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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.

rs142216439

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:39540036 (GRCh38.p14) 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>A / C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000015 (4/264690, TOPMED)
G=0.000025 (6/241748, GnomAD_exome)
G=0.000007 (1/140174, GnomAD) (+ 6 more)
G=0.000033 (4/120750, ExAC)
G=0.00000 (0/79484, ALFA)
G=0.00005 (4/78700, PAGE_STUDY)
G=0.00008 (1/13006, GO-ESP)
G=0.0003 (2/6404, 1000G_30x)
G=0.0002 (1/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
KIF6 : Missense Variant
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 79484 C=1.00000 G=0.00000
European Sub 69394 C=1.00000 G=0.00000
African Sub 3698 C=1.0000 G=0.0000
African Others Sub 166 C=1.000 G=0.000
African American Sub 3532 C=1.0000 G=0.0000
Asian Sub 3274 C=1.0000 G=0.0000
East Asian Sub 2648 C=1.0000 G=0.0000
Other Asian Sub 626 C=1.000 G=0.000
Latin American 1 Sub 436 C=1.000 G=0.000
Latin American 2 Sub 928 C=1.000 G=0.000
South Asian Sub 274 C=1.000 G=0.000
Other Sub 1480 C=1.0000 G=0.0000


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=0.999985 G=0.000015
gnomAD - Exomes Global Study-wide 241748 C=0.999975 G=0.000025
gnomAD - Exomes European Sub 132436 C=0.999985 G=0.000015
gnomAD - Exomes Asian Sub 45650 C=1.00000 G=0.00000
gnomAD - Exomes American Sub 32124 C=0.99991 G=0.00009
gnomAD - Exomes African Sub 16128 C=0.99994 G=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 9514 C=1.0000 G=0.0000
gnomAD - Exomes Other Sub 5896 C=1.0000 G=0.0000
gnomAD - Genomes Global Study-wide 140174 C=0.999993 G=0.000007
gnomAD - Genomes European Sub 75916 C=0.99999 G=0.00001
gnomAD - Genomes African Sub 42002 C=1.00000 G=0.00000
gnomAD - Genomes American Sub 13650 C=1.00000 G=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2150 C=1.0000 G=0.0000
ExAC Global Study-wide 120750 C=0.999967 G=0.000033
ExAC Europe Sub 73176 C=0.99997 G=0.00003
ExAC Asian Sub 24696 C=1.00000 G=0.00000
ExAC American Sub 11572 C=0.99991 G=0.00009
ExAC African Sub 10402 C=0.99990 G=0.00010
ExAC Other Sub 904 C=1.000 G=0.000
Allele Frequency Aggregator Total Global 79484 C=1.00000 G=0.00000
Allele Frequency Aggregator European Sub 69394 C=1.00000 G=0.00000
Allele Frequency Aggregator African Sub 3698 C=1.0000 G=0.0000
Allele Frequency Aggregator Asian Sub 3274 C=1.0000 G=0.0000
Allele Frequency Aggregator Other Sub 1480 C=1.0000 G=0.0000
Allele Frequency Aggregator Latin American 2 Sub 928 C=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 436 C=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 274 C=1.000 G=0.000
The PAGE Study Global Study-wide 78700 C=0.99995 G=0.00005
The PAGE Study AfricanAmerican Sub 32514 C=0.99997 G=0.00003
The PAGE Study Mexican Sub 10810 C=1.00000 G=0.00000
The PAGE Study Asian Sub 8318 C=1.0000 G=0.0000
The PAGE Study PuertoRican Sub 7918 C=1.0000 G=0.0000
The PAGE Study NativeHawaiian Sub 4534 C=1.0000 G=0.0000
The PAGE Study Cuban Sub 4230 C=0.9995 G=0.0005
The PAGE Study Dominican Sub 3828 C=1.0000 G=0.0000
The PAGE Study CentralAmerican Sub 2450 C=0.9996 G=0.0004
The PAGE Study SouthAmerican Sub 1982 C=1.0000 G=0.0000
The PAGE Study NativeAmerican Sub 1260 C=1.0000 G=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 G=0.000
GO Exome Sequencing Project Global Study-wide 13006 C=0.99992 G=0.00008
GO Exome Sequencing Project European American Sub 8600 C=1.0000 G=0.0000
GO Exome Sequencing Project African American Sub 4406 C=0.9998 G=0.0002
1000Genomes_30x Global Study-wide 6404 C=0.9997 G=0.0003
1000Genomes_30x African Sub 1786 C=1.0000 G=0.0000
1000Genomes_30x Europe Sub 1266 C=1.0000 G=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 G=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 G=0.0000
1000Genomes_30x American Sub 980 C=0.998 G=0.002
1000Genomes Global Study-wide 5008 C=0.9998 G=0.0002
1000Genomes African Sub 1322 C=1.0000 G=0.0000
1000Genomes East Asian Sub 1008 C=1.0000 G=0.0000
1000Genomes Europe Sub 1006 C=1.0000 G=0.0000
1000Genomes South Asian Sub 978 C=1.000 G=0.000
1000Genomes American Sub 694 C=0.999 G=0.001
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.p14 chr 6 NC_000006.12:g.39540036C>A
GRCh38.p14 chr 6 NC_000006.12:g.39540036C>G
GRCh37.p13 chr 6 NC_000006.11:g.39507812C>A
GRCh37.p13 chr 6 NC_000006.11:g.39507812C>G
KIF6 RefSeqGene NG_054928.1:g.190389G>T
KIF6 RefSeqGene NG_054928.1:g.190389G>C
Gene: KIF6, kinesin family member 6 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
KIF6 transcript variant 3 NM_001289021.3:c.1477+446…

NM_001289021.3:c.1477+4468G>T

N/A Intron Variant
KIF6 transcript variant 4 NM_001289024.3:c. N/A Genic Upstream Transcript Variant
KIF6 transcript variant 5 NM_001351566.2:c. N/A Genic Upstream Transcript Variant
KIF6 transcript variant 6 NM_001351503.2:c. N/A Genic Downstream Transcript Variant
KIF6 transcript variant 1 NM_145027.6:c.1612G>T G [GGG] > W [TGG] Coding Sequence Variant
kinesin-like protein KIF6 isoform 1 NP_659464.3:p.Gly538Trp G (Gly) > W (Trp) Missense Variant
KIF6 transcript variant 1 NM_145027.6:c.1612G>C G [GGG] > R [CGG] Coding Sequence Variant
kinesin-like protein KIF6 isoform 1 NP_659464.3:p.Gly538Arg G (Gly) > R (Arg) Missense Variant
KIF6 transcript variant 2 NM_001289020.3:c.1612G>T G [GGG] > W [TGG] Coding Sequence Variant
kinesin-like protein KIF6 isoform 2 NP_001275949.1:p.Gly538Trp G (Gly) > W (Trp) Missense Variant
KIF6 transcript variant 2 NM_001289020.3:c.1612G>C G [GGG] > R [CGG] Coding Sequence Variant
kinesin-like protein KIF6 isoform 2 NP_001275949.1:p.Gly538Arg G (Gly) > R (Arg) Missense Variant
KIF6 transcript variant X6 XM_047418331.1:c. N/A Genic Upstream Transcript Variant
KIF6 transcript variant X7 XM_011514361.3:c. N/A Genic Downstream Transcript Variant
KIF6 transcript variant X1 XM_005248904.5:c.1612G>T G [GGG] > W [TGG] Coding Sequence Variant
kinesin-like protein KIF6 isoform X1 XP_005248961.1:p.Gly538Trp G (Gly) > W (Trp) Missense Variant
KIF6 transcript variant X1 XM_005248904.5:c.1612G>C G [GGG] > R [CGG] Coding Sequence Variant
kinesin-like protein KIF6 isoform X1 XP_005248961.1:p.Gly538Arg G (Gly) > R (Arg) Missense Variant
KIF6 transcript variant X2 XM_011514357.4:c.1612G>T G [GGG] > W [TGG] Coding Sequence Variant
kinesin-like protein KIF6 isoform X2 XP_011512659.1:p.Gly538Trp G (Gly) > W (Trp) Missense Variant
KIF6 transcript variant X2 XM_011514357.4:c.1612G>C G [GGG] > R [CGG] Coding Sequence Variant
kinesin-like protein KIF6 isoform X2 XP_011512659.1:p.Gly538Arg G (Gly) > R (Arg) Missense Variant
KIF6 transcript variant X3 XM_011514358.4:c.1612G>T G [GGG] > W [TGG] Coding Sequence Variant
kinesin-like protein KIF6 isoform X3 XP_011512660.1:p.Gly538Trp G (Gly) > W (Trp) Missense Variant
KIF6 transcript variant X3 XM_011514358.4:c.1612G>C G [GGG] > R [CGG] Coding Sequence Variant
kinesin-like protein KIF6 isoform X3 XP_011512660.1:p.Gly538Arg G (Gly) > R (Arg) Missense Variant
KIF6 transcript variant X4 XM_047418330.1:c.1612G>T G [GGG] > W [TGG] Coding Sequence Variant
kinesin-like protein KIF6 isoform X4 XP_047274286.1:p.Gly538Trp G (Gly) > W (Trp) Missense Variant
KIF6 transcript variant X4 XM_047418330.1:c.1612G>C G [GGG] > R [CGG] Coding Sequence Variant
kinesin-like protein KIF6 isoform X4 XP_047274286.1:p.Gly538Arg G (Gly) > R (Arg) Missense Variant
KIF6 transcript variant X5 XR_001743238.2:n.1710G>T N/A Non Coding Transcript Variant
KIF6 transcript variant X5 XR_001743238.2:n.1710G>C N/A Non Coding 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
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= A G
GRCh38.p14 chr 6 NC_000006.12:g.39540036= NC_000006.12:g.39540036C>A NC_000006.12:g.39540036C>G
GRCh37.p13 chr 6 NC_000006.11:g.39507812= NC_000006.11:g.39507812C>A NC_000006.11:g.39507812C>G
KIF6 RefSeqGene NG_054928.1:g.190389= NG_054928.1:g.190389G>T NG_054928.1:g.190389G>C
KIF6 transcript variant 1 NM_145027.6:c.1612= NM_145027.6:c.1612G>T NM_145027.6:c.1612G>C
KIF6 transcript variant 1 NM_145027.5:c.1612= NM_145027.5:c.1612G>T NM_145027.5:c.1612G>C
KIF6 transcript variant 1 NM_145027.4:c.1612= NM_145027.4:c.1612G>T NM_145027.4:c.1612G>C
KIF6 transcript variant 2 NM_001289020.3:c.1612= NM_001289020.3:c.1612G>T NM_001289020.3:c.1612G>C
KIF6 transcript variant 2 NM_001289020.2:c.1612= NM_001289020.2:c.1612G>T NM_001289020.2:c.1612G>C
KIF6 transcript variant 2 NM_001289020.1:c.1612= NM_001289020.1:c.1612G>T NM_001289020.1:c.1612G>C
KIF6 transcript variant X1 XM_005248904.5:c.1612= XM_005248904.5:c.1612G>T XM_005248904.5:c.1612G>C
KIF6 transcript variant X1 XM_005248904.4:c.1612= XM_005248904.4:c.1612G>T XM_005248904.4:c.1612G>C
KIF6 transcript variant X1 XM_005248904.3:c.1612= XM_005248904.3:c.1612G>T XM_005248904.3:c.1612G>C
KIF6 transcript variant X1 XM_005248904.2:c.1612= XM_005248904.2:c.1612G>T XM_005248904.2:c.1612G>C
KIF6 transcript variant X1 XM_005248904.1:c.1612= XM_005248904.1:c.1612G>T XM_005248904.1:c.1612G>C
KIF6 transcript variant X2 XM_011514357.4:c.1612= XM_011514357.4:c.1612G>T XM_011514357.4:c.1612G>C
KIF6 transcript variant X2 XM_011514357.3:c.1612= XM_011514357.3:c.1612G>T XM_011514357.3:c.1612G>C
KIF6 transcript variant X2 XM_011514357.2:c.1612= XM_011514357.2:c.1612G>T XM_011514357.2:c.1612G>C
KIF6 transcript variant X2 XM_011514357.1:c.1612= XM_011514357.1:c.1612G>T XM_011514357.1:c.1612G>C
KIF6 transcript variant X3 XM_011514358.4:c.1612= XM_011514358.4:c.1612G>T XM_011514358.4:c.1612G>C
KIF6 transcript variant X3 XM_011514358.3:c.1612= XM_011514358.3:c.1612G>T XM_011514358.3:c.1612G>C
KIF6 transcript variant X3 XM_011514358.2:c.1612= XM_011514358.2:c.1612G>T XM_011514358.2:c.1612G>C
KIF6 transcript variant X3 XM_011514358.1:c.1612= XM_011514358.1:c.1612G>T XM_011514358.1:c.1612G>C
KIF6 transcript variant X5 XR_001743238.2:n.1710= XR_001743238.2:n.1710G>T XR_001743238.2:n.1710G>C
KIF6 transcript variant X7 XR_001743238.1:n.1707= XR_001743238.1:n.1707G>T XR_001743238.1:n.1707G>C
KIF6 transcript variant X4 XM_047418330.1:c.1612= XM_047418330.1:c.1612G>T XM_047418330.1:c.1612G>C
kinesin-like protein KIF6 isoform 1 NP_659464.3:p.Gly538= NP_659464.3:p.Gly538Trp NP_659464.3:p.Gly538Arg
kinesin-like protein KIF6 isoform 2 NP_001275949.1:p.Gly538= NP_001275949.1:p.Gly538Trp NP_001275949.1:p.Gly538Arg
kinesin-like protein KIF6 isoform X1 XP_005248961.1:p.Gly538= XP_005248961.1:p.Gly538Trp XP_005248961.1:p.Gly538Arg
kinesin-like protein KIF6 isoform X2 XP_011512659.1:p.Gly538= XP_011512659.1:p.Gly538Trp XP_011512659.1:p.Gly538Arg
kinesin-like protein KIF6 isoform X3 XP_011512660.1:p.Gly538= XP_011512660.1:p.Gly538Trp XP_011512660.1:p.Gly538Arg
kinesin-like protein KIF6 isoform X4 XP_047274286.1:p.Gly538= XP_047274286.1:p.Gly538Trp XP_047274286.1:p.Gly538Arg
KIF6 transcript variant 3 NM_001289021.3:c.1477+4468= NM_001289021.3:c.1477+4468G>T NM_001289021.3:c.1477+4468G>C
KIF6 transcript variant X3 XM_005248906.1:c.1477+4468= XM_005248906.1:c.1477+4468G>T XM_005248906.1:c.1477+4468G>C
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#.

36 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342211318 May 09, 2011 (134)
2 1000GENOMES ss488835912 May 04, 2012 (137)
3 EXOME_CHIP ss491385449 May 04, 2012 (137)
4 ILLUMINA ss780849023 Aug 21, 2014 (142)
5 ILLUMINA ss783532779 Aug 21, 2014 (142)
6 1000GENOMES ss1319796281 Aug 21, 2014 (142)
7 EVA_EXAC ss1688305173 Apr 01, 2015 (144)
8 ILLUMINA ss1752635884 Sep 08, 2015 (146)
9 ILLUMINA ss1917805136 Feb 12, 2016 (147)
10 ILLUMINA ss1946177296 Feb 12, 2016 (147)
11 ILLUMINA ss1958902433 Feb 12, 2016 (147)
12 HUMAN_LONGEVITY ss2283392180 Dec 20, 2016 (150)
13 GNOMAD ss2735763968 Nov 08, 2017 (151)
14 AFFY ss2985367111 Nov 08, 2017 (151)
15 ILLUMINA ss3022613839 Nov 08, 2017 (151)
16 ILLUMINA ss3629529306 Oct 12, 2018 (152)
17 ILLUMINA ss3635063989 Oct 12, 2018 (152)
18 ILLUMINA ss3640771288 Oct 12, 2018 (152)
19 ILLUMINA ss3644910340 Oct 12, 2018 (152)
20 ILLUMINA ss3653130333 Oct 12, 2018 (152)
21 ILLUMINA ss3654132387 Oct 12, 2018 (152)
22 ILLUMINA ss3726340536 Jul 13, 2019 (153)
23 ILLUMINA ss3744553707 Jul 13, 2019 (153)
24 ILLUMINA ss3745363918 Jul 13, 2019 (153)
25 PAGE_CC ss3771288385 Jul 13, 2019 (153)
26 ILLUMINA ss3772857535 Jul 13, 2019 (153)
27 EVA ss3824185096 Apr 26, 2020 (154)
28 GNOMAD ss4140310058 Apr 26, 2021 (155)
29 TOPMED ss4700142693 Apr 26, 2021 (155)
30 1000G_HIGH_COVERAGE ss5268153926 Oct 17, 2022 (156)
31 EVA ss5365090220 Oct 17, 2022 (156)
32 EVA ss5512430339 Oct 17, 2022 (156)
33 1000G_HIGH_COVERAGE ss5553904462 Oct 17, 2022 (156)
34 EVA ss5848094829 Oct 17, 2022 (156)
35 EVA ss5883479742 Oct 17, 2022 (156)
36 EVA ss5968728515 Oct 17, 2022 (156)
37 1000Genomes NC_000006.11 - 39507812 Oct 12, 2018 (152)
38 1000Genomes_30x NC_000006.12 - 39540036 Oct 17, 2022 (156)
39 ExAC NC_000006.11 - 39507812 Oct 12, 2018 (152)
40 gnomAD - Genomes NC_000006.12 - 39540036 Apr 26, 2021 (155)
41 gnomAD - Exomes NC_000006.11 - 39507812 Jul 13, 2019 (153)
42 GO Exome Sequencing Project NC_000006.11 - 39507812 Oct 12, 2018 (152)
43 The PAGE Study NC_000006.12 - 39540036 Jul 13, 2019 (153)
44 TopMed NC_000006.12 - 39540036 Apr 26, 2021 (155)
45 ALFA NC_000006.12 - 39540036 Apr 26, 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
ss5512430339 NC_000006.11:39507811:C:A NC_000006.12:39540035:C:A
31572915, 8336323, 4906597, 643117, ss342211318, ss488835912, ss491385449, ss780849023, ss783532779, ss1319796281, ss1688305173, ss1752635884, ss1917805136, ss1946177296, ss1958902433, ss2735763968, ss2985367111, ss3022613839, ss3629529306, ss3635063989, ss3640771288, ss3644910340, ss3653130333, ss3654132387, ss3744553707, ss3745363918, ss3772857535, ss3824185096, ss5365090220, ss5848094829, ss5968728515 NC_000006.11:39507811:C:G NC_000006.12:39540035:C:G (self)
41430397, 222798250, 509854, 537520251, 4172976008, ss2283392180, ss3726340536, ss3771288385, ss4140310058, ss4700142693, ss5268153926, ss5553904462, ss5883479742 NC_000006.12:39540035:C:G NC_000006.12:39540035:C:G (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 rs142216439

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.post761+d5e8e07