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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.

rs114390380

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1180168 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.015052 (3984/264690, TOPMED)
A=0.015889 (3785/238208, GnomAD_exome)
A=0.016857 (2363/140182, GnomAD) (+ 16 more)
A=0.02051 (1963/95730, ExAC)
A=0.02299 (1680/73068, ALFA)
A=0.00012 (2/16760, 8.3KJPN)
A=0.02019 (262/12976, GO-ESP)
A=0.0058 (29/5008, 1000G)
A=0.0283 (127/4480, Estonian)
A=0.0246 (95/3854, ALSPAC)
A=0.0191 (71/3708, TWINSUK)
A=0.0007 (2/2916, KOREAN)
A=0.0005 (1/1822, Korea1K)
A=0.018 (11/600, NorthernSweden)
A=0.008 (2/244, FINRISK)
G=0.5 (2/4, SGDP_PRJ)
A=0.5 (2/4, SGDP_PRJ)
G=0.5 (2/4, Siberian)
A=0.5 (2/4, Siberian)
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.1180168G>A
GRCh37.p13 chr 1 NC_000001.10:g.1115548G>A
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.115G>A G [GGA] > R [AGA] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform 2 NP_694986.2:p.Gly39Arg G (Gly) > R (Arg) Missense Variant
TTLL10 transcript variant 1 NM_001130045.2:c.334G>A G [GGA] > R [AGA] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform 1 NP_001123517.1:p.Gly112Arg G (Gly) > R (Arg) Missense Variant
TTLL10 transcript variant 3 NM_001371649.1:c.334G>A G [GGA] > R [AGA] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform 1 NP_001358578.1:p.Gly112Arg G (Gly) > R (Arg) Missense Variant
TTLL10 transcript variant X10 XM_005244738.1:c.115G>A G [GGA] > R [AGA] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X8 XP_005244795.1:p.Gly39Arg G (Gly) > R (Arg) Missense Variant
TTLL10 transcript variant X1 XM_017000906.1:c.253G>A G [GGA] > R [AGA] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X1 XP_016856395.1:p.Gly85Arg G (Gly) > R (Arg) Missense Variant
TTLL10 transcript variant X2 XM_017000907.1:c.334G>A G [GGA] > R [AGA] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X2 XP_016856396.1:p.Gly112Arg G (Gly) > R (Arg) Missense Variant
TTLL10 transcript variant X3 XM_017000908.1:c.334G>A G [GGA] > R [AGA] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X3 XP_016856397.1:p.Gly112Arg G (Gly) > R (Arg) Missense Variant
TTLL10 transcript variant X4 XM_017000909.1:c.334G>A G [GGA] > R [AGA] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X4 XP_016856398.1:p.Gly112Arg G (Gly) > R (Arg) Missense Variant
TTLL10 transcript variant X6 XM_017000911.1:c.334G>A G [GGA] > R [AGA] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X6 XP_016856400.1:p.Gly112Arg G (Gly) > R (Arg) Missense Variant
TTLL10 transcript variant X7 XM_011541177.2:c.334G>A G [GGA] > R [AGA] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X7 XP_011539479.1:p.Gly112Arg G (Gly) > R (Arg) Missense Variant
TTLL10 transcript variant X8 XM_017000912.1:c.334G>A G [GGA] > R [AGA] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X7 XP_016856401.1:p.Gly112Arg G (Gly) > R (Arg) Missense Variant
TTLL10 transcript variant X5 XM_017000910.2:c.334G>A G [GGA] > R [AGA] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X5 XP_016856399.1:p.Gly112Arg G (Gly) > R (Arg) Missense Variant
TTLL10 transcript variant X9 XR_001737088.1:n.644G>A N/A Non Coding Transcript Variant
TTLL10 transcript variant X11 XR_001737089.1:n.1034G>A 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 73068 G=0.97701 A=0.02299
European Sub 58798 G=0.97459 A=0.02541
African Sub 3632 G=0.9953 A=0.0047
African Others Sub 122 G=1.000 A=0.000
African American Sub 3510 G=0.9952 A=0.0048
Asian Sub 194 G=1.000 A=0.000
East Asian Sub 112 G=1.000 A=0.000
Other Asian Sub 82 G=1.00 A=0.00
Latin American 1 Sub 500 G=0.996 A=0.004
Latin American 2 Sub 648 G=0.983 A=0.017
South Asian Sub 98 G=0.99 A=0.01
Other Sub 9198 G=0.9831 A=0.0169


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 G=0.984948 A=0.015052
gnomAD - Exomes Global Study-wide 238208 G=0.984111 A=0.015889
gnomAD - Exomes European Sub 125772 G=0.974215 A=0.025785
gnomAD - Exomes Asian Sub 48088 G=0.99844 A=0.00156
gnomAD - Exomes American Sub 33980 G=0.99220 A=0.00780
gnomAD - Exomes African Sub 14886 G=0.99631 A=0.00369
gnomAD - Exomes Ashkenazi Jewish Sub 9684 G=0.9935 A=0.0065
gnomAD - Exomes Other Sub 5798 G=0.9855 A=0.0145
gnomAD - Genomes Global Study-wide 140182 G=0.983143 A=0.016857
gnomAD - Genomes European Sub 75908 G=0.97500 A=0.02500
gnomAD - Genomes African Sub 42010 G=0.99493 A=0.00507
gnomAD - Genomes American Sub 13660 G=0.98463 A=0.01537
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.9931 A=0.0069
gnomAD - Genomes East Asian Sub 3130 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 G=0.9912 A=0.0088
ExAC Global Study-wide 95730 G=0.97949 A=0.02051
ExAC Europe Sub 57230 G=0.96836 A=0.03164
ExAC Asian Sub 21296 G=0.99807 A=0.00193
ExAC American Sub 9188 G=0.9931 A=0.0069
ExAC African Sub 7354 G=0.9948 A=0.0052
ExAC Other Sub 662 G=0.985 A=0.015
8.3KJPN JAPANESE Study-wide 16760 G=0.99988 A=0.00012
GO Exome Sequencing Project Global Study-wide 12976 G=0.97981 A=0.02019
GO Exome Sequencing Project European American Sub 8588 G=0.9723 A=0.0277
GO Exome Sequencing Project African American Sub 4388 G=0.9945 A=0.0055
1000Genomes Global Study-wide 5008 G=0.9942 A=0.0058
1000Genomes African Sub 1322 G=0.9985 A=0.0015
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9841 A=0.0159
1000Genomes South Asian Sub 978 G=0.996 A=0.004
1000Genomes American Sub 694 G=0.990 A=0.010
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9717 A=0.0283
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9754 A=0.0246
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9809 A=0.0191
KOREAN population from KRGDB KOREAN Study-wide 2916 G=0.9993 A=0.0007
Korean Genome Project KOREAN Study-wide 1822 G=0.9995 A=0.0005
Northern Sweden ACPOP Study-wide 600 G=0.982 A=0.018
FINRISK Finnish from FINRISK project Study-wide 244 G=0.992 A=0.008
SGDP_PRJ Global Study-wide 4 G=0.5 A=0.5
Siberian Global Study-wide 4 G=0.5 A=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 G= A
GRCh38.p13 chr 1 NC_000001.11:g.1180168= NC_000001.11:g.1180168G>A
GRCh37.p13 chr 1 NC_000001.10:g.1115548= NC_000001.10:g.1115548G>A
TTLL10 transcript variant 2 NM_153254.3:c.115= NM_153254.3:c.115G>A
TTLL10 transcript variant 2 NM_153254.2:c.115= NM_153254.2:c.115G>A
TTLL10 transcript variant X7 XM_011541177.2:c.334= XM_011541177.2:c.334G>A
TTLL10 transcript variant 1 NM_001130045.2:c.334= NM_001130045.2:c.334G>A
TTLL10 transcript variant 1 NM_001130045.1:c.334= NM_001130045.1:c.334G>A
TTLL10 transcript variant X5 XM_017000910.2:c.334= XM_017000910.2:c.334G>A
TTLL10 transcript variant X1 XM_017000906.1:c.253= XM_017000906.1:c.253G>A
TTLL10 transcript variant 3 NM_001371649.1:c.334= NM_001371649.1:c.334G>A
TTLL10 transcript variant X8 XM_017000912.1:c.334= XM_017000912.1:c.334G>A
TTLL10 transcript variant X4 XM_017000909.1:c.334= XM_017000909.1:c.334G>A
TTLL10 transcript variant X10 XM_005244738.1:c.115= XM_005244738.1:c.115G>A
TTLL10 transcript variant X9 XR_001737088.1:n.644= XR_001737088.1:n.644G>A
TTLL10 transcript variant X3 XM_017000908.1:c.334= XM_017000908.1:c.334G>A
TTLL10 transcript variant X2 XM_017000907.1:c.334= XM_017000907.1:c.334G>A
TTLL10 transcript variant X6 XM_017000911.1:c.334= XM_017000911.1:c.334G>A
TTLL10 transcript variant X11 XR_001737089.1:n.1034= XR_001737089.1:n.1034G>A
inactive polyglycylase TTLL10 isoform 2 NP_694986.2:p.Gly39= NP_694986.2:p.Gly39Arg
inactive polyglycylase TTLL10 isoform X7 XP_011539479.1:p.Gly112= XP_011539479.1:p.Gly112Arg
inactive polyglycylase TTLL10 isoform 1 NP_001123517.1:p.Gly112= NP_001123517.1:p.Gly112Arg
inactive polyglycylase TTLL10 isoform X5 XP_016856399.1:p.Gly112= XP_016856399.1:p.Gly112Arg
inactive polyglycylase TTLL10 isoform X1 XP_016856395.1:p.Gly85= XP_016856395.1:p.Gly85Arg
inactive polyglycylase TTLL10 isoform 1 NP_001358578.1:p.Gly112= NP_001358578.1:p.Gly112Arg
inactive polyglycylase TTLL10 isoform X7 XP_016856401.1:p.Gly112= XP_016856401.1:p.Gly112Arg
inactive polyglycylase TTLL10 isoform X4 XP_016856398.1:p.Gly112= XP_016856398.1:p.Gly112Arg
inactive polyglycylase TTLL10 isoform X8 XP_005244795.1:p.Gly39= XP_005244795.1:p.Gly39Arg
inactive polyglycylase TTLL10 isoform X3 XP_016856397.1:p.Gly112= XP_016856397.1:p.Gly112Arg
inactive polyglycylase TTLL10 isoform X2 XP_016856396.1:p.Gly112= XP_016856396.1:p.Gly112Arg
inactive polyglycylase TTLL10 isoform X6 XP_016856400.1:p.Gly112= XP_016856400.1:p.Gly112Arg
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#.

49 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss217314369 Jul 14, 2010 (132)
2 1000GENOMES ss217410441 Jul 14, 2010 (132)
3 1000GENOMES ss328359983 May 09, 2011 (134)
4 NHLBI-ESP ss341924374 May 09, 2011 (134)
5 MPI_MOLGEN ss469105688 Sep 17, 2011 (135)
6 1000GENOMES ss489714587 May 04, 2012 (137)
7 EXOME_CHIP ss491284055 May 04, 2012 (137)
8 CLINSEQ_SNP ss491581869 May 04, 2012 (137)
9 ILLUMINA ss533153835 Sep 08, 2015 (146)
10 ILLUMINA ss783435124 Sep 08, 2015 (146)
11 EVA-GONL ss974772645 Aug 21, 2014 (142)
12 1000GENOMES ss1289352909 Aug 21, 2014 (142)
13 EVA_FINRISK ss1584003645 Apr 01, 2015 (144)
14 EVA_DECODE ss1584132569 Apr 01, 2015 (144)
15 EVA_UK10K_ALSPAC ss1599383773 Apr 01, 2015 (144)
16 EVA_UK10K_TWINSUK ss1642377806 Apr 01, 2015 (144)
17 EVA_EXAC ss1685225665 Apr 01, 2015 (144)
18 ILLUMINA ss1917720987 Feb 12, 2016 (147)
19 ILLUMINA ss1958230895 Feb 12, 2016 (147)
20 JJLAB ss2019500188 Sep 14, 2016 (149)
21 USC_VALOUEV ss2147487057 Dec 20, 2016 (150)
22 HUMAN_LONGEVITY ss2159391489 Dec 20, 2016 (150)
23 TOPMED ss2321530710 Dec 20, 2016 (150)
24 GNOMAD ss2730999802 Nov 08, 2017 (151)
25 GNOMAD ss2746174192 Nov 08, 2017 (151)
26 GNOMAD ss2750679128 Nov 08, 2017 (151)
27 AFFY ss2984841269 Nov 08, 2017 (151)
28 SWEGEN ss2986155452 Nov 08, 2017 (151)
29 ILLUMINA ss3021043849 Nov 08, 2017 (151)
30 TOPMED ss3066487779 Nov 08, 2017 (151)
31 ILLUMINA ss3634302092 Oct 11, 2018 (152)
32 ILLUMINA ss3640009458 Oct 11, 2018 (152)
33 ILLUMINA ss3644477686 Oct 11, 2018 (152)
34 ILLUMINA ss3651365902 Oct 11, 2018 (152)
35 ILLUMINA ss3653615035 Oct 11, 2018 (152)
36 EGCUT_WGS ss3654266495 Jul 12, 2019 (153)
37 EVA_DECODE ss3685999327 Jul 12, 2019 (153)
38 ACPOP ss3726719297 Jul 12, 2019 (153)
39 ILLUMINA ss3744337415 Jul 12, 2019 (153)
40 ILLUMINA ss3744603023 Jul 12, 2019 (153)
41 EVA ss3823543026 Apr 25, 2020 (154)
42 EVA ss3825549313 Apr 25, 2020 (154)
43 SGDP_PRJ ss3848005819 Apr 25, 2020 (154)
44 KRGDB ss3892848782 Apr 25, 2020 (154)
45 KOGIC ss3943637757 Apr 25, 2020 (154)
46 EVA ss3986091284 Apr 25, 2021 (155)
47 TOPMED ss4436539244 Apr 25, 2021 (155)
48 TOMMO_GENOMICS ss5142070037 Apr 25, 2021 (155)
49 EVA ss5237258296 Apr 25, 2021 (155)
50 1000Genomes NC_000001.10 - 1115548 Oct 11, 2018 (152)
51 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 1115548 Oct 11, 2018 (152)
52 Genetic variation in the Estonian population NC_000001.10 - 1115548 Oct 11, 2018 (152)
53 ExAC NC_000001.10 - 1115548 Oct 11, 2018 (152)
54 FINRISK NC_000001.10 - 1115548 Apr 25, 2020 (154)
55 gnomAD - Genomes NC_000001.11 - 1180168 Apr 25, 2021 (155)
56 gnomAD - Exomes NC_000001.10 - 1115548 Jul 12, 2019 (153)
57 GO Exome Sequencing Project NC_000001.10 - 1115548 Oct 11, 2018 (152)
58 KOREAN population from KRGDB NC_000001.10 - 1115548 Apr 25, 2020 (154)
59 Korean Genome Project NC_000001.11 - 1180168 Apr 25, 2020 (154)
60 Northern Sweden NC_000001.10 - 1115548 Jul 12, 2019 (153)
61 SGDP_PRJ NC_000001.10 - 1115548 Apr 25, 2020 (154)
62 Siberian NC_000001.10 - 1115548 Apr 25, 2020 (154)
63 8.3KJPN NC_000001.10 - 1115548 Apr 25, 2021 (155)
64 TopMed NC_000001.11 - 1180168 Apr 25, 2021 (155)
65 UK 10K study - Twins NC_000001.10 - 1115548 Oct 11, 2018 (152)
66 ALFA NC_000001.11 - 1180168 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
ss217314369, ss217410441, ss469105688, ss491581869, ss1584132569 NC_000001.9:1105410:G:A NC_000001.11:1180167:G:A (self)
18094, 6215, 4743, 4399317, 106, 14628, 1763, 26176, 4162, 22799, 3411, 39344, 6215, ss328359983, ss341924374, ss489714587, ss491284055, ss533153835, ss783435124, ss974772645, ss1289352909, ss1584003645, ss1599383773, ss1642377806, ss1685225665, ss1917720987, ss1958230895, ss2019500188, ss2147487057, ss2321530710, ss2730999802, ss2746174192, ss2750679128, ss2984841269, ss2986155452, ss3021043849, ss3634302092, ss3640009458, ss3644477686, ss3651365902, ss3653615035, ss3654266495, ss3726719297, ss3744337415, ss3744603023, ss3823543026, ss3825549313, ss3848005819, ss3892848782, ss3986091284, ss5142070037, ss5237258296 NC_000001.10:1115547:G:A NC_000001.11:1180167:G:A (self)
158742, 15758, 83528, 145579, 2709128483, ss2159391489, ss3066487779, ss3685999327, ss3943637757, ss4436539244 NC_000001.11:1180167:G:A NC_000001.11:1180167:G: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 rs114390380

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