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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.

rs74475385

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1185108 (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
A>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.020114 (5324/264690, TOPMED)
C=0.005122 (1277/249316, GnomAD_exome)
C=0.002771 (395/142530, ALFA) (+ 9 more)
C=0.019351 (2714/140250, GnomAD)
C=0.006398 (761/118942, ExAC)
C=0.02868 (2257/78698, PAGE_STUDY)
C=0.02199 (286/13006, GO-ESP)
C=0.0218 (109/5008, 1000G)
C=0.0002 (1/4480, Estonian)
C=0.005 (1/216, Qatari)
A=0.5 (5/10, SGDP_PRJ)
C=0.5 (5/10, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TTLL10 : Missense 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.1185108A>C
GRCh37.p13 chr 1 NC_000001.10:g.1120488A>C
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.1181A>C K [AAG] > T [ACG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform 2 NP_694986.2:p.Lys394Thr K (Lys) > T (Thr) Missense Variant
TTLL10 transcript variant 1 NM_001130045.2:c.1400A>C K [AAG] > T [ACG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform 1 NP_001123517.1:p.Lys467Thr K (Lys) > T (Thr) Missense Variant
TTLL10 transcript variant 3 NM_001371649.1:c.1400A>C K [AAG] > T [ACG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform 1 NP_001358578.1:p.Lys467Thr K (Lys) > T (Thr) Missense Variant
TTLL10 transcript variant X10 XM_005244738.1:c.1181A>C K [AAG] > T [ACG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X8 XP_005244795.1:p.Lys394Thr K (Lys) > T (Thr) Missense Variant
TTLL10 transcript variant X1 XM_017000906.1:c.1319A>C K [AAG] > T [ACG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X1 XP_016856395.1:p.Lys440Thr K (Lys) > T (Thr) Missense Variant
TTLL10 transcript variant X2 XM_017000907.1:c.1400A>C K [AAG] > T [ACG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X2 XP_016856396.1:p.Lys467Thr K (Lys) > T (Thr) Missense Variant
TTLL10 transcript variant X3 XM_017000908.1:c.1400A>C K [AAG] > T [ACG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X3 XP_016856397.1:p.Lys467Thr K (Lys) > T (Thr) Missense Variant
TTLL10 transcript variant X4 XM_017000909.1:c.1400A>C K [AAG] > T [ACG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X4 XP_016856398.1:p.Lys467Thr K (Lys) > T (Thr) Missense Variant
TTLL10 transcript variant X6 XM_017000911.1:c.1400A>C K [AAG] > T [ACG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X6 XP_016856400.1:p.Lys467Thr K (Lys) > T (Thr) Missense Variant
TTLL10 transcript variant X7 XM_011541177.2:c.1400A>C K [AAG] > T [ACG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X7 XP_011539479.1:p.Lys467Thr K (Lys) > T (Thr) Missense Variant
TTLL10 transcript variant X8 XM_017000912.1:c.1400A>C K [AAG] > T [ACG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X7 XP_016856401.1:p.Lys467Thr K (Lys) > T (Thr) Missense Variant
TTLL10 transcript variant X5 XM_017000910.2:c.1400A>C K [AAG] > T [ACG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X5 XP_016856399.1:p.Lys467Thr K (Lys) > T (Thr) Missense Variant
TTLL10 transcript variant X9 XR_001737088.1:n.1727A>C N/A Non Coding Transcript Variant
TTLL10 transcript variant X11 XR_001737089.1:n. N/A Genic Downstream 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 142530 A=0.997229 C=0.002771
European Sub 115868 A=0.999275 C=0.000725
African Sub 4494 A=0.9437 C=0.0563
African Others Sub 124 A=0.944 C=0.056
African American Sub 4370 A=0.9437 C=0.0563
Asian Sub 3214 A=1.0000 C=0.0000
East Asian Sub 1960 A=1.0000 C=0.0000
Other Asian Sub 1254 A=1.0000 C=0.0000
Latin American 1 Sub 530 A=0.981 C=0.019
Latin American 2 Sub 690 A=0.996 C=0.004
South Asian Sub 120 A=1.000 C=0.000
Other Sub 17614 A=0.99745 C=0.00255


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
TopMed Global Study-wide 264690 A=0.979886 C=0.020114
gnomAD - Exomes Global Study-wide 249316 A=0.994878 C=0.005122
gnomAD - Exomes European Sub 133806 A=0.999193 C=0.000807
gnomAD - Exomes Asian Sub 48940 A=0.99986 C=0.00014
gnomAD - Exomes American Sub 34322 A=0.99639 C=0.00361
gnomAD - Exomes African Sub 16146 A=0.93683 C=0.06317
gnomAD - Exomes Ashkenazi Jewish Sub 10016 A=0.99990 C=0.00010
gnomAD - Exomes Other Sub 6086 A=0.9972 C=0.0028
gnomAD - Genomes Global Study-wide 140250 A=0.980649 C=0.019351
gnomAD - Genomes European Sub 75940 A=0.99924 C=0.00076
gnomAD - Genomes African Sub 42048 A=0.94016 C=0.05984
gnomAD - Genomes American Sub 13652 A=0.99253 C=0.00747
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3132 A=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2154 A=0.9824 C=0.0176
ExAC Global Study-wide 118942 A=0.993602 C=0.006398
ExAC Europe Sub 71436 A=0.99929 C=0.00071
ExAC Asian Sub 24956 A=0.99996 C=0.00004
ExAC American Sub 11464 A=0.99712 C=0.00288
ExAC African Sub 10224 A=0.93417 C=0.06583
ExAC Other Sub 862 A=0.997 C=0.003
The PAGE Study Global Study-wide 78698 A=0.97132 C=0.02868
The PAGE Study AfricanAmerican Sub 32514 A=0.94322 C=0.05678
The PAGE Study Mexican Sub 10810 A=0.99611 C=0.00389
The PAGE Study Asian Sub 8318 A=0.9999 C=0.0001
The PAGE Study PuertoRican Sub 7918 A=0.9830 C=0.0170
The PAGE Study NativeHawaiian Sub 4534 A=0.9985 C=0.0015
The PAGE Study Cuban Sub 4228 A=0.9884 C=0.0116
The PAGE Study Dominican Sub 3828 A=0.9692 C=0.0308
The PAGE Study CentralAmerican Sub 2450 A=0.9886 C=0.0114
The PAGE Study SouthAmerican Sub 1982 A=0.9934 C=0.0066
The PAGE Study NativeAmerican Sub 1260 A=0.9857 C=0.0143
The PAGE Study SouthAsian Sub 856 A=1.000 C=0.000
GO Exome Sequencing Project Global Study-wide 13006 A=0.97801 C=0.02199
GO Exome Sequencing Project European American Sub 8600 A=0.9995 C=0.0005
GO Exome Sequencing Project African American Sub 4406 A=0.9360 C=0.0640
1000Genomes Global Study-wide 5008 A=0.9782 C=0.0218
1000Genomes African Sub 1322 A=0.9221 C=0.0779
1000Genomes East Asian Sub 1008 A=1.0000 C=0.0000
1000Genomes Europe Sub 1006 A=0.9990 C=0.0010
1000Genomes South Asian Sub 978 A=1.000 C=0.000
1000Genomes American Sub 694 A=0.993 C=0.007
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9998 C=0.0002
Qatari Global Study-wide 216 A=0.995 C=0.005
SGDP_PRJ Global Study-wide 10 A=0.5 C=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 A= C
GRCh38.p13 chr 1 NC_000001.11:g.1185108= NC_000001.11:g.1185108A>C
GRCh37.p13 chr 1 NC_000001.10:g.1120488= NC_000001.10:g.1120488A>C
TTLL10 transcript variant 2 NM_153254.3:c.1181= NM_153254.3:c.1181A>C
TTLL10 transcript variant 2 NM_153254.2:c.1181= NM_153254.2:c.1181A>C
TTLL10 transcript variant X7 XM_011541177.2:c.1400= XM_011541177.2:c.1400A>C
TTLL10 transcript variant 1 NM_001130045.2:c.1400= NM_001130045.2:c.1400A>C
TTLL10 transcript variant 1 NM_001130045.1:c.1400= NM_001130045.1:c.1400A>C
TTLL10 transcript variant X5 XM_017000910.2:c.1400= XM_017000910.2:c.1400A>C
TTLL10 transcript variant X1 XM_017000906.1:c.1319= XM_017000906.1:c.1319A>C
TTLL10 transcript variant 3 NM_001371649.1:c.1400= NM_001371649.1:c.1400A>C
TTLL10 transcript variant X8 XM_017000912.1:c.1400= XM_017000912.1:c.1400A>C
TTLL10 transcript variant X4 XM_017000909.1:c.1400= XM_017000909.1:c.1400A>C
TTLL10 transcript variant X10 XM_005244738.1:c.1181= XM_005244738.1:c.1181A>C
TTLL10 transcript variant X9 XR_001737088.1:n.1727= XR_001737088.1:n.1727A>C
TTLL10 transcript variant X3 XM_017000908.1:c.1400= XM_017000908.1:c.1400A>C
TTLL10 transcript variant X2 XM_017000907.1:c.1400= XM_017000907.1:c.1400A>C
TTLL10 transcript variant X6 XM_017000911.1:c.1400= XM_017000911.1:c.1400A>C
inactive polyglycylase TTLL10 isoform 2 NP_694986.2:p.Lys394= NP_694986.2:p.Lys394Thr
inactive polyglycylase TTLL10 isoform X7 XP_011539479.1:p.Lys467= XP_011539479.1:p.Lys467Thr
inactive polyglycylase TTLL10 isoform 1 NP_001123517.1:p.Lys467= NP_001123517.1:p.Lys467Thr
inactive polyglycylase TTLL10 isoform X5 XP_016856399.1:p.Lys467= XP_016856399.1:p.Lys467Thr
inactive polyglycylase TTLL10 isoform X1 XP_016856395.1:p.Lys440= XP_016856395.1:p.Lys440Thr
inactive polyglycylase TTLL10 isoform 1 NP_001358578.1:p.Lys467= NP_001358578.1:p.Lys467Thr
inactive polyglycylase TTLL10 isoform X7 XP_016856401.1:p.Lys467= XP_016856401.1:p.Lys467Thr
inactive polyglycylase TTLL10 isoform X4 XP_016856398.1:p.Lys467= XP_016856398.1:p.Lys467Thr
inactive polyglycylase TTLL10 isoform X8 XP_005244795.1:p.Lys394= XP_005244795.1:p.Lys394Thr
inactive polyglycylase TTLL10 isoform X3 XP_016856397.1:p.Lys467= XP_016856397.1:p.Lys467Thr
inactive polyglycylase TTLL10 isoform X2 XP_016856396.1:p.Lys467= XP_016856396.1:p.Lys467Thr
inactive polyglycylase TTLL10 isoform X6 XP_016856400.1:p.Lys467= XP_016856400.1:p.Lys467Thr
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#.

51 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 ILLUMINA ss161037387 Dec 01, 2009 (131)
2 1000GENOMES ss217405755 Jul 14, 2010 (132)
3 1000GENOMES ss217410907 Jul 14, 2010 (132)
4 1000GENOMES ss218192293 Jul 14, 2010 (132)
5 NHLBI-ESP ss341924449 May 09, 2011 (134)
6 ILLUMINA ss479218455 Sep 08, 2015 (146)
7 1000GENOMES ss489714634 May 04, 2012 (137)
8 EXOME_CHIP ss491284081 May 04, 2012 (137)
9 CLINSEQ_SNP ss491581884 May 04, 2012 (137)
10 ILLUMINA ss534048531 Sep 08, 2015 (146)
11 TISHKOFF ss553714424 Apr 25, 2013 (138)
12 ILLUMINA ss780767188 Aug 21, 2014 (142)
13 ILLUMINA ss783446578 Aug 21, 2014 (142)
14 1000GENOMES ss1289353176 Aug 21, 2014 (142)
15 EVA_DECODE ss1584132620 Apr 01, 2015 (144)
16 EVA_EXAC ss1685226086 Apr 01, 2015 (144)
17 ILLUMINA ss1751863633 Sep 08, 2015 (146)
18 ILLUMINA ss1917721008 Feb 12, 2016 (147)
19 WEILL_CORNELL_DGM ss1917964783 Feb 12, 2016 (147)
20 ILLUMINA ss1945981842 Feb 12, 2016 (147)
21 ILLUMINA ss1958230934 Feb 12, 2016 (147)
22 HUMAN_LONGEVITY ss2159391949 Dec 20, 2016 (150)
23 TOPMED ss2321531160 Dec 20, 2016 (150)
24 GNOMAD ss2731000422 Nov 08, 2017 (151)
25 GNOMAD ss2746174411 Nov 08, 2017 (151)
26 GNOMAD ss2750679726 Nov 08, 2017 (151)
27 AFFY ss2984841297 Nov 08, 2017 (151)
28 SWEGEN ss2986155555 Nov 08, 2017 (151)
29 ILLUMINA ss3021043888 Nov 08, 2017 (151)
30 TOPMED ss3066489037 Nov 08, 2017 (151)
31 ILLUMINA ss3626007226 Oct 11, 2018 (152)
32 ILLUMINA ss3626007227 Oct 11, 2018 (152)
33 ILLUMINA ss3634302113 Oct 11, 2018 (152)
34 ILLUMINA ss3635978743 Oct 11, 2018 (152)
35 ILLUMINA ss3640009479 Oct 11, 2018 (152)
36 ILLUMINA ss3644477706 Oct 11, 2018 (152)
37 ILLUMINA ss3651365943 Oct 11, 2018 (152)
38 ILLUMINA ss3653615063 Oct 11, 2018 (152)
39 EGCUT_WGS ss3654266586 Jul 12, 2019 (153)
40 EVA_DECODE ss3685999426 Jul 12, 2019 (153)
41 ILLUMINA ss3724988544 Jul 12, 2019 (153)
42 ILLUMINA ss3744337436 Jul 12, 2019 (153)
43 ILLUMINA ss3744603044 Jul 12, 2019 (153)
44 PAGE_CC ss3770778903 Jul 12, 2019 (153)
45 ILLUMINA ss3772104801 Jul 12, 2019 (153)
46 KHV_HUMAN_GENOMES ss3798747778 Jul 12, 2019 (153)
47 EVA ss3823543137 Apr 25, 2020 (154)
48 EVA ss3825982912 Apr 25, 2020 (154)
49 SGDP_PRJ ss3848005957 Apr 25, 2020 (154)
50 EVA ss3986091338 Apr 25, 2021 (155)
51 TOPMED ss4436540791 Apr 25, 2021 (155)
52 1000Genomes NC_000001.10 - 1120488 Oct 11, 2018 (152)
53 Genetic variation in the Estonian population NC_000001.10 - 1120488 Oct 11, 2018 (152)
54 ExAC NC_000001.10 - 1120488 Oct 11, 2018 (152)
55 gnomAD - Genomes NC_000001.11 - 1185108 Apr 25, 2021 (155)
56 gnomAD - Exomes NC_000001.10 - 1120488 Jul 12, 2019 (153)
57 GO Exome Sequencing Project NC_000001.10 - 1120488 Oct 11, 2018 (152)
58 The PAGE Study NC_000001.11 - 1185108 Jul 12, 2019 (153)
59 Qatari NC_000001.10 - 1120488 Apr 25, 2020 (154)
60 SGDP_PRJ NC_000001.10 - 1120488 Apr 25, 2020 (154)
61 TopMed NC_000001.11 - 1185108 Apr 25, 2021 (155)
62 ALFA NC_000001.11 - 1185108 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
ss161037387, ss217405755, ss217410907, ss491581884, ss1584132620 NC_000001.9:1110350:A:C NC_000001.11:1185107:A:C (self)
18361, 4834, 4399776, 15269, 1874, 6713, 22937, ss218192293, ss341924449, ss479218455, ss489714634, ss491284081, ss534048531, ss553714424, ss780767188, ss783446578, ss1289353176, ss1685226086, ss1751863633, ss1917721008, ss1917964783, ss1945981842, ss1958230934, ss2321531160, ss2731000422, ss2746174411, ss2750679726, ss2984841297, ss2986155555, ss3021043888, ss3626007226, ss3626007227, ss3634302113, ss3635978743, ss3640009479, ss3644477706, ss3651365943, ss3653615063, ss3654266586, ss3744337436, ss3744603044, ss3772104801, ss3823543137, ss3825982912, ss3848005957, ss3986091338 NC_000001.10:1120487:A:C NC_000001.11:1185107:A:C (self)
160069, 372, 84511, 147126, 3081281610, ss2159391949, ss3066489037, ss3685999426, ss3724988544, ss3770778903, ss3798747778, ss4436540791 NC_000001.11:1185107:A:C NC_000001.11:1185107:A:C (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 rs74475385

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