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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.

rs114359609

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1180130 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.006290 (1665/264690, TOPMED)
T=0.002227 (531/238412, GnomAD_exome)
T=0.001253 (247/197116, ALFA) (+ 10 more)
T=0.005385 (755/140192, GnomAD)
T=0.00240 (233/96922, ExAC)
T=0.00859 (673/78374, PAGE_STUDY)
T=0.00477 (62/12998, GO-ESP)
T=0.0046 (23/5008, 1000G)
T=0.0005 (2/3854, ALSPAC)
T=0.0003 (1/3708, TWINSUK)
T=0.005 (1/216, Qatari)
C=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TTLL10 : Missense Variant
TTLL10-AS1 : 2KB Upstream Variant
Publications
0 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.1180130C>T
GRCh37.p13 chr 1 NC_000001.10:g.1115510C>T
Gene: TTLL10, tubulin tyrosine ligase like 10 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TTLL10 transcript variant 2 NM_153254.3:c.77C>T P [CCG] > L [CTG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform 2 NP_694986.2:p.Pro26Leu P (Pro) > L (Leu) Missense Variant
TTLL10 transcript variant 1 NM_001130045.2:c.296C>T P [CCG] > L [CTG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform 1 NP_001123517.1:p.Pro99Leu P (Pro) > L (Leu) Missense Variant
TTLL10 transcript variant 3 NM_001371649.1:c.296C>T P [CCG] > L [CTG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform 1 NP_001358578.1:p.Pro99Leu P (Pro) > L (Leu) Missense Variant
TTLL10 transcript variant X10 XM_005244738.1:c.77C>T P [CCG] > L [CTG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X8 XP_005244795.1:p.Pro26Leu P (Pro) > L (Leu) Missense Variant
TTLL10 transcript variant X1 XM_017000906.1:c.215C>T P [CCG] > L [CTG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X1 XP_016856395.1:p.Pro72Leu P (Pro) > L (Leu) Missense Variant
TTLL10 transcript variant X2 XM_017000907.1:c.296C>T P [CCG] > L [CTG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X2 XP_016856396.1:p.Pro99Leu P (Pro) > L (Leu) Missense Variant
TTLL10 transcript variant X3 XM_017000908.1:c.296C>T P [CCG] > L [CTG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X3 XP_016856397.1:p.Pro99Leu P (Pro) > L (Leu) Missense Variant
TTLL10 transcript variant X4 XM_017000909.1:c.296C>T P [CCG] > L [CTG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X4 XP_016856398.1:p.Pro99Leu P (Pro) > L (Leu) Missense Variant
TTLL10 transcript variant X6 XM_017000911.1:c.296C>T P [CCG] > L [CTG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X6 XP_016856400.1:p.Pro99Leu P (Pro) > L (Leu) Missense Variant
TTLL10 transcript variant X7 XM_011541177.2:c.296C>T P [CCG] > L [CTG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X7 XP_011539479.1:p.Pro99Leu P (Pro) > L (Leu) Missense Variant
TTLL10 transcript variant X8 XM_017000912.1:c.296C>T P [CCG] > L [CTG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X7 XP_016856401.1:p.Pro99Leu P (Pro) > L (Leu) Missense Variant
TTLL10 transcript variant X5 XM_017000910.2:c.296C>T P [CCG] > L [CTG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X5 XP_016856399.1:p.Pro99Leu P (Pro) > L (Leu) Missense Variant
TTLL10 transcript variant X9 XR_001737088.1:n.606C>T N/A Non Coding Transcript Variant
TTLL10 transcript variant X11 XR_001737089.1:n.996C>T N/A Non Coding Transcript Variant
Gene: TTLL10-AS1, uncharacterized TTLL10-AS1 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
TTLL10-AS1 transcript variant X2 XR_132470.6:n. N/A Upstream Transcript Variant
TTLL10-AS1 transcript variant X1 XR_946813.2:n. N/A Upstream 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

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 197116 C=0.998747 T=0.001253
European Sub 167906 C=0.999089 T=0.000911
African Sub 4954 C=0.9885 T=0.0115
African Others Sub 176 C=0.994 T=0.006
African American Sub 4778 C=0.9883 T=0.0117
Asian Sub 6326 C=1.0000 T=0.0000
East Asian Sub 4480 C=1.0000 T=0.0000
Other Asian Sub 1846 C=1.0000 T=0.0000
Latin American 1 Sub 796 C=0.989 T=0.011
Latin American 2 Sub 968 C=0.999 T=0.001
South Asian Sub 280 C=0.996 T=0.004
Other Sub 15886 C=0.99836 T=0.00164


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=0.993710 T=0.006290
gnomAD - Exomes Global Study-wide 238412 C=0.997773 T=0.002227
gnomAD - Exomes European Sub 125876 C=0.999206 T=0.000794
gnomAD - Exomes Asian Sub 48070 C=0.99958 T=0.00042
gnomAD - Exomes American Sub 33950 C=0.99523 T=0.00477
gnomAD - Exomes African Sub 15054 C=0.98572 T=0.01428
gnomAD - Exomes Ashkenazi Jewish Sub 9652 C=0.9990 T=0.0010
gnomAD - Exomes Other Sub 5810 C=0.9959 T=0.0041
gnomAD - Genomes Global Study-wide 140192 C=0.994615 T=0.005385
gnomAD - Genomes European Sub 75924 C=0.99929 T=0.00071
gnomAD - Genomes African Sub 42002 C=0.98591 T=0.01409
gnomAD - Genomes American Sub 13660 C=0.99312 T=0.00688
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.9997 T=0.0003
gnomAD - Genomes East Asian Sub 3134 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2150 C=0.9935 T=0.0065
ExAC Global Study-wide 96922 C=0.99760 T=0.00240
ExAC Europe Sub 58236 C=0.99902 T=0.00098
ExAC Asian Sub 21188 C=0.99934 T=0.00066
ExAC American Sub 9146 C=0.9955 T=0.0045
ExAC African Sub 7680 C=0.9844 T=0.0156
ExAC Other Sub 672 C=0.999 T=0.001
The PAGE Study Global Study-wide 78374 C=0.99141 T=0.00859
The PAGE Study AfricanAmerican Sub 32342 C=0.98704 T=0.01296
The PAGE Study Mexican Sub 10790 C=0.99416 T=0.00584
The PAGE Study Asian Sub 8288 C=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7898 C=0.9899 T=0.0101
The PAGE Study NativeHawaiian Sub 4494 C=0.9991 T=0.0009
The PAGE Study Cuban Sub 4214 C=0.9903 T=0.0097
The PAGE Study Dominican Sub 3822 C=0.9916 T=0.0084
The PAGE Study CentralAmerican Sub 2446 C=0.9935 T=0.0065
The PAGE Study SouthAmerican Sub 1980 C=0.9924 T=0.0076
The PAGE Study NativeAmerican Sub 1258 C=0.9976 T=0.0024
The PAGE Study SouthAsian Sub 842 C=1.000 T=0.000
GO Exome Sequencing Project Global Study-wide 12998 C=0.99523 T=0.00477
GO Exome Sequencing Project European American Sub 8592 C=0.9992 T=0.0008
GO Exome Sequencing Project African American Sub 4406 C=0.9875 T=0.0125
1000Genomes Global Study-wide 5008 C=0.9954 T=0.0046
1000Genomes African Sub 1322 C=0.9871 T=0.0129
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=0.9980 T=0.0020
1000Genomes South Asian Sub 978 C=0.999 T=0.001
1000Genomes American Sub 694 C=0.996 T=0.004
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9995 T=0.0005
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9997 T=0.0003
Qatari Global Study-wide 216 C=0.995 T=0.005
SGDP_PRJ Global Study-wide 2 C=0.5 T=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 C= T
GRCh38.p13 chr 1 NC_000001.11:g.1180130= NC_000001.11:g.1180130C>T
GRCh37.p13 chr 1 NC_000001.10:g.1115510= NC_000001.10:g.1115510C>T
TTLL10 transcript variant 2 NM_153254.3:c.77= NM_153254.3:c.77C>T
TTLL10 transcript variant 2 NM_153254.2:c.77= NM_153254.2:c.77C>T
TTLL10 transcript variant X7 XM_011541177.2:c.296= XM_011541177.2:c.296C>T
TTLL10 transcript variant 1 NM_001130045.2:c.296= NM_001130045.2:c.296C>T
TTLL10 transcript variant 1 NM_001130045.1:c.296= NM_001130045.1:c.296C>T
TTLL10 transcript variant X5 XM_017000910.2:c.296= XM_017000910.2:c.296C>T
TTLL10 transcript variant X1 XM_017000906.1:c.215= XM_017000906.1:c.215C>T
TTLL10 transcript variant 3 NM_001371649.1:c.296= NM_001371649.1:c.296C>T
TTLL10 transcript variant X8 XM_017000912.1:c.296= XM_017000912.1:c.296C>T
TTLL10 transcript variant X4 XM_017000909.1:c.296= XM_017000909.1:c.296C>T
TTLL10 transcript variant X10 XM_005244738.1:c.77= XM_005244738.1:c.77C>T
TTLL10 transcript variant X9 XR_001737088.1:n.606= XR_001737088.1:n.606C>T
TTLL10 transcript variant X3 XM_017000908.1:c.296= XM_017000908.1:c.296C>T
TTLL10 transcript variant X2 XM_017000907.1:c.296= XM_017000907.1:c.296C>T
TTLL10 transcript variant X6 XM_017000911.1:c.296= XM_017000911.1:c.296C>T
TTLL10 transcript variant X11 XR_001737089.1:n.996= XR_001737089.1:n.996C>T
inactive polyglycylase TTLL10 isoform 2 NP_694986.2:p.Pro26= NP_694986.2:p.Pro26Leu
inactive polyglycylase TTLL10 isoform X7 XP_011539479.1:p.Pro99= XP_011539479.1:p.Pro99Leu
inactive polyglycylase TTLL10 isoform 1 NP_001123517.1:p.Pro99= NP_001123517.1:p.Pro99Leu
inactive polyglycylase TTLL10 isoform X5 XP_016856399.1:p.Pro99= XP_016856399.1:p.Pro99Leu
inactive polyglycylase TTLL10 isoform X1 XP_016856395.1:p.Pro72= XP_016856395.1:p.Pro72Leu
inactive polyglycylase TTLL10 isoform 1 NP_001358578.1:p.Pro99= NP_001358578.1:p.Pro99Leu
inactive polyglycylase TTLL10 isoform X7 XP_016856401.1:p.Pro99= XP_016856401.1:p.Pro99Leu
inactive polyglycylase TTLL10 isoform X4 XP_016856398.1:p.Pro99= XP_016856398.1:p.Pro99Leu
inactive polyglycylase TTLL10 isoform X8 XP_005244795.1:p.Pro26= XP_005244795.1:p.Pro26Leu
inactive polyglycylase TTLL10 isoform X3 XP_016856397.1:p.Pro99= XP_016856397.1:p.Pro99Leu
inactive polyglycylase TTLL10 isoform X2 XP_016856396.1:p.Pro99= XP_016856396.1:p.Pro99Leu
inactive polyglycylase TTLL10 isoform X6 XP_016856400.1:p.Pro99= XP_016856400.1:p.Pro99Leu
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#.

44 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss217410868 Jul 14, 2010 (132)
2 1000GENOMES ss218192271 Jul 14, 2010 (132)
3 NHLBI-ESP ss341924371 May 09, 2011 (134)
4 1000GENOMES ss489714585 May 04, 2012 (137)
5 EXOME_CHIP ss491284054 May 04, 2012 (137)
6 ILLUMINA ss780756378 Sep 08, 2015 (146)
7 ILLUMINA ss783434803 Sep 08, 2015 (146)
8 JMKIDD_LAB ss1067414434 Aug 21, 2014 (142)
9 JMKIDD_LAB ss1067614012 Aug 21, 2014 (142)
10 1000GENOMES ss1289352908 Aug 21, 2014 (142)
11 EVA_UK10K_ALSPAC ss1599383772 Apr 01, 2015 (144)
12 EVA_UK10K_TWINSUK ss1642377805 Apr 01, 2015 (144)
13 EVA_EXAC ss1685225658 Apr 01, 2015 (144)
14 ILLUMINA ss1751863269 Sep 08, 2015 (146)
15 ILLUMINA ss1917720986 Feb 12, 2016 (147)
16 WEILL_CORNELL_DGM ss1917964720 Feb 12, 2016 (147)
17 ILLUMINA ss1945981821 Feb 12, 2016 (147)
18 ILLUMINA ss1958230894 Feb 12, 2016 (147)
19 HUMAN_LONGEVITY ss2159391488 Dec 20, 2016 (150)
20 TOPMED ss2321530706 Dec 20, 2016 (150)
21 GNOMAD ss2730999792 Nov 08, 2017 (151)
22 GNOMAD ss2746174189 Nov 08, 2017 (151)
23 GNOMAD ss2750679125 Nov 08, 2017 (151)
24 AFFY ss2984841268 Nov 08, 2017 (151)
25 ILLUMINA ss3021043847 Nov 08, 2017 (151)
26 TOPMED ss3066487768 Nov 08, 2017 (151)
27 ILLUMINA ss3626007197 Oct 11, 2018 (152)
28 ILLUMINA ss3634302091 Oct 11, 2018 (152)
29 ILLUMINA ss3640009457 Oct 11, 2018 (152)
30 ILLUMINA ss3644477685 Oct 11, 2018 (152)
31 ILLUMINA ss3651365900 Oct 11, 2018 (152)
32 ILLUMINA ss3653615034 Oct 11, 2018 (152)
33 EVA_DECODE ss3685999325 Jul 12, 2019 (153)
34 ILLUMINA ss3724988516 Jul 12, 2019 (153)
35 ILLUMINA ss3744337414 Jul 12, 2019 (153)
36 ILLUMINA ss3744603022 Jul 12, 2019 (153)
37 PAGE_CC ss3770778880 Jul 12, 2019 (153)
38 ILLUMINA ss3772104780 Jul 12, 2019 (153)
39 KHV_HUMAN_GENOMES ss3798747718 Jul 12, 2019 (153)
40 EVA ss3823543021 Apr 25, 2020 (154)
41 EVA ss3825549312 Apr 25, 2020 (154)
42 SGDP_PRJ ss3848005817 Apr 25, 2020 (154)
43 EVA ss3986091283 Apr 25, 2021 (155)
44 TOPMED ss4436539228 Apr 25, 2021 (155)
45 1000Genomes NC_000001.10 - 1115510 Oct 11, 2018 (152)
46 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 1115510 Oct 11, 2018 (152)
47 ExAC NC_000001.10 - 1115510 Oct 11, 2018 (152)
48 gnomAD - Genomes NC_000001.11 - 1180130 Apr 25, 2021 (155)
49 gnomAD - Exomes NC_000001.10 - 1115510 Jul 12, 2019 (153)
50 GO Exome Sequencing Project NC_000001.10 - 1115510 Oct 11, 2018 (152)
51 The PAGE Study NC_000001.11 - 1180130 Jul 12, 2019 (153)
52 Qatari NC_000001.10 - 1115510 Apr 25, 2020 (154)
53 SGDP_PRJ NC_000001.10 - 1115510 Apr 25, 2020 (154)
54 TopMed NC_000001.11 - 1180130 Apr 25, 2021 (155)
55 UK 10K study - Twins NC_000001.10 - 1115510 Oct 11, 2018 (152)
56 ALFA NC_000001.11 - 1180130 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
ss217410868 NC_000001.9:1105372:C:T NC_000001.11:1180129:C:T (self)
18092, 6214, 4399308, 14615, 1758, 6650, 22797, 6214, ss218192271, ss341924371, ss489714585, ss491284054, ss780756378, ss783434803, ss1067414434, ss1067614012, ss1289352908, ss1599383772, ss1642377805, ss1685225658, ss1751863269, ss1917720986, ss1917964720, ss1945981821, ss1958230894, ss2321530706, ss2730999792, ss2746174189, ss2750679125, ss2984841268, ss3021043847, ss3626007197, ss3634302091, ss3640009457, ss3644477685, ss3651365900, ss3653615034, ss3744337414, ss3744603022, ss3772104780, ss3823543021, ss3825549312, ss3848005817, ss3986091283 NC_000001.10:1115509:C:T NC_000001.11:1180129:C:T (self)
158733, 349, 83518, 145563, 5157734884, ss2159391488, ss3066487768, ss3685999325, ss3724988516, ss3770778880, ss3798747718, ss4436539228 NC_000001.11:1180129:C:T NC_000001.11:1180129: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.

No publications for rs114359609

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