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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs45487699

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr10:86681680 (GRCh38.p7) 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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00066 (161/245636, GnomAD)
T=0.00056 (70/125568, TOPMED)
T=0.00057 (68/119136, ExAC) (+ 4 more)
T=0.0004 (13/30946, GnomAD)
T=0.001 (3/5008, 1000G)
T=0.002 (6/3854, ALSPAC)
T=0.001 (4/3708, TWINSUK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
LDB3 : Missense Variant
Publications
8 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.p7 chr 10 NC_000010.11:g.86681680C>T
GRCh37.p13 chr 10 NC_000010.10:g.88441437C>T
LDB3 RefSeqGene (LRG_385) NG_008876.1:g.18117C>T
Gene: LDB3, LIM domain binding 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LDB3 transcript variant 2 NM_001080114.1:c. N/A Intron Variant
LDB3 transcript variant 4 NM_001080116.1:c. N/A Intron Variant
LDB3 transcript variant 1 NM_007078.2:c.566C>T S [TCG] > L [TTG] Coding Sequence Variant
LIM domain-binding protein 3 isoform 1 NP_009009.1:p.Ser...

NP_009009.1:p.Ser189Leu

S (Ser) > L (Leu) Missense Variant
LDB3 transcript variant 3 NM_001080115.1:c....

NM_001080115.1:c.566C>T

S [TCG] > L [TTG] Coding Sequence Variant
LIM domain-binding protein 3 isoform 3 NP_001073584.1:p....

NP_001073584.1:p.Ser189Leu

S (Ser) > L (Leu) Missense Variant
LDB3 transcript variant 5 NM_001171610.1:c....

NM_001171610.1:c.566C>T

S [TCG] > L [TTG] Coding Sequence Variant
LIM domain-binding protein 3 isoform 5 NP_001165081.1:p....

NP_001165081.1:p.Ser189Leu

S (Ser) > L (Leu) Missense Variant
LDB3 transcript variant 6 NM_001171611.1:c....

NM_001171611.1:c.566C>T

S [TCG] > L [TTG] Coding Sequence Variant
LIM domain-binding protein 3 isoform 6 NP_001165082.1:p....

NP_001165082.1:p.Ser189Leu

S (Ser) > L (Leu) Missense Variant
LDB3 transcript variant X9 XM_011539189.1:c. N/A Intron Variant
LDB3 transcript variant X9 XM_011539190.1:c. N/A Intron Variant
LDB3 transcript variant X12 XM_011539191.2:c. N/A Intron Variant
LDB3 transcript variant X14 XM_011539193.1:c. N/A Intron Variant
LDB3 transcript variant X16 XM_011539194.1:c. N/A Intron Variant
LDB3 transcript variant X21 XM_017015609.1:c. N/A Intron Variant
LDB3 transcript variant X15 XM_017015607.1:c. N/A Genic Upstream Transcript Variant
LDB3 transcript variant X1 XM_011539184.2:c....

XM_011539184.2:c.566C>T

S [TCG] > L [TTG] Coding Sequence Variant
LIM domain-binding protein 3 isoform X1 XP_011537486.1:p....

XP_011537486.1:p.Ser189Leu

S (Ser) > L (Leu) Missense Variant
LDB3 transcript variant X2 XM_011539185.2:c....

XM_011539185.2:c.566C>T

S [TCG] > L [TTG] Coding Sequence Variant
LIM domain-binding protein 3 isoform X1 XP_011537487.1:p....

XP_011537487.1:p.Ser189Leu

S (Ser) > L (Leu) Missense Variant
LDB3 transcript variant X3 XM_011539186.2:c....

XM_011539186.2:c.566C>T

S [TCG] > L [TTG] Coding Sequence Variant
LIM domain-binding protein 3 isoform X2 XP_011537488.1:p....

XP_011537488.1:p.Ser189Leu

S (Ser) > L (Leu) Missense Variant
LDB3 transcript variant X4 XM_011539187.2:c....

XM_011539187.2:c.566C>T

S [TCG] > L [TTG] Coding Sequence Variant
LIM domain-binding protein 3 isoform X3 XP_011537489.1:p....

XP_011537489.1:p.Ser189Leu

S (Ser) > L (Leu) Missense Variant
LDB3 transcript variant X5 XM_011539188.2:c....

XM_011539188.2:c.566C>T

S [TCG] > L [TTG] Coding Sequence Variant
LIM domain-binding protein 3 isoform X4 XP_011537490.1:p....

XP_011537490.1:p.Ser189Leu

S (Ser) > L (Leu) Missense Variant
LDB3 transcript variant X6 XM_017015606.1:c....

XM_017015606.1:c.566C>T

S [TCG] > L [TTG] Coding Sequence Variant
LIM domain-binding protein 3 isoform X4 XP_016871095.1:p....

XP_016871095.1:p.Ser189Leu

S (Ser) > L (Leu) Missense Variant
LDB3 transcript variant X7 XM_005269464.4:c....

XM_005269464.4:c.566C>T

S [TCG] > L [TTG] Coding Sequence Variant
LIM domain-binding protein 3 isoform X5 XP_005269521.1:p....

XP_005269521.1:p.Ser189Leu

S (Ser) > L (Leu) Missense Variant
LDB3 transcript variant X11 XM_005269466.4:c....

XM_005269466.4:c.566C>T

S [TCG] > L [TTG] Coding Sequence Variant
LIM domain-binding protein 3 isoform X8 XP_005269523.1:p....

XP_005269523.1:p.Ser189Leu

S (Ser) > L (Leu) Missense Variant
LDB3 transcript variant X17 XM_011539195.2:c....

XM_011539195.2:c.566C>T

S [TCG] > L [TTG] Coding Sequence Variant
LIM domain-binding protein 3 isoform X13 XP_011537497.1:p....

XP_011537497.1:p.Ser189Leu

S (Ser) > L (Leu) Missense Variant
LDB3 transcript variant X18 XM_005269468.4:c....

XM_005269468.4:c.566C>T

S [TCG] > L [TTG] Coding Sequence Variant
LIM domain-binding protein 3 isoform X14 XP_005269525.1:p....

XP_005269525.1:p.Ser189Leu

S (Ser) > L (Leu) Missense Variant
LDB3 transcript variant X19 XM_017015608.1:c....

XM_017015608.1:c.566C>T

S [TCG] > L [TTG] Coding Sequence Variant
LIM domain-binding protein 3 isoform X14 XP_016871097.1:p....

XP_016871097.1:p.Ser189Leu

S (Ser) > L (Leu) 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: 19770 )
ClinVar Accession Disease Names Clinical Significance
RCV000004996.3 Dilated cardiomyopathy 1C Pathogenic
RCV000038759.4 not specified Uncertain-Significance
RCV000170300.3 Familial hypertrophic cardiomyopathy 24 Pathogenic
RCV000172555.2 not provided Likely-Benign
RCV000234541.4 Myofibrillar myopathy, ZASP-related Uncertain-Significance
RCV000618756.1 Cardiovascular phenotype Uncertain-Significance
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
The Genome Aggregation Database Global Study-wide 245636 C=0.99934 T=0.00066
The Genome Aggregation Database European Sub 133530 C=0.99926 T=0.00074
The Genome Aggregation Database Asian Sub 48002 C=0.9994 T=0.0006
The Genome Aggregation Database American Sub 33576 C=0.9992 T=0.0008
The Genome Aggregation Database African Sub 15234 C=0.9999 T=0.0001
The Genome Aggregation Database Ashkenazi Jewish Sub 9826 C=1.000 T=0.000
The Genome Aggregation Database Other Sub 5468 C=0.999 T=0.001
Trans-Omics for Precision Medicine Global Study-wide 125568 C=0.99944 T=0.00056
The Exome Aggregation Consortium Global Study-wide 119136 C=0.99943 T=0.00057
The Exome Aggregation Consortium Europe Sub 71922 C=0.9993 T=0.0007
The Exome Aggregation Consortium Asian Sub 24966 C=0.9995 T=0.0005
The Exome Aggregation Consortium American Sub 11544 C=0.9994 T=0.0006
The Exome Aggregation Consortium African Sub 9814 C=1.000 T=0.000
The Exome Aggregation Consortium Other Sub 890 C=1.00 T=0.00
The Genome Aggregation Database Global Study-wide 30946 C=0.9996 T=0.0004
The Genome Aggregation Database European Sub 18474 C=0.9994 T=0.0006
The Genome Aggregation Database African Sub 8728 C=1.000 T=0.000
The Genome Aggregation Database East Asian Sub 1622 C=1.000 T=0.000
The Genome Aggregation Database Other Sub 982 C=1.00 T=0.00
The Genome Aggregation Database American Sub 838 C=1.00 T=0.00
The Genome Aggregation Database Ashkenazi Jewish Sub 302 C=1.00 T=0.00
1000Genomes Global Study-wide 5008 C=0.999 T=0.001
1000Genomes African Sub 1322 C=1.000 T=0.000
1000Genomes East Asian Sub 1008 C=1.000 T=0.000
1000Genomes Europe Sub 1006 C=0.998 T=0.002
1000Genomes South Asian Sub 978 C=1.00 T=0.00
1000Genomes American Sub 694 C=1.00 T=0.00
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.998 T=0.002
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.999 T=0.001
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= T Note
GRCh38.p7 chr 10 NC_000010.11:g.86681680C= NC_000010.11:g.86681680C>T
GRCh37.p13 chr 10 NC_000010.10:g.88441437C= NC_000010.10:g.88441437C>T
LDB3 RefSeqGene (LRG_385) NG_008876.1:g.18117C= NG_008876.1:g.18117C>T
LDB3 transcript variant 1 NM_007078.2:c.566C= NM_007078.2:c.566C>T
LDB3 transcript variant 5 NM_001171610.1:c.566C= NM_001171610.1:c.566C>T
LDB3 transcript variant 6 NM_001171611.1:c.566C= NM_001171611.1:c.566C>T
LDB3 transcript variant 3 NM_001080115.1:c.566C= NM_001080115.1:c.566C>T
LDB3 transcript variant X7 XM_005269464.4:c.566C= XM_005269464.4:c.566C>T
LDB3 transcript variant X1 XM_005269464.1:c.566C= XM_005269464.1:c.566C>T
LDB3 transcript variant X11 XM_005269466.4:c.566C= XM_005269466.4:c.566C>T
LDB3 transcript variant X3 XM_005269466.1:c.566C= XM_005269466.1:c.566C>T
LDB3 transcript variant X18 XM_005269468.4:c.566C= XM_005269468.4:c.566C>T
LDB3 transcript variant X5 XM_005269468.1:c.566C= XM_005269468.1:c.566C>T
LDB3 transcript variant X2 XM_011539185.2:c.566C= XM_011539185.2:c.566C>T
LDB3 transcript variant X1 XM_011539184.2:c.566C= XM_011539184.2:c.566C>T
LDB3 transcript variant X3 XM_011539186.2:c.566C= XM_011539186.2:c.566C>T
LDB3 transcript variant X4 XM_011539187.2:c.566C= XM_011539187.2:c.566C>T
LDB3 transcript variant X5 XM_011539188.2:c.566C= XM_011539188.2:c.566C>T
LDB3 transcript variant X17 XM_011539195.2:c.566C= XM_011539195.2:c.566C>T
LDB3 transcript variant X6 XM_017015606.1:c.566C= XM_017015606.1:c.566C>T
LDB3 transcript variant X19 XM_017015608.1:c.566C= XM_017015608.1:c.566C>T
LIM domain-binding protein 3 isoform 1 NP_009009.1:p.Ser189= NP_009009.1:p.Ser189Leu
LIM domain-binding protein 3 isoform 5 NP_001165081.1:p.Ser189= NP_001165081.1:p.Ser189Leu
LIM domain-binding protein 3 isoform 6 NP_001165082.1:p.Ser189= NP_001165082.1:p.Ser189Leu
LIM domain-binding protein 3 isoform 3 NP_001073584.1:p.Ser189= NP_001073584.1:p.Ser189Leu
LIM domain-binding protein 3 isoform X5 XP_005269521.1:p.Ser189= XP_005269521.1:p.Ser189Leu
LIM domain-binding protein 3 isoform X8 XP_005269523.1:p.Ser189= XP_005269523.1:p.Ser189Leu
LIM domain-binding protein 3 isoform X14 XP_005269525.1:p.Ser189= XP_005269525.1:p.Ser189Leu
LIM domain-binding protein 3 isoform X1 XP_011537487.1:p.Ser189= XP_011537487.1:p.Ser189Leu
LIM domain-binding protein 3 isoform X1 XP_011537486.1:p.Ser189= XP_011537486.1:p.Ser189Leu
LIM domain-binding protein 3 isoform X2 XP_011537488.1:p.Ser189= XP_011537488.1:p.Ser189Leu
LIM domain-binding protein 3 isoform X3 XP_011537489.1:p.Ser189= XP_011537489.1:p.Ser189Leu
LIM domain-binding protein 3 isoform X4 XP_011537490.1:p.Ser189= XP_011537490.1:p.Ser189Leu
LIM domain-binding protein 3 isoform X13 XP_011537497.1:p.Ser189= XP_011537497.1:p.Ser189Leu
LIM domain-binding protein 3 isoform X4 XP_016871095.1:p.Ser189= XP_016871095.1:p.Ser189Leu
LIM domain-binding protein 3 isoform X14 XP_016871097.1:p.Ser189= XP_016871097.1:p.Ser189Leu
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#.

6 ClinVar, 7 Frequency, 29 SubSNP submissions
No Submitter Submission ID Date (Build)
1 RSG_UW ss70458287 May 17, 2007 (127)
2 OMIM-CURATED-RECORDS ss262861278 Sep 23, 2010 (133)
3 NHLBI-ESP ss342302671 May 09, 2011 (134)
4 1000GENOMES ss488935932 May 04, 2012 (137)
5 EXOME_CHIP ss491437713 May 04, 2012 (137)
6 CLINSEQ_SNP ss491628618 May 04, 2012 (137)
7 ILLUMINA ss780888295 Sep 08, 2015 (146)
8 ILLUMINA ss783574504 Sep 08, 2015 (146)
9 1000GENOMES ss1338408744 Aug 21, 2014 (142)
10 EVA_UK10K_ALSPAC ss1625081822 Apr 01, 2015 (144)
11 EVA_UK10K_TWINSUK ss1668075855 Apr 01, 2015 (144)
12 EVA_EXAC ss1689981922 Apr 01, 2015 (144)
13 EVA_MGP ss1711263694 Apr 01, 2015 (144)
14 ILLUMINA ss1751985095 Sep 08, 2015 (146)
15 ILLUMINA ss1917849042 Feb 12, 2016 (147)
16 ILLUMINA ss1946288156 Feb 12, 2016 (147)
17 ILLUMINA ss1959280431 Feb 12, 2016 (147)
18 HUMAN_LONGEVITY ss2176721335 Dec 20, 2016 (150)
19 TOPMED ss2339805328 Dec 20, 2016 (150)
20 GNOMAD ss2738373802 Nov 08, 2017 (151)
21 GNOMAD ss2748427854 Nov 08, 2017 (151)
22 GNOMAD ss2891508970 Nov 08, 2017 (151)
23 AFFY ss2984918411 Nov 08, 2017 (151)
24 SWEGEN ss3006874904 Nov 08, 2017 (151)
25 TOPMED ss3126091534 Nov 08, 2017 (151)
26 ILLUMINA ss3626498109 Jul 20, 2018 (151)
27 ILLUMINA ss3634414871 Jul 20, 2018 (151)
28 ILLUMINA ss3640122213 Jul 20, 2018 (151)
29 ILLUMINA ss3644540884 Jul 20, 2018 (151)
30 1000Genomes NC_000010.10 - 88441437 Jul 20, 2018 (151)
31 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 88441437 Jul 20, 2018 (151)
32 The Exome Aggregation Consortium NC_000010.10 - 88441437 Jul 20, 2018 (151)
33 The Genome Aggregation Database NC_000010.10 - 88441437 Jul 20, 2018 (151)
34 The Genome Aggregation Database NC_000010.10 - 88441437 Jul 20, 2018 (151)
35 Trans-Omics for Precision Medicine NC_000010.11 - 86681680 Jul 20, 2018 (151)
36 UK 10K study - Twins NC_000010.10 - 88441437 Jul 20, 2018 (151)
37 ClinVar RCV000004996.3 Jul 20, 2018 (151)
38 ClinVar RCV000038759.4 Jul 20, 2018 (151)
39 ClinVar RCV000170300.3 Jul 20, 2018 (151)
40 ClinVar RCV000172555.2 Jul 20, 2018 (151)
41 ClinVar RCV000234541.4 Jul 20, 2018 (151)
42 ClinVar RCV000618756.1 Jul 20, 2018 (151)
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
ss491628618 NC_000010.9:88431416:C= NC_000010.11:86681679:C= (self)
50831734, 28219146, 208899, 25210491, 7388537, 28219146, ss342302671, ss488935932, ss491437713, ss780888295, ss783574504, ss1338408744, ss1625081822, ss1668075855, ss1689981922, ss1711263694, ss1751985095, ss1917849042, ss1946288156, ss1959280431, ss2339805328, ss2738373802, ss2748427854, ss2891508970, ss2984918411, ss3006874904, ss3626498109, ss3634414871, ss3640122213, ss3644540884 NC_000010.10:88441436:C= NC_000010.11:86681679:C= (self)
47957248, ss262861278, ss2176721335, ss3126091534 NC_000010.11:86681679:C= NC_000010.11:86681679:C= (self)
ss70458287 NT_030059.13:39245900:C= NC_000010.11:86681679:C= (self)
ss491628618 NC_000010.9:88431416:C>T NC_000010.11:86681679:C>T (self)
50831734, 28219146, 208899, 25210491, 7388537, 28219146, ss342302671, ss488935932, ss491437713, ss780888295, ss783574504, ss1338408744, ss1625081822, ss1668075855, ss1689981922, ss1711263694, ss1751985095, ss1917849042, ss1946288156, ss1959280431, ss2339805328, ss2738373802, ss2748427854, ss2891508970, ss2984918411, ss3006874904, ss3626498109, ss3634414871, ss3640122213, ss3644540884 NC_000010.10:88441436:C>T NC_000010.11:86681679:C>T (self)
RCV000004996.3, RCV000038759.4, RCV000170300.3, RCV000172555.2, RCV000234541.4, RCV000618756.1, 47957248, ss262861278, ss2176721335, ss3126091534 NC_000010.11:86681679:C>T NC_000010.11:86681679:C>T (self)
ss70458287 NT_030059.13:39245900:C>T NC_000010.11:86681679: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.

8 citations for rs45487699
PMID Title Author Year Journal
14662268 Mutations in Cypher/ZASP in patients with dilated cardiomyopathy and left ventricular non-compaction. Vatta M et al. 2003 Journal of the American College of Cardiology
17097056 Echocardiographic-determined septal morphology in Z-disc hypertrophic cardiomyopathy. Theis JL et al. 2006 Biochemical and biophysical research communications
19377068 Impaired binding of ZASP/Cypher with phosphoglucomutase 1 is associated with dilated cardiomyopathy. Arimura T et al. 2009 Cardiovascular research
20852297 A ZASP missense mutation, S196L, leads to cytoskeletal and electrical abnormalities in a mouse model of cardiomyopathy. Li Z et al. 2010 Circulation. Arrhythmia and electrophysiology
22337857 Evaluating pathogenicity of rare variants from dilated cardiomyopathy in the exome era. Norton N et al. 2012 Circulation. Cardiovascular genetics
23785128 Targeted sequence capture and GS-FLX Titanium sequencing of 23 hypertrophic and dilated cardiomyopathy genes: implementation into diagnostics. Mook OR et al. 2013 Journal of medical genetics
23861362 Interpreting secondary cardiac disease variants in an exome cohort. Ng D et al. 2013 Circulation. Cardiovascular genetics
24033266 A systematic approach to assessing the clinical significance of genetic variants. Duzkale H et al. 2013 Clinical genetics

Genomic regions, transcripts, and products
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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: 0.1.4.post833+d3ba21e