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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.

rs116383664

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1180081 (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=0.009422 (2494/264690, TOPMED)
T=0.002314 (533/230344, GnomAD_exome)
T=0.001709 (241/141048, ALFA) (+ 9 more)
T=0.008806 (1235/140238, GnomAD)
T=0.00331 (276/83324, ExAC)
T=0.01378 (1063/77164, PAGE_STUDY)
T=0.00840 (109/12982, GO-ESP)
T=0.0118 (59/5008, 1000G)
T=0.0002 (1/4480, Estonian)
T=0.019 (4/216, Qatari)
C=0.5 (2/4, SGDP_PRJ)
T=0.5 (2/4, 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.1180081C>T
GRCh37.p13 chr 1 NC_000001.10:g.1115461C>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.28C>T R [CGG] > W [TGG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform 2 NP_694986.2:p.Arg10Trp R (Arg) > W (Trp) Missense Variant
TTLL10 transcript variant 1 NM_001130045.2:c.247C>T R [CGG] > W [TGG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform 1 NP_001123517.1:p.Arg83Trp R (Arg) > W (Trp) Missense Variant
TTLL10 transcript variant 3 NM_001371649.1:c.247C>T R [CGG] > W [TGG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform 1 NP_001358578.1:p.Arg83Trp R (Arg) > W (Trp) Missense Variant
TTLL10 transcript variant X10 XM_005244738.1:c.28C>T R [CGG] > W [TGG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X8 XP_005244795.1:p.Arg10Trp R (Arg) > W (Trp) Missense Variant
TTLL10 transcript variant X1 XM_017000906.1:c.166C>T R [CGG] > W [TGG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X1 XP_016856395.1:p.Arg56Trp R (Arg) > W (Trp) Missense Variant
TTLL10 transcript variant X2 XM_017000907.1:c.247C>T R [CGG] > W [TGG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X2 XP_016856396.1:p.Arg83Trp R (Arg) > W (Trp) Missense Variant
TTLL10 transcript variant X3 XM_017000908.1:c.247C>T R [CGG] > W [TGG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X3 XP_016856397.1:p.Arg83Trp R (Arg) > W (Trp) Missense Variant
TTLL10 transcript variant X4 XM_017000909.1:c.247C>T R [CGG] > W [TGG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X4 XP_016856398.1:p.Arg83Trp R (Arg) > W (Trp) Missense Variant
TTLL10 transcript variant X6 XM_017000911.1:c.247C>T R [CGG] > W [TGG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X6 XP_016856400.1:p.Arg83Trp R (Arg) > W (Trp) Missense Variant
TTLL10 transcript variant X7 XM_011541177.2:c.247C>T R [CGG] > W [TGG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X7 XP_011539479.1:p.Arg83Trp R (Arg) > W (Trp) Missense Variant
TTLL10 transcript variant X8 XM_017000912.1:c.247C>T R [CGG] > W [TGG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X7 XP_016856401.1:p.Arg83Trp R (Arg) > W (Trp) Missense Variant
TTLL10 transcript variant X5 XM_017000910.2:c.247C>T R [CGG] > W [TGG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X5 XP_016856399.1:p.Arg83Trp R (Arg) > W (Trp) Missense Variant
TTLL10 transcript variant X9 XR_001737088.1:n.557C>T N/A Non Coding Transcript Variant
TTLL10 transcript variant X11 XR_001737089.1:n.947C>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 141048 C=0.998291 T=0.001709
European Sub 122488 C=0.999151 T=0.000849
African Sub 3888 C=0.9748 T=0.0252
African Others Sub 134 C=0.978 T=0.022
African American Sub 3754 C=0.9747 T=0.0253
Asian Sub 208 C=1.000 T=0.000
East Asian Sub 126 C=1.000 T=0.000
Other Asian Sub 82 C=1.00 T=0.00
Latin American 1 Sub 516 C=0.990 T=0.010
Latin American 2 Sub 718 C=0.997 T=0.003
South Asian Sub 114 C=1.000 T=0.000
Other Sub 13116 C=0.99756 T=0.00244


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=0.990578 T=0.009422
gnomAD - Exomes Global Study-wide 230344 C=0.997686 T=0.002314
gnomAD - Exomes European Sub 120304 C=0.999269 T=0.000731
gnomAD - Exomes Asian Sub 46898 C=0.99979 T=0.00021
gnomAD - Exomes American Sub 33538 C=0.99905 T=0.00095
gnomAD - Exomes African Sub 14804 C=0.97339 T=0.02661
gnomAD - Exomes Ashkenazi Jewish Sub 9190 C=0.9999 T=0.0001
gnomAD - Exomes Other Sub 5610 C=0.9986 T=0.0014
gnomAD - Genomes Global Study-wide 140238 C=0.991194 T=0.008806
gnomAD - Genomes European Sub 75940 C=0.99922 T=0.00078
gnomAD - Genomes African Sub 42026 C=0.97314 T=0.02686
gnomAD - Genomes American Sub 13662 C=0.99758 T=0.00242
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 C=0.9935 T=0.0065
ExAC Global Study-wide 83324 C=0.99669 T=0.00331
ExAC Europe Sub 52272 C=0.99922 T=0.00078
ExAC Asian Sub 15646 C=0.99974 T=0.00026
ExAC American Sub 7732 C=0.9990 T=0.0010
ExAC African Sub 7078 C=0.9688 T=0.0312
ExAC Other Sub 596 C=0.997 T=0.003
The PAGE Study Global Study-wide 77164 C=0.98622 T=0.01378
The PAGE Study AfricanAmerican Sub 31586 C=0.97341 T=0.02659
The PAGE Study Mexican Sub 10726 C=0.99786 T=0.00214
The PAGE Study Asian Sub 8132 C=0.9991 T=0.0009
The PAGE Study PuertoRican Sub 7834 C=0.9925 T=0.0075
The PAGE Study NativeHawaiian Sub 4430 C=0.9984 T=0.0016
The PAGE Study Cuban Sub 4202 C=0.9936 T=0.0064
The PAGE Study Dominican Sub 3772 C=0.9809 T=0.0191
The PAGE Study CentralAmerican Sub 2434 C=0.9955 T=0.0045
The PAGE Study SouthAmerican Sub 1974 C=0.9975 T=0.0025
The PAGE Study NativeAmerican Sub 1252 C=0.9928 T=0.0072
The PAGE Study SouthAsian Sub 822 C=0.996 T=0.004
GO Exome Sequencing Project Global Study-wide 12982 C=0.99160 T=0.00840
GO Exome Sequencing Project European American Sub 8586 C=0.9995 T=0.0005
GO Exome Sequencing Project African American Sub 4396 C=0.9761 T=0.0239
1000Genomes Global Study-wide 5008 C=0.9882 T=0.0118
1000Genomes African Sub 1322 C=0.9554 T=0.0446
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=1.000 T=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9998 T=0.0002
Qatari Global Study-wide 216 C=0.981 T=0.019
SGDP_PRJ Global Study-wide 4 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.1180081= NC_000001.11:g.1180081C>T
GRCh37.p13 chr 1 NC_000001.10:g.1115461= NC_000001.10:g.1115461C>T
TTLL10 transcript variant 2 NM_153254.3:c.28= NM_153254.3:c.28C>T
TTLL10 transcript variant 2 NM_153254.2:c.28= NM_153254.2:c.28C>T
TTLL10 transcript variant X7 XM_011541177.2:c.247= XM_011541177.2:c.247C>T
TTLL10 transcript variant 1 NM_001130045.2:c.247= NM_001130045.2:c.247C>T
TTLL10 transcript variant 1 NM_001130045.1:c.247= NM_001130045.1:c.247C>T
TTLL10 transcript variant X5 XM_017000910.2:c.247= XM_017000910.2:c.247C>T
TTLL10 transcript variant X1 XM_017000906.1:c.166= XM_017000906.1:c.166C>T
TTLL10 transcript variant 3 NM_001371649.1:c.247= NM_001371649.1:c.247C>T
TTLL10 transcript variant X8 XM_017000912.1:c.247= XM_017000912.1:c.247C>T
TTLL10 transcript variant X4 XM_017000909.1:c.247= XM_017000909.1:c.247C>T
TTLL10 transcript variant X10 XM_005244738.1:c.28= XM_005244738.1:c.28C>T
TTLL10 transcript variant X9 XR_001737088.1:n.557= XR_001737088.1:n.557C>T
TTLL10 transcript variant X3 XM_017000908.1:c.247= XM_017000908.1:c.247C>T
TTLL10 transcript variant X2 XM_017000907.1:c.247= XM_017000907.1:c.247C>T
TTLL10 transcript variant X6 XM_017000911.1:c.247= XM_017000911.1:c.247C>T
TTLL10 transcript variant X11 XR_001737089.1:n.947= XR_001737089.1:n.947C>T
inactive polyglycylase TTLL10 isoform 2 NP_694986.2:p.Arg10= NP_694986.2:p.Arg10Trp
inactive polyglycylase TTLL10 isoform X7 XP_011539479.1:p.Arg83= XP_011539479.1:p.Arg83Trp
inactive polyglycylase TTLL10 isoform 1 NP_001123517.1:p.Arg83= NP_001123517.1:p.Arg83Trp
inactive polyglycylase TTLL10 isoform X5 XP_016856399.1:p.Arg83= XP_016856399.1:p.Arg83Trp
inactive polyglycylase TTLL10 isoform X1 XP_016856395.1:p.Arg56= XP_016856395.1:p.Arg56Trp
inactive polyglycylase TTLL10 isoform 1 NP_001358578.1:p.Arg83= NP_001358578.1:p.Arg83Trp
inactive polyglycylase TTLL10 isoform X7 XP_016856401.1:p.Arg83= XP_016856401.1:p.Arg83Trp
inactive polyglycylase TTLL10 isoform X4 XP_016856398.1:p.Arg83= XP_016856398.1:p.Arg83Trp
inactive polyglycylase TTLL10 isoform X8 XP_005244795.1:p.Arg10= XP_005244795.1:p.Arg10Trp
inactive polyglycylase TTLL10 isoform X3 XP_016856397.1:p.Arg83= XP_016856397.1:p.Arg83Trp
inactive polyglycylase TTLL10 isoform X2 XP_016856396.1:p.Arg83= XP_016856396.1:p.Arg83Trp
inactive polyglycylase TTLL10 isoform X6 XP_016856400.1:p.Arg83= XP_016856400.1:p.Arg83Trp
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#.

52 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss217405716 Jul 14, 2010 (132)
2 1000GENOMES ss217410862 Jul 14, 2010 (132)
3 1000GENOMES ss218192270 Jul 14, 2010 (132)
4 NHLBI-ESP ss341924366 May 09, 2011 (134)
5 ILLUMINA ss480877550 May 04, 2012 (137)
6 ILLUMINA ss482067654 May 04, 2012 (137)
7 1000GENOMES ss489714581 May 04, 2012 (137)
8 EXOME_CHIP ss491284051 May 04, 2012 (137)
9 ILLUMINA ss533998456 Sep 08, 2015 (146)
10 TISHKOFF ss553714383 Apr 25, 2013 (138)
11 ILLUMINA ss779236830 Sep 08, 2015 (146)
12 ILLUMINA ss780755887 Sep 08, 2015 (146)
13 ILLUMINA ss781340910 Sep 08, 2015 (146)
14 ILLUMINA ss783434278 Sep 08, 2015 (146)
15 ILLUMINA ss834703067 Sep 08, 2015 (146)
16 JMKIDD_LAB ss1067414433 Aug 21, 2014 (142)
17 1000GENOMES ss1289352906 Aug 21, 2014 (142)
18 EVA_EXAC ss1685225645 Apr 01, 2015 (144)
19 ILLUMINA ss1751863264 Sep 08, 2015 (146)
20 ILLUMINA ss1917720983 Feb 12, 2016 (147)
21 WEILL_CORNELL_DGM ss1917964718 Feb 12, 2016 (147)
22 ILLUMINA ss1945981818 Feb 12, 2016 (147)
23 ILLUMINA ss1958230890 Feb 12, 2016 (147)
24 HUMAN_LONGEVITY ss2159391480 Dec 20, 2016 (150)
25 TOPMED ss2321530700 Dec 20, 2016 (150)
26 ILLUMINA ss2632465818 Nov 08, 2017 (151)
27 GNOMAD ss2730999776 Nov 08, 2017 (151)
28 GNOMAD ss2746174182 Nov 08, 2017 (151)
29 GNOMAD ss2750679118 Nov 08, 2017 (151)
30 AFFY ss2984841266 Nov 08, 2017 (151)
31 SWEGEN ss2986155450 Nov 08, 2017 (151)
32 ILLUMINA ss3021043844 Nov 08, 2017 (151)
33 TOPMED ss3066487757 Nov 08, 2017 (151)
34 ILLUMINA ss3626007192 Oct 11, 2018 (152)
35 ILLUMINA ss3626007193 Oct 11, 2018 (152)
36 ILLUMINA ss3630505831 Oct 11, 2018 (152)
37 ILLUMINA ss3634302088 Oct 11, 2018 (152)
38 ILLUMINA ss3640009454 Oct 11, 2018 (152)
39 ILLUMINA ss3644477682 Oct 11, 2018 (152)
40 ILLUMINA ss3651365897 Oct 11, 2018 (152)
41 ILLUMINA ss3653615032 Oct 11, 2018 (152)
42 EGCUT_WGS ss3654266493 Jul 12, 2019 (153)
43 EVA_DECODE ss3685999323 Jul 12, 2019 (153)
44 ILLUMINA ss3744337411 Jul 12, 2019 (153)
45 ILLUMINA ss3744603019 Jul 12, 2019 (153)
46 PAGE_CC ss3770778878 Jul 12, 2019 (153)
47 ILLUMINA ss3772104777 Jul 12, 2019 (153)
48 EVA ss3823543017 Apr 25, 2020 (154)
49 SGDP_PRJ ss3848005815 Apr 25, 2020 (154)
50 FSA-LAB ss3983910751 Apr 25, 2021 (155)
51 EVA ss3986091281 Apr 25, 2021 (155)
52 TOPMED ss4436539213 Apr 25, 2021 (155)
53 1000Genomes NC_000001.10 - 1115461 Oct 11, 2018 (152)
54 Genetic variation in the Estonian population NC_000001.10 - 1115461 Oct 11, 2018 (152)
55 ExAC NC_000001.10 - 1115461 Oct 11, 2018 (152)
56 gnomAD - Genomes NC_000001.11 - 1180081 Apr 25, 2021 (155)
57 gnomAD - Exomes NC_000001.10 - 1115461 Jul 12, 2019 (153)
58 GO Exome Sequencing Project NC_000001.10 - 1115461 Oct 11, 2018 (152)
59 The PAGE Study NC_000001.11 - 1180081 Jul 12, 2019 (153)
60 Qatari NC_000001.10 - 1115461 Apr 25, 2020 (154)
61 SGDP_PRJ NC_000001.10 - 1115461 Apr 25, 2020 (154)
62 TopMed NC_000001.11 - 1180081 Apr 25, 2021 (155)
63 ALFA NC_000001.11 - 1180081 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
ss217405716, ss217410862, ss482067654 NC_000001.9:1105323:C:T NC_000001.11:1180080:C:T (self)
18090, 4741, 4399295, 14600, 1754, 6648, 22795, ss218192270, ss341924366, ss480877550, ss489714581, ss491284051, ss533998456, ss553714383, ss779236830, ss780755887, ss781340910, ss783434278, ss834703067, ss1067414433, ss1289352906, ss1685225645, ss1751863264, ss1917720983, ss1917964718, ss1945981818, ss1958230890, ss2321530700, ss2632465818, ss2730999776, ss2746174182, ss2750679118, ss2984841266, ss2986155450, ss3021043844, ss3626007192, ss3626007193, ss3630505831, ss3634302088, ss3640009454, ss3644477682, ss3651365897, ss3653615032, ss3654266493, ss3744337411, ss3744603019, ss3772104777, ss3823543017, ss3848005815, ss3983910751, ss3986091281 NC_000001.10:1115460:C:T NC_000001.11:1180080:C:T (self)
158723, 347, 83507, 145548, 12582477119, ss2159391480, ss3066487757, ss3685999323, ss3770778878, ss4436539213 NC_000001.11:1180080:C:T NC_000001.11:1180080: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 rs116383664

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
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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: 2.0.1.post596+ae089ad