Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs1480860602

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:236465662 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000004 (1/264690, TOPMED)
T=0.000004 (1/248910, GnomAD_exome)
T=0.00000 (0/10680, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
IQCA1 : 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 10680 C=1.00000 T=0.00000 1.0 0.0 0.0 N/A
European Sub 6962 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Sub 2294 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 84 C=1.00 T=0.00 1.0 0.0 0.0 N/A
African American Sub 2210 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 C=1.000 T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 C=1.000 T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 C=1.000 T=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Sub 466 C=1.000 T=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 C=0.999996 T=0.000004
gnomAD - Exomes Global Study-wide 248910 C=0.999996 T=0.000004
gnomAD - Exomes European Sub 134316 C=1.000000 T=0.000000
gnomAD - Exomes Asian Sub 48532 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34486 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 15478 C=0.99994 T=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10054 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6044 C=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 10680 C=1.00000 T=0.00000
Allele Frequency Aggregator European Sub 6962 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2294 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Other Sub 466 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 108 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 94 C=1.00 T=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 2 NC_000002.12:g.236465662C>T
GRCh37.p13 chr 2 NC_000002.11:g.237374305C>T
Gene: IQCA1, IQ motif containing with AAA domain 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
IQCA1 transcript variant 1 NM_024726.5:c.769G>A E [GAA] > K [AAA] Coding Sequence Variant
dynein regulatory complex protein 11 isoform 1 NP_079002.3:p.Glu257Lys E (Glu) > K (Lys) Missense Variant
IQCA1 transcript variant 3 NM_001270585.2:c.790G>A E [GAA] > K [AAA] Coding Sequence Variant
dynein regulatory complex protein 11 isoform 3 NP_001257514.1:p.Glu264Lys E (Glu) > K (Lys) Missense Variant
IQCA1 transcript variant 2 NM_001270584.2:c.769G>A E [GAA] > K [AAA] Coding Sequence Variant
dynein regulatory complex protein 11 isoform 2 NP_001257513.1:p.Glu257Lys E (Glu) > K (Lys) Missense Variant
IQCA1 transcript variant 4 NR_073043.2:n.978G>A N/A Non Coding Transcript Variant
IQCA1 transcript variant X2 XM_011511864.3:c.790G>A E [GAA] > K [AAA] Coding Sequence Variant
dynein regulatory complex protein 11 isoform X1 XP_011510166.1:p.Glu264Lys E (Glu) > K (Lys) Missense Variant
IQCA1 transcript variant X3 XM_011511865.4:c.769G>A E [GAA] > K [AAA] Coding Sequence Variant
dynein regulatory complex protein 11 isoform X2 XP_011510167.1:p.Glu257Lys E (Glu) > K (Lys) Missense Variant
IQCA1 transcript variant X4 XM_011511866.2:c.790G>A E [GAA] > K [AAA] Coding Sequence Variant
dynein regulatory complex protein 11 isoform X3 XP_011510168.1:p.Glu264Lys E (Glu) > K (Lys) Missense Variant
IQCA1 transcript variant X5 XM_017004960.2:c.790G>A E [GAA] > K [AAA] Coding Sequence Variant
dynein regulatory complex protein 11 isoform X4 XP_016860449.1:p.Glu264Lys E (Glu) > K (Lys) Missense Variant
IQCA1 transcript variant X6 XM_047445852.1:c.769G>A E [GAA] > K [AAA] Coding Sequence Variant
dynein regulatory complex protein 11 isoform X5 XP_047301808.1:p.Glu257Lys E (Glu) > K (Lys) Missense Variant
IQCA1 transcript variant X1 XR_007081589.1:n.822G>A 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= T
GRCh38.p14 chr 2 NC_000002.12:g.236465662= NC_000002.12:g.236465662C>T
GRCh37.p13 chr 2 NC_000002.11:g.237374305= NC_000002.11:g.237374305C>T
IQCA1 transcript variant 1 NM_024726.5:c.769= NM_024726.5:c.769G>A
IQCA1 transcript variant 1 NM_024726.4:c.769= NM_024726.4:c.769G>A
IQCA1 transcript variant X3 XM_011511865.4:c.769= XM_011511865.4:c.769G>A
IQCA1 transcript variant X2 XM_011511865.3:c.769= XM_011511865.3:c.769G>A
IQCA1 transcript variant X2 XM_011511865.2:c.769= XM_011511865.2:c.769G>A
IQCA1 transcript variant X2 XM_011511865.1:c.769= XM_011511865.1:c.769G>A
IQCA1 transcript variant X2 XM_011511864.3:c.790= XM_011511864.3:c.790G>A
IQCA1 transcript variant X1 XM_011511864.2:c.790= XM_011511864.2:c.790G>A
IQCA1 transcript variant X1 XM_011511864.1:c.790= XM_011511864.1:c.790G>A
IQCA1 transcript variant 4 NR_073043.2:n.978= NR_073043.2:n.978G>A
IQCA1 transcript variant 4 NR_073043.1:n.1037= NR_073043.1:n.1037G>A
IQCA1 transcript variant 2 NM_001270584.2:c.769= NM_001270584.2:c.769G>A
IQCA1 transcript variant 2 NM_001270584.1:c.769= NM_001270584.1:c.769G>A
IQCA1 transcript variant 3 NM_001270585.2:c.790= NM_001270585.2:c.790G>A
IQCA1 transcript variant 3 NM_001270585.1:c.790= NM_001270585.1:c.790G>A
IQCA1 transcript variant X4 XM_011511866.2:c.790= XM_011511866.2:c.790G>A
IQCA1 transcript variant X3 XM_011511866.1:c.790= XM_011511866.1:c.790G>A
IQCA1 transcript variant X5 XM_017004960.2:c.790= XM_017004960.2:c.790G>A
IQCA1 transcript variant X4 XM_017004960.1:c.790= XM_017004960.1:c.790G>A
IQCA1 transcript variant X1 XR_007081589.1:n.822= XR_007081589.1:n.822G>A
IQCA1 transcript variant X6 XM_047445852.1:c.769= XM_047445852.1:c.769G>A
dynein regulatory complex protein 11 isoform 1 NP_079002.3:p.Glu257= NP_079002.3:p.Glu257Lys
dynein regulatory complex protein 11 isoform X2 XP_011510167.1:p.Glu257= XP_011510167.1:p.Glu257Lys
dynein regulatory complex protein 11 isoform X1 XP_011510166.1:p.Glu264= XP_011510166.1:p.Glu264Lys
dynein regulatory complex protein 11 isoform 2 NP_001257513.1:p.Glu257= NP_001257513.1:p.Glu257Lys
dynein regulatory complex protein 11 isoform 3 NP_001257514.1:p.Glu264= NP_001257514.1:p.Glu264Lys
dynein regulatory complex protein 11 isoform X3 XP_011510168.1:p.Glu264= XP_011510168.1:p.Glu264Lys
dynein regulatory complex protein 11 isoform X4 XP_016860449.1:p.Glu264= XP_016860449.1:p.Glu264Lys
dynein regulatory complex protein 11 isoform X5 XP_047301808.1:p.Glu257= XP_047301808.1:p.Glu257Lys
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#.

2 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2733442303 Nov 08, 2017 (151)
2 TOPMED ss4549534296 Apr 27, 2021 (155)
3 gnomAD - Exomes NC_000002.11 - 237374305 Jul 13, 2019 (153)
4 TopMed NC_000002.12 - 236465662 Apr 27, 2021 (155)
5 ALFA NC_000002.12 - 236465662 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
2511537, ss2733442303 NC_000002.11:237374304:C:T NC_000002.12:236465661:C:T (self)
353357175, 11773358795, ss4549534296 NC_000002.12:236465661:C:T NC_000002.12:236465661:C:T (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 rs1480860602

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