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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.

rs114587574

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1183035 (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=0.000094 (25/264690, TOPMED)
A=0.000109 (25/229426, GnomAD_exome)
A=0.000043 (6/140224, GnomAD) (+ 5 more)
A=0.00019 (13/68884, ExAC)
A=0.00066 (11/16760, 8.3KJPN)
A=0.00000 (0/14050, ALFA)
A=0.0006 (3/5008, 1000G)
A=0.0007 (2/2916, KOREAN)
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.1183035G>A
GRCh37.p13 chr 1 NC_000001.10:g.1118415G>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.857G>A R [CGG] > Q [CAG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform 2 NP_694986.2:p.Arg286Gln R (Arg) > Q (Gln) Missense Variant
TTLL10 transcript variant 1 NM_001130045.2:c.1076G>A R [CGG] > Q [CAG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform 1 NP_001123517.1:p.Arg359Gln R (Arg) > Q (Gln) Missense Variant
TTLL10 transcript variant 3 NM_001371649.1:c.1076G>A R [CGG] > Q [CAG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform 1 NP_001358578.1:p.Arg359Gln R (Arg) > Q (Gln) Missense Variant
TTLL10 transcript variant X10 XM_005244738.1:c.857G>A R [CGG] > Q [CAG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X8 XP_005244795.1:p.Arg286Gln R (Arg) > Q (Gln) Missense Variant
TTLL10 transcript variant X1 XM_017000906.1:c.995G>A R [CGG] > Q [CAG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X1 XP_016856395.1:p.Arg332Gln R (Arg) > Q (Gln) Missense Variant
TTLL10 transcript variant X2 XM_017000907.1:c.1076G>A R [CGG] > Q [CAG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X2 XP_016856396.1:p.Arg359Gln R (Arg) > Q (Gln) Missense Variant
TTLL10 transcript variant X3 XM_017000908.1:c.1076G>A R [CGG] > Q [CAG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X3 XP_016856397.1:p.Arg359Gln R (Arg) > Q (Gln) Missense Variant
TTLL10 transcript variant X4 XM_017000909.1:c.1076G>A R [CGG] > Q [CAG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X4 XP_016856398.1:p.Arg359Gln R (Arg) > Q (Gln) Missense Variant
TTLL10 transcript variant X6 XM_017000911.1:c.1076G>A R [CGG] > Q [CAG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X6 XP_016856400.1:p.Arg359Gln R (Arg) > Q (Gln) Missense Variant
TTLL10 transcript variant X7 XM_011541177.2:c.1076G>A R [CGG] > Q [CAG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X7 XP_011539479.1:p.Arg359Gln R (Arg) > Q (Gln) Missense Variant
TTLL10 transcript variant X8 XM_017000912.1:c.1076G>A R [CGG] > Q [CAG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X7 XP_016856401.1:p.Arg359Gln R (Arg) > Q (Gln) Missense Variant
TTLL10 transcript variant X5 XM_017000910.2:c.1076G>A R [CGG] > Q [CAG] Coding Sequence Variant
inactive polyglycylase TTLL10 isoform X5 XP_016856399.1:p.Arg359Gln R (Arg) > Q (Gln) Missense Variant
TTLL10 transcript variant X9 XR_001737088.1:n.1386G>A 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 14050 G=1.00000 A=0.00000
European Sub 9690 G=1.0000 A=0.0000
African Sub 2898 G=1.0000 A=0.0000
African Others Sub 114 G=1.000 A=0.000
African American Sub 2784 G=1.0000 A=0.0000
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 496 G=1.000 A=0.000


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 G=0.999906 A=0.000094
gnomAD - Exomes Global Study-wide 229426 G=0.999891 A=0.000109
gnomAD - Exomes European Sub 121090 G=0.999959 A=0.000041
gnomAD - Exomes Asian Sub 45978 G=0.99957 A=0.00043
gnomAD - Exomes American Sub 33446 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 13730 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 9536 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 5646 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140224 G=0.999957 A=0.000043
gnomAD - Genomes European Sub 75916 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 42044 G=1.00000 A=0.00000
gnomAD - Genomes American Sub 13664 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3130 G=0.9984 A=0.0016
gnomAD - Genomes Other Sub 2146 G=0.9995 A=0.0005
ExAC Global Study-wide 68884 G=0.99981 A=0.00019
ExAC Europe Sub 39880 G=0.99990 A=0.00010
ExAC Asian Sub 15950 G=0.99950 A=0.00050
ExAC American Sub 7090 G=0.9999 A=0.0001
ExAC African Sub 5474 G=1.0000 A=0.0000
ExAC Other Sub 490 G=1.000 A=0.000
8.3KJPN JAPANESE Study-wide 16760 G=0.99934 A=0.00066
1000Genomes Global Study-wide 5008 G=0.9994 A=0.0006
1000Genomes African Sub 1322 G=0.9992 A=0.0008
1000Genomes East Asian Sub 1008 G=0.9990 A=0.0010
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=0.999 A=0.001
1000Genomes American Sub 694 G=1.000 A=0.000
KOREAN population from KRGDB KOREAN Study-wide 2916 G=0.9993 A=0.0007
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.1183035= NC_000001.11:g.1183035G>A
GRCh37.p13 chr 1 NC_000001.10:g.1118415= NC_000001.10:g.1118415G>A
TTLL10 transcript variant 2 NM_153254.3:c.857= NM_153254.3:c.857G>A
TTLL10 transcript variant 2 NM_153254.2:c.857= NM_153254.2:c.857G>A
TTLL10 transcript variant X7 XM_011541177.2:c.1076= XM_011541177.2:c.1076G>A
TTLL10 transcript variant 1 NM_001130045.2:c.1076= NM_001130045.2:c.1076G>A
TTLL10 transcript variant 1 NM_001130045.1:c.1076= NM_001130045.1:c.1076G>A
TTLL10 transcript variant X5 XM_017000910.2:c.1076= XM_017000910.2:c.1076G>A
TTLL10 transcript variant X1 XM_017000906.1:c.995= XM_017000906.1:c.995G>A
TTLL10 transcript variant 3 NM_001371649.1:c.1076= NM_001371649.1:c.1076G>A
TTLL10 transcript variant X8 XM_017000912.1:c.1076= XM_017000912.1:c.1076G>A
TTLL10 transcript variant X4 XM_017000909.1:c.1076= XM_017000909.1:c.1076G>A
TTLL10 transcript variant X10 XM_005244738.1:c.857= XM_005244738.1:c.857G>A
TTLL10 transcript variant X9 XR_001737088.1:n.1386= XR_001737088.1:n.1386G>A
TTLL10 transcript variant X3 XM_017000908.1:c.1076= XM_017000908.1:c.1076G>A
TTLL10 transcript variant X2 XM_017000907.1:c.1076= XM_017000907.1:c.1076G>A
TTLL10 transcript variant X6 XM_017000911.1:c.1076= XM_017000911.1:c.1076G>A
inactive polyglycylase TTLL10 isoform 2 NP_694986.2:p.Arg286= NP_694986.2:p.Arg286Gln
inactive polyglycylase TTLL10 isoform X7 XP_011539479.1:p.Arg359= XP_011539479.1:p.Arg359Gln
inactive polyglycylase TTLL10 isoform 1 NP_001123517.1:p.Arg359= NP_001123517.1:p.Arg359Gln
inactive polyglycylase TTLL10 isoform X5 XP_016856399.1:p.Arg359= XP_016856399.1:p.Arg359Gln
inactive polyglycylase TTLL10 isoform X1 XP_016856395.1:p.Arg332= XP_016856395.1:p.Arg332Gln
inactive polyglycylase TTLL10 isoform 1 NP_001358578.1:p.Arg359= NP_001358578.1:p.Arg359Gln
inactive polyglycylase TTLL10 isoform X7 XP_016856401.1:p.Arg359= XP_016856401.1:p.Arg359Gln
inactive polyglycylase TTLL10 isoform X4 XP_016856398.1:p.Arg359= XP_016856398.1:p.Arg359Gln
inactive polyglycylase TTLL10 isoform X8 XP_005244795.1:p.Arg286= XP_005244795.1:p.Arg286Gln
inactive polyglycylase TTLL10 isoform X3 XP_016856397.1:p.Arg359= XP_016856397.1:p.Arg359Gln
inactive polyglycylase TTLL10 isoform X2 XP_016856396.1:p.Arg359= XP_016856396.1:p.Arg359Gln
inactive polyglycylase TTLL10 isoform X6 XP_016856400.1:p.Arg359= XP_016856400.1:p.Arg359Gln
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#.

14 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss217390814 Jul 14, 2010 (132)
2 1000GENOMES ss1289353066 Aug 21, 2014 (142)
3 EVA_EXAC ss1685225944 Apr 01, 2015 (144)
4 HUMAN_LONGEVITY ss2159391736 Dec 20, 2016 (150)
5 TOPMED ss2321530971 Dec 20, 2016 (150)
6 GNOMAD ss2731000242 Nov 08, 2017 (151)
7 GNOMAD ss2746174353 Nov 08, 2017 (151)
8 GNOMAD ss2750679482 Nov 08, 2017 (151)
9 TOPMED ss3066488540 Nov 08, 2017 (151)
10 EVA ss3745725101 Jul 12, 2019 (153)
11 KRGDB ss3892848870 Apr 25, 2020 (154)
12 TOPMED ss4436540177 Apr 25, 2021 (155)
13 TOMMO_GENOMICS ss5142070195 Apr 25, 2021 (155)
14 EVA ss5236862470 Apr 25, 2021 (155)
15 1000Genomes NC_000001.10 - 1118415 Oct 11, 2018 (152)
16 ExAC NC_000001.10 - 1118415 Oct 11, 2018 (152)
17 gnomAD - Genomes NC_000001.11 - 1183035 Apr 25, 2021 (155)
18 gnomAD - Exomes NC_000001.10 - 1118415 Jul 12, 2019 (153)
19 KOREAN population from KRGDB NC_000001.10 - 1118415 Apr 25, 2020 (154)
20 8.3KJPN NC_000001.10 - 1118415 Apr 25, 2021 (155)
21 TopMed NC_000001.11 - 1183035 Apr 25, 2021 (155)
22 ALFA NC_000001.11 - 1183035 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
ss217390814 NC_000001.9:1108277:G:A NC_000001.11:1183034:G:A (self)
18252, 4399624, 15073, 26264, 39502, ss1289353066, ss1685225944, ss2321530971, ss2731000242, ss2746174353, ss2750679482, ss3745725101, ss3892848870, ss5142070195 NC_000001.10:1118414:G:A NC_000001.11:1183034:G:A (self)
159531, 84120, 146512, 5765325767, ss2159391736, ss3066488540, ss4436540177, ss5236862470 NC_000001.11:1183034:G:A NC_000001.11:1183034: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 rs114587574

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