.999996 A=0.000004
gnomAD - Exomes European Sub 134384 C=0.999993 A=0.000007
gnomAD - Exomes Asian Sub 48718 C=1.00000 A=0.00000
gnomAD - Exomes American Sub 34234 C=1.00000 A=0.00000
gnomAD - Exomes African Sub 16202 C=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10004 C=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6068 C=1.0000 A=0.0000
Allele Frequency Aggregator Total Global 14050 C=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 9690 C=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2898 C=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 A=0.000
Allele Frequency Aggregator Other Sub 496 C=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 A=0.00
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 1 NC_000001.11:g.220631035C>A
GRCh37.p13 chr 1 NC_000001.10:g.220804377C>A
Gene: MARK1, microtubule affinity regulating kinase 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MARK1 transcript variant 5 NM_001286129.2:c. N/A Genic Downstream Transcript Variant
MARK1 transcript variant 2 NM_018650.5:c.910C>A Q [CAA] > K [AAA] Coding Sequence Variant
serine/threonine-protein kinase MARK1 isoform 2 NP_061120.3:p.Gln304Lys Q (Gln) > K (Lys) Missense Variant
MARK1 transcript variant 4 NM_001286128.2:c.844C>A Q [CAA] > K [AAA] Coding Sequence Variant
serine/threonine-protein kinase MARK1 isoform 4 NP_001273057.1:p.Gln282Lys Q (Gln) > K (Lys) Missense Variant
MARK1 transcript variant 3 NM_001286126.2:c.910C>A Q [CAA] > K [AAA] Coding Sequence Variant
serine/threonine-protein kinase MARK1 isoform 3 NP_001273055.1:p.Gln304Lys Q (Gln) > K (Lys) Missense Variant
MARK1 transcript variant 1 NM_001286124.2:c.910C>A Q [CAA] > K [AAA] Coding Sequence Variant
serine/threonine-protein kinase MARK1 isoform 1 NP_001273053.1:p.Gln304Lys Q (Gln) > K (Lys) Missense Variant
MARK1 transcript variant X7 XM_024447090.2:c. N/A Genic Downstream Transcript Variant
MARK1 transcript variant X1 XM_011509561.4:c.886C>A Q [CAA] > K [AAA] Coding Sequence Variant
serine/threonine-protein kinase MARK1 isoform X1 XP_011507863.1:p.Gln296Lys Q (Gln) > K (Lys) Missense Variant
MARK1 transcript variant X2 XM_047420844.1:c.886C>A Q [CAA] > K [AAA] Coding Sequence Variant
serine/threonine-protein kinase MARK1 isoform X2 XP_047276800.1:p.Gln296Lys Q (Gln) > K (Lys) Missense Variant
MARK1 transcript variant X3 XM_005273134.6:c.910C>A Q [CAA] > K [AAA] Coding Sequence Variant
serine/threonine-protein kinase MARK1 isoform X3 XP_005273191.1:p.Gln304Lys Q (Gln) > K (Lys) Missense Variant
MARK1 transcript variant X4 XM_006711326.5:c.646C>A Q [CAA] > K [AAA] Coding Sequence Variant
serine/threonine-protein kinase MARK1 isoform X4 XP_006711389.1:p.Gln216Lys Q (Gln) > K (Lys) Missense Variant
MARK1 transcript variant X5 XM_017001305.3:c.580C>A Q [CAA] > K [AAA] Coding Sequence Variant
serine/threonine-protein kinase MARK1 isoform X5 XP_016856794.1:p.Gln194Lys Q (Gln) > K (Lys) Missense Variant
MARK1 transcript variant X6 XM_011509562.4:c.580C>A Q [CAA] > K [AAA] Coding Sequence Variant
serine/threonine-protein kinase MARK1 isoform X5 XP_011507864.1:p.Gln194Lys Q (Gln) > K (Lys) 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.

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 C= A
GRCh38.p14 chr 1 NC_000001.11:g.220631035= NC_000001.11:g.220631035C>A
GRCh37.p13 chr 1 NC_000001.10:g.220804377= NC_000001.10:g.220804377C>A
MARK1 transcript variant X3 XM_005273134.6:c.910= XM_005273134.6:c.910C>A
MARK1 transcript variant X2 XM_005273134.5:c.910= XM_005273134.5:c.910C>A
MARK1 transcript variant X2 XM_005273134.4:c.910= XM_005273134.4:c.910C>A
MARK1 transcript variant X2 XM_005273134.3:c.910= XM_005273134.3:c.910C>A
MARK1 transcript variant X2 XM_005273134.2:c.910= XM_005273134.2:c.910C>A
MARK1 transcript variant X2 XM_005273134.1:c.910= XM_005273134.1:c.910C>A
MARK1 transcript variant 2 NM_018650.5:c.910= NM_018650.5:c.910C>A
MARK1 transcript variant 2 NM_018650.4:c.910= NM_018650.4:c.910C>A
MARK1 transcript NM_018650.3:c.910= NM_018650.3:c.910C>A
MARK1 transcript variant X4 XM_006711326.5:c.646= XM_006711326.5:c.646C>A
MARK1 transcript variant X3 XM_006711326.4:c.646= XM_006711326.4:c.646C>A
MARK1 transcript variant X3 XM_006711326.3:c.646= XM_006711326.3:c.646C>A
MARK1 transcript variant X3 XM_006711326.2:c.646= XM_006711326.2:c.646C>A
MARK1 transcript variant X3 XM_006711326.1:c.646= XM_006711326.1:c.646C>A
MARK1 transcript variant X1 XM_011509561.4:c.886= XM_011509561.4:c.886C>A
MARK1 transcript variant X1 XM_011509561.3:c.886= XM_011509561.3:c.886C>A
MARK1 transcript variant X1 XM_011509561.2:c.886= XM_011509561.2:c.886C>A
MARK1 transcript variant X1 XM_011509561.1:c.886= XM_011509561.1:c.886C>A
MARK1 transcript variant X6 XM_011509562.4:c.580= XM_011509562.4:c.580C>A
MARK1 transcript variant X5 XM_011509562.3:c.580= XM_011509562.3:c.580C>A
MARK1 transcript variant X5 XM_011509562.2:c.580= XM_011509562.2:c.580C>A
MARK1 transcript variant X4 XM_011509562.1:c.580= XM_011509562.1:c.580C>A
MARK1 transcript variant X5 XM_017001305.3:c.580= XM_017001305.3:c.580C>A
MARK1 transcript variant X4 XM_017001305.2:c.580= XM_017001305.2:c.580C>A
MARK1 transcript variant X4 XM_017001305.1:c.580= XM_017001305.1:c.580C>A
MARK1 transcript variant 1 NM_001286124.2:c.910= NM_001286124.2:c.910C>A
MARK1 transcript variant 1 NM_001286124.1:c.910= NM_001286124.1:c.910C>A
MARK1 transcript variant 3 NM_001286126.2:c.910= NM_001286126.2:c.910C>A
MARK1 transcript variant 3 NM_001286126.1:c.910= NM_001286126.1:c.910C>A
MARK1 transcript variant 4 NM_001286128.2:c.844= NM_001286128.2:c.844C>A
MARK1 transcript variant 4 NM_001286128.1:c.844= NM_001286128.1:c.844C>A
MARK1 transcript variant X2 XM_047420844.1:c.886= XM_047420844.1:c.886C>A
serine/threonine-protein kinase MARK1 isoform X3 XP_005273191.1:p.Gln304= XP_005273191.1:p.Gln304Lys
serine/threonine-protein kinase MARK1 isoform 2 NP_061120.3:p.Gln304= NP_061120.3:p.Gln304Lys
serine/threonine-protein kinase MARK1 isoform X4 XP_006711389.1:p.Gln216= XP_006711389.1:p.Gln216Lys
serine/threonine-protein kinase MARK1 isoform X1 XP_011507863.1:p.Gln296= XP_011507863.1:p.Gln296Lys
serine/threonine-protein kinase MARK1 isoform X5 XP_011507864.1:p.Gln194= XP_011507864.1:p.Gln194Lys
serine/threonine-protein kinase MARK1 isoform X5 XP_016856794.1:p.Gln194= XP_016856794.1:p.Gln194Lys
serine/threonine-protein kinase MARK1 isoform 1 NP_001273053.1:p.Gln304= NP_001273053.1:p.Gln304Lys
serine/threonine-protein kinase MARK1 isoform 3 NP_001273055.1:p.Gln304= NP_001273055.1:p.Gln304Lys
serine/threonine-protein kinase MARK1 isoform 4 NP_001273057.1:p.Gln282= NP_001273057.1:p.Gln282Lys
serine/threonine-protein kinase MARK1 isoform X2 XP_047276800.1:p.Gln296= XP_047276800.1:p.Gln296Lys
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#.

2 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2732288841 Nov 08, 2017 (151)
2 TOPMED ss4484519380 Apr 25, 2021 (155)
3 gnomAD - Exomes NC_000001.10 - 220804377 Jul 12, 2019 (153)
4 TopMed NC_000001.11 - 220631035 Apr 25, 2021 (155)
5 ALFA NC_000001.11 - 220631035 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
1325089, ss2732288841 NC_000001.10:220804376:C:A NC_000001.11:220631034:C:A (self)
48125715, 631837276, ss4484519380 NC_000001.11:220631034:C:A NC_000001.11:220631034:C:A (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 rs1460753925

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