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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.

rs1484562228

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:51379466 (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
dupA
Variation Type
Indel Insertion and Deletion
Frequency
dupA=0.000004 (1/264690, TOPMED)
dupA=0.00000 (0/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DOCK3 : Frameshift 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 11862 A=1.00000 AA=0.00000 1.0 0.0 0.0 N/A
European Sub 7618 A=1.0000 AA=0.0000 1.0 0.0 0.0 N/A
African Sub 2816 A=1.0000 AA=0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 A=1.000 AA=0.000 1.0 0.0 0.0 N/A
African American Sub 2708 A=1.0000 AA=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 A=1.000 AA=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 A=1.00 AA=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 A=1.00 AA=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 A=1.000 AA=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 A=1.000 AA=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 A=1.00 AA=0.00 1.0 0.0 0.0 N/A
Other Sub 470 A=1.000 AA=0.000 1.0 0.0 0.0 N/A


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 -

No frequency provided

dupA=0.000004
Allele Frequency Aggregator Total Global 11862 A=1.00000 dupA=0.00000
Allele Frequency Aggregator European Sub 7618 A=1.0000 dupA=0.0000
Allele Frequency Aggregator African Sub 2816 A=1.0000 dupA=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 A=1.000 dupA=0.000
Allele Frequency Aggregator Other Sub 470 A=1.000 dupA=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=1.000 dupA=0.000
Allele Frequency Aggregator Asian Sub 108 A=1.000 dupA=0.000
Allele Frequency Aggregator South Asian Sub 94 A=1.00 dupA=0.00
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 3 NC_000003.12:g.51379466dup
GRCh37.p13 chr 3 NC_000003.11:g.51416897dup
DOCK3 RefSeqGene NG_028012.2:g.709226dup
GRCh37.p13 chr 3 fix patch HG186_PATCH NW_003315910.1:g.789dup
Gene: DOCK3, dedicator of cytokinesis 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
DOCK3 transcript NM_004947.5:c.5501-659dup N/A Intron Variant
DOCK3 transcript variant X19 XM_006713010.4:c.5501-158…

XM_006713010.4:c.5501-1584dup

N/A Intron Variant
DOCK3 transcript variant X9 XM_017005825.3:c.5483-659…

XM_017005825.3:c.5483-659dup

N/A Intron Variant
DOCK3 transcript variant X11 XM_047447597.1:c.5474-659…

XM_047447597.1:c.5474-659dup

N/A Intron Variant
DOCK3 transcript variant X12 XM_047447598.1:c.5456-659…

XM_047447598.1:c.5456-659dup

N/A Intron Variant
DOCK3 transcript variant X14 XM_047447600.1:c.5438-659…

XM_047447600.1:c.5438-659dup

N/A Intron Variant
DOCK3 transcript variant X15 XM_047447601.1:c.5414-659…

XM_047447601.1:c.5414-659dup

N/A Intron Variant
DOCK3 transcript variant X16 XM_047447602.1:c.5414-659…

XM_047447602.1:c.5414-659dup

N/A Intron Variant
DOCK3 transcript variant X17 XM_047447603.1:c.5396-659…

XM_047447603.1:c.5396-659dup

N/A Intron Variant
DOCK3 transcript variant X20 XM_047447604.1:c.5456-158…

XM_047447604.1:c.5456-1584dup

N/A Intron Variant
DOCK3 transcript variant X18 XM_017005826.3:c. N/A Genic Downstream Transcript Variant
DOCK3 transcript variant X1 XM_005264914.4:c.5518dup S [AGC] > K [AAGC] Coding Sequence Variant
dedicator of cytokinesis protein 3 isoform X1 XP_005264971.1:p.Ser1840fs S (Ser) > K (Lys) Frameshift Variant
DOCK3 transcript variant X2 XM_005264915.4:c.5500dup S [AGC] > K [AAGC] Coding Sequence Variant
dedicator of cytokinesis protein 3 isoform X2 XP_005264972.1:p.Ser1834fs S (Ser) > K (Lys) Frameshift Variant
DOCK3 transcript variant X3 XM_005264916.5:c.5491dup S [AGC] > K [AAGC] Coding Sequence Variant
dedicator of cytokinesis protein 3 isoform X3 XP_005264973.1:p.Ser1831fs S (Ser) > K (Lys) Frameshift Variant
DOCK3 transcript variant X4 XM_005264917.4:c.5476dup S [AGC] > K [AAGC] Coding Sequence Variant
dedicator of cytokinesis protein 3 isoform X4 XP_005264974.1:p.Ser1826fs S (Ser) > K (Lys) Frameshift Variant
DOCK3 transcript variant X5 XM_006713008.4:c.5455dup S [AGC] > K [AAGC] Coding Sequence Variant
dedicator of cytokinesis protein 3 isoform X5 XP_006713071.1:p.Ser1819fs S (Ser) > K (Lys) Frameshift Variant
DOCK3 transcript variant X6 XM_047447595.1:c.5449dup S [AGC] > K [AAGC] Coding Sequence Variant
dedicator of cytokinesis protein 3 isoform X6 XP_047303551.1:p.Ser1817fs S (Ser) > K (Lys) Frameshift Variant
DOCK3 transcript variant X7 XM_047447596.1:c.5431dup S [AGC] > K [AAGC] Coding Sequence Variant
dedicator of cytokinesis protein 3 isoform X7 XP_047303552.1:p.Ser1811fs S (Ser) > K (Lys) Frameshift Variant
DOCK3 transcript variant X8 XM_006713009.4:c.5431dup S [AGC] > K [AAGC] Coding Sequence Variant
dedicator of cytokinesis protein 3 isoform X8 XP_006713072.1:p.Ser1811fs S (Ser) > K (Lys) Frameshift Variant
DOCK3 transcript variant X10 XM_005264918.5:c.5371dup S [AGC] > K [AAGC] Coding Sequence Variant
dedicator of cytokinesis protein 3 isoform X10 XP_005264975.1:p.Ser1791fs S (Ser) > K (Lys) Frameshift Variant
DOCK3 transcript variant X13 XM_047447599.1:c.5344dup S [AGC] > K [AAGC] Coding Sequence Variant
dedicator of cytokinesis protein 3 isoform X13 XP_047303555.1:p.Ser1782fs S (Ser) > K (Lys) Frameshift Variant
DOCK3 transcript variant X21 XM_047447605.1:c.5164dup S [AGC] > K [AAGC] Coding Sequence Variant
dedicator of cytokinesis protein 3 isoform X21 XP_047303561.1:p.Ser1722fs S (Ser) > K (Lys) Frameshift Variant
DOCK3 transcript variant X22 XM_017005827.3:c.4705dup S [AGC] > K [AAGC] Coding Sequence Variant
dedicator of cytokinesis protein 3 isoform X22 XP_016861316.1:p.Ser1569fs S (Ser) > K (Lys) Frameshift Variant
DOCK3 transcript variant X23 XM_011533441.4:c.4483dup S [AGC] > K [AAGC] Coding Sequence Variant
dedicator of cytokinesis protein 3 isoform X23 XP_011531743.1:p.Ser1495fs S (Ser) > K (Lys) Frameshift Variant
DOCK3 transcript variant X24 XM_047447606.1:c.4357dup S [AGC] > K [AAGC] Coding Sequence Variant
dedicator of cytokinesis protein 3 isoform X24 XP_047303562.1:p.Ser1453fs S (Ser) > K (Lys) Frameshift Variant
DOCK3 transcript variant X25 XM_011533443.3:c.2830dup S [AGC] > K [AAGC] Coding Sequence Variant
dedicator of cytokinesis protein 3 isoform X25 XP_011531745.1:p.Ser944fs S (Ser) > K (Lys) Frameshift Variant
DOCK3 transcript variant X26 XM_011533444.3:c.2830dup S [AGC] > K [AAGC] Coding Sequence Variant
dedicator of cytokinesis protein 3 isoform X25 XP_011531746.1:p.Ser944fs S (Ser) > K (Lys) Frameshift Variant
DOCK3 transcript variant X27 XM_011533445.3:c.2656dup S [AGC] > K [AAGC] Coding Sequence Variant
dedicator of cytokinesis protein 3 isoform X26 XP_011531747.1:p.Ser886fs S (Ser) > K (Lys) Frameshift 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 A= dupA
GRCh38.p14 chr 3 NC_000003.12:g.51379466= NC_000003.12:g.51379466dup
GRCh37.p13 chr 3 NC_000003.11:g.51416897= NC_000003.11:g.51416897dup
DOCK3 RefSeqGene NG_028012.2:g.709226= NG_028012.2:g.709226dup
GRCh37.p13 chr 3 fix patch HG186_PATCH NW_003315910.1:g.789= NW_003315910.1:g.789dup
DOCK3 transcript variant X3 XM_005264916.5:c.5491= XM_005264916.5:c.5491dup
DOCK3 transcript variant X3 XM_005264916.4:c.5491= XM_005264916.4:c.5491dup
DOCK3 transcript variant X3 XM_005264916.3:c.5491= XM_005264916.3:c.5491dup
DOCK3 transcript variant X3 XM_005264916.2:c.5491= XM_005264916.2:c.5491dup
DOCK3 transcript variant X3 XM_005264916.1:c.5491= XM_005264916.1:c.5491dup
DOCK3 transcript variant X10 XM_005264918.5:c.5371= XM_005264918.5:c.5371dup
DOCK3 transcript variant X8 XM_005264918.4:c.5371= XM_005264918.4:c.5371dup
DOCK3 transcript variant X8 XM_005264918.3:c.5371= XM_005264918.3:c.5371dup
DOCK3 transcript variant X7 XM_005264918.2:c.5371= XM_005264918.2:c.5371dup
DOCK3 transcript variant X5 XM_005264918.1:c.5371= XM_005264918.1:c.5371dup
DOCK3 transcript variant X23 XM_011533441.4:c.4483= XM_011533441.4:c.4483dup
DOCK3 transcript variant X12 XM_011533441.3:c.4483= XM_011533441.3:c.4483dup
DOCK3 transcript variant X12 XM_011533441.2:c.4483= XM_011533441.2:c.4483dup
DOCK3 transcript variant X9 XM_011533441.1:c.4483= XM_011533441.1:c.4483dup
DOCK3 transcript variant X1 XM_005264914.4:c.5518= XM_005264914.4:c.5518dup
DOCK3 transcript variant X1 XM_005264914.3:c.5518= XM_005264914.3:c.5518dup
DOCK3 transcript variant X1 XM_005264914.2:c.5518= XM_005264914.2:c.5518dup
DOCK3 transcript variant X1 XM_005264914.1:c.5518= XM_005264914.1:c.5518dup
DOCK3 transcript variant X2 XM_005264915.4:c.5500= XM_005264915.4:c.5500dup
DOCK3 transcript variant X2 XM_005264915.3:c.5500= XM_005264915.3:c.5500dup
DOCK3 transcript variant X2 XM_005264915.2:c.5500= XM_005264915.2:c.5500dup
DOCK3 transcript variant X2 XM_005264915.1:c.5500= XM_005264915.1:c.5500dup
DOCK3 transcript variant X4 XM_005264917.4:c.5476= XM_005264917.4:c.5476dup
DOCK3 transcript variant X4 XM_005264917.3:c.5476= XM_005264917.3:c.5476dup
DOCK3 transcript variant X4 XM_005264917.2:c.5476= XM_005264917.2:c.5476dup
DOCK3 transcript variant X4 XM_005264917.1:c.5476= XM_005264917.1:c.5476dup
DOCK3 transcript variant X5 XM_006713008.4:c.5455= XM_006713008.4:c.5455dup
DOCK3 transcript variant X5 XM_006713008.3:c.5455= XM_006713008.3:c.5455dup
DOCK3 transcript variant X5 XM_006713008.2:c.5455= XM_006713008.2:c.5455dup
DOCK3 transcript variant X6 XM_006713008.1:c.5455= XM_006713008.1:c.5455dup
DOCK3 transcript variant X8 XM_006713009.4:c.5431= XM_006713009.4:c.5431dup
DOCK3 transcript variant X6 XM_006713009.3:c.5431= XM_006713009.3:c.5431dup
DOCK3 transcript variant X6 XM_006713009.2:c.5431= XM_006713009.2:c.5431dup
DOCK3 transcript variant X7 XM_006713009.1:c.5431= XM_006713009.1:c.5431dup
DOCK3 transcript variant X22 XM_017005827.3:c.4705= XM_017005827.3:c.4705dup
DOCK3 transcript variant X11 XM_017005827.2:c.4705= XM_017005827.2:c.4705dup
DOCK3 transcript variant X11 XM_017005827.1:c.4705= XM_017005827.1:c.4705dup
DOCK3 transcript variant X25 XM_011533443.3:c.2830= XM_011533443.3:c.2830dup
DOCK3 transcript variant X13 XM_011533443.2:c.2830= XM_011533443.2:c.2830dup
DOCK3 transcript variant X11 XM_011533443.1:c.2830= XM_011533443.1:c.2830dup
DOCK3 transcript variant X27 XM_011533445.3:c.2656= XM_011533445.3:c.2656dup
DOCK3 transcript variant X15 XM_011533445.2:c.2656= XM_011533445.2:c.2656dup
DOCK3 transcript variant X13 XM_011533445.1:c.2656= XM_011533445.1:c.2656dup
DOCK3 transcript variant X26 XM_011533444.3:c.2830= XM_011533444.3:c.2830dup
DOCK3 transcript variant X14 XM_011533444.2:c.2830= XM_011533444.2:c.2830dup
DOCK3 transcript variant X12 XM_011533444.1:c.2830= XM_011533444.1:c.2830dup
DOCK3 transcript variant X6 XM_047447595.1:c.5449= XM_047447595.1:c.5449dup
DOCK3 transcript variant X7 XM_047447596.1:c.5431= XM_047447596.1:c.5431dup
DOCK3 transcript variant X13 XM_047447599.1:c.5344= XM_047447599.1:c.5344dup
DOCK3 transcript variant X21 XM_047447605.1:c.5164= XM_047447605.1:c.5164dup
DOCK3 transcript variant X24 XM_047447606.1:c.4357= XM_047447606.1:c.4357dup
dedicator of cytokinesis protein 3 isoform X3 XP_005264973.1:p.Ser1831= XP_005264973.1:p.Ser1831fs
dedicator of cytokinesis protein 3 isoform X10 XP_005264975.1:p.Ser1791= XP_005264975.1:p.Ser1791fs
dedicator of cytokinesis protein 3 isoform X23 XP_011531743.1:p.Ser1495= XP_011531743.1:p.Ser1495fs
dedicator of cytokinesis protein 3 isoform X1 XP_005264971.1:p.Ser1840= XP_005264971.1:p.Ser1840fs
dedicator of cytokinesis protein 3 isoform X2 XP_005264972.1:p.Ser1834= XP_005264972.1:p.Ser1834fs
dedicator of cytokinesis protein 3 isoform X4 XP_005264974.1:p.Ser1826= XP_005264974.1:p.Ser1826fs
dedicator of cytokinesis protein 3 isoform X5 XP_006713071.1:p.Ser1819= XP_006713071.1:p.Ser1819fs
dedicator of cytokinesis protein 3 isoform X8 XP_006713072.1:p.Ser1811= XP_006713072.1:p.Ser1811fs
dedicator of cytokinesis protein 3 isoform X22 XP_016861316.1:p.Ser1569= XP_016861316.1:p.Ser1569fs
dedicator of cytokinesis protein 3 isoform X25 XP_011531745.1:p.Ser944= XP_011531745.1:p.Ser944fs
dedicator of cytokinesis protein 3 isoform X26 XP_011531747.1:p.Ser886= XP_011531747.1:p.Ser886fs
dedicator of cytokinesis protein 3 isoform X25 XP_011531746.1:p.Ser944= XP_011531746.1:p.Ser944fs
dedicator of cytokinesis protein 3 isoform X6 XP_047303551.1:p.Ser1817= XP_047303551.1:p.Ser1817fs
dedicator of cytokinesis protein 3 isoform X7 XP_047303552.1:p.Ser1811= XP_047303552.1:p.Ser1811fs
dedicator of cytokinesis protein 3 isoform X13 XP_047303555.1:p.Ser1782= XP_047303555.1:p.Ser1782fs
dedicator of cytokinesis protein 3 isoform X21 XP_047303561.1:p.Ser1722= XP_047303561.1:p.Ser1722fs
dedicator of cytokinesis protein 3 isoform X24 XP_047303562.1:p.Ser1453= XP_047303562.1:p.Ser1453fs
DOCK3 transcript NM_004947.4:c.5501-659= NM_004947.4:c.5501-659dup
DOCK3 transcript NM_004947.5:c.5501-659= NM_004947.5:c.5501-659dup
DOCK3 transcript variant X19 XM_006713010.4:c.5501-1584= XM_006713010.4:c.5501-1584dup
DOCK3 transcript variant X9 XM_017005825.3:c.5483-659= XM_017005825.3:c.5483-659dup
DOCK3 transcript variant X11 XM_047447597.1:c.5474-659= XM_047447597.1:c.5474-659dup
DOCK3 transcript variant X12 XM_047447598.1:c.5456-659= XM_047447598.1:c.5456-659dup
DOCK3 transcript variant X14 XM_047447600.1:c.5438-659= XM_047447600.1:c.5438-659dup
DOCK3 transcript variant X15 XM_047447601.1:c.5414-659= XM_047447601.1:c.5414-659dup
DOCK3 transcript variant X16 XM_047447602.1:c.5414-659= XM_047447602.1:c.5414-659dup
DOCK3 transcript variant X17 XM_047447603.1:c.5396-659= XM_047447603.1:c.5396-659dup
DOCK3 transcript variant X20 XM_047447604.1:c.5456-1584= XM_047447604.1:c.5456-1584dup
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#.

1 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 TOPMED ss4564189067 Apr 27, 2021 (155)
2 TopMed NC_000003.12 - 51379466 Apr 27, 2021 (155)
3 ALFA NC_000003.12 - 51379466 Apr 27, 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
401566622, ss4564189067 NC_000003.12:51379465::A NC_000003.12:51379465:A:AA (self)
6973677319 NC_000003.12:51379465:A:AA NC_000003.12:51379465:A:AA (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 rs1484562228

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.post820+afb47a3d