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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.

rs63749796

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr16:16159505 (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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.00005 (4/77894, PAGE_STUDY)
Clinical Significance
Reported in ClinVar
Gene : Consequence
ABCC6 : Missense Variant
Publications
1 citation
Genomic View
See rs on genome
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
The PAGE Study Global Study-wide 77894 C=0.99995 G=0.00005
The PAGE Study AfricanAmerican Sub 31952 C=0.99994 G=0.00006
The PAGE Study Mexican Sub 10780 C=1.00000 G=0.00000
The PAGE Study Asian Sub 8278 C=1.0000 G=0.0000
The PAGE Study PuertoRican Sub 7874 C=0.9999 G=0.0001
The PAGE Study NativeHawaiian Sub 4476 C=0.9998 G=0.0002
The PAGE Study Cuban Sub 4216 C=1.0000 G=0.0000
The PAGE Study Dominican Sub 3796 C=1.0000 G=0.0000
The PAGE Study CentralAmerican Sub 2442 C=1.0000 G=0.0000
The PAGE Study SouthAmerican Sub 1978 C=1.0000 G=0.0000
The PAGE Study NativeAmerican Sub 1258 C=1.0000 G=0.0000
The PAGE Study SouthAsian Sub 844 C=1.000 G=0.000
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 16 NC_000016.10:g.16159505C>G
GRCh37.p13 chr 16 NC_000016.9:g.16253362C>G
ABCC6 RefSeqGene (LRG_1115) NG_007558.3:g.69113G>C
GRCh38.p14 chr 16 alt locus HSCHR16_1_CTG1 NT_187607.1:g.1817433C>G
Gene: ABCC6, ATP binding cassette subfamily C member 6 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ABCC6 transcript variant 2 NM_001079528.4:c. N/A Genic Downstream Transcript Variant
ABCC6 transcript variant 3 NM_001351800.1:c.3370G>C D [GAC] > H [CAC] Coding Sequence Variant
ATP-binding cassette sub-family C member 6 isoform 3 NP_001338729.1:p.Asp1124H…

NP_001338729.1:p.Asp1124His

D (Asp) > H (His) Missense Variant
ABCC6 transcript variant 1 NM_001171.6:c.3712G>C D [GAC] > H [CAC] Coding Sequence Variant
ATP-binding cassette sub-family C member 6 isoform 1 NP_001162.5:p.Asp1238His D (Asp) > H (His) Missense Variant
ABCC6 transcript variant 4 NR_147784.1:n.3374G>C N/A Non Coding Transcript Variant
ABCC6 transcript variant X10 XM_011522482.4:c. N/A Genic Downstream Transcript Variant
ABCC6 transcript variant X8 XM_017023214.2:c. N/A Genic Downstream Transcript Variant
ABCC6 transcript variant X9 XM_047434069.1:c. N/A Genic Downstream Transcript Variant
ABCC6 transcript variant X3 XM_011522480.1:c.3370G>C D [GAC] > H [CAC] Coding Sequence Variant
ATP-binding cassette sub-family C member 6 isoform X3 XP_011520782.1:p.Asp1124H…

XP_011520782.1:p.Asp1124His

D (Asp) > H (His) Missense Variant
ABCC6 transcript variant X1 XM_011522479.3:c.3679G>C D [GAC] > H [CAC] Coding Sequence Variant
ATP-binding cassette sub-family C member 6 isoform X1 XP_011520781.1:p.Asp1227H…

XP_011520781.1:p.Asp1227His

D (Asp) > H (His) Missense Variant
ABCC6 transcript variant X2 XM_017023212.2:c.3544G>C D [GAC] > H [CAC] Coding Sequence Variant
ATP-binding cassette sub-family C member 6 isoform X2 XP_016878701.1:p.Asp1182H…

XP_016878701.1:p.Asp1182His

D (Asp) > H (His) Missense Variant
ABCC6 transcript variant X4 XM_011522481.4:c.3370G>C D [GAC] > H [CAC] Coding Sequence Variant
ATP-binding cassette sub-family C member 6 isoform X3 XP_011520783.1:p.Asp1124H…

XP_011520783.1:p.Asp1124His

D (Asp) > H (His) Missense Variant
ABCC6 transcript variant X5 XR_932836.3:n.3772G>C N/A Non Coding Transcript Variant
ABCC6 transcript variant X6 XR_932838.4:n.3572G>C N/A Non Coding Transcript Variant
ABCC6 transcript variant X7 XR_932837.4:n.3572G>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.

Allele: G (allele ID: 21620 )
ClinVar Accession Disease Names Clinical Significance
RCV000006959.7 Pseudoxanthoma elasticum Pathogenic-Likely-Pathogenic
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= G
GRCh38.p14 chr 16 NC_000016.10:g.16159505= NC_000016.10:g.16159505C>G
GRCh37.p13 chr 16 NC_000016.9:g.16253362= NC_000016.9:g.16253362C>G
ABCC6 RefSeqGene (LRG_1115) NG_007558.3:g.69113= NG_007558.3:g.69113G>C
ABCC6 transcript variant 1 NM_001171.6:c.3712= NM_001171.6:c.3712G>C
ABCC6 transcript variant 1 NM_001171.5:c.3712= NM_001171.5:c.3712G>C
ABCC6 transcript variant 3 NM_001351800.1:c.3370= NM_001351800.1:c.3370G>C
ABCC6 transcript variant 4 NR_147784.1:n.3374= NR_147784.1:n.3374G>C
GRCh38.p14 chr 16 alt locus HSCHR16_1_CTG1 NT_187607.1:g.1817433= NT_187607.1:g.1817433C>G
ABCC6 transcript variant X4 XM_011522481.4:c.3370= XM_011522481.4:c.3370G>C
ABCC6 transcript variant X5 XM_011522481.3:c.3370= XM_011522481.3:c.3370G>C
ABCC6 transcript variant X6 XM_011522481.2:c.3370= XM_011522481.2:c.3370G>C
ABCC6 transcript variant X3 XM_011522481.1:c.3370= XM_011522481.1:c.3370G>C
ABCC6 transcript variant X6 XR_932838.4:n.3572= XR_932838.4:n.3572G>C
ABCC6 transcript variant X7 XR_932838.3:n.3693= XR_932838.3:n.3693G>C
ABCC6 transcript variant X8 XR_932838.2:n.3693= XR_932838.2:n.3693G>C
ABCC6 transcript variant X5 XR_932838.1:n.3748= XR_932838.1:n.3748G>C
ABCC6 transcript variant X7 XR_932837.4:n.3572= XR_932837.4:n.3572G>C
ABCC6 transcript variant X6 XR_932837.3:n.3693= XR_932837.3:n.3693G>C
ABCC6 transcript variant X7 XR_932837.2:n.3692= XR_932837.2:n.3692G>C
ABCC6 transcript variant X4 XR_932837.1:n.3748= XR_932837.1:n.3748G>C
ABCC6 transcript variant X1 XM_011522479.3:c.3679= XM_011522479.3:c.3679G>C
ABCC6 transcript variant X1 XM_011522479.2:c.3679= XM_011522479.2:c.3679G>C
ABCC6 transcript variant X6 XM_011522479.1:c.3679= XM_011522479.1:c.3679G>C
ABCC6 transcript variant X5 XR_932836.3:n.3772= XR_932836.3:n.3772G>C
ABCC6 transcript variant X3 XR_932836.2:n.3893= XR_932836.2:n.3893G>C
ABCC6 transcript variant X1 XR_932836.1:n.3947= XR_932836.1:n.3947G>C
ABCC6 transcript variant X2 XM_017023212.2:c.3544= XM_017023212.2:c.3544G>C
ABCC6 transcript variant X2 XM_017023212.1:c.3544= XM_017023212.1:c.3544G>C
ABCC6 transcript variant X3 XM_011522480.1:c.3370= XM_011522480.1:c.3370G>C
ATP-binding cassette sub-family C member 6 isoform 1 NP_001162.5:p.Asp1238= NP_001162.5:p.Asp1238His
ATP-binding cassette sub-family C member 6 isoform 3 NP_001338729.1:p.Asp1124= NP_001338729.1:p.Asp1124His
ATP-binding cassette sub-family C member 6 isoform X3 XP_011520783.1:p.Asp1124= XP_011520783.1:p.Asp1124His
ATP-binding cassette sub-family C member 6 isoform X1 XP_011520781.1:p.Asp1227= XP_011520781.1:p.Asp1227His
ATP-binding cassette sub-family C member 6 isoform X2 XP_016878701.1:p.Asp1182= XP_016878701.1:p.Asp1182His
ATP-binding cassette sub-family C member 6 isoform X3 XP_011520782.1:p.Asp1124= XP_011520782.1:p.Asp1124His
multidrug resistance-associated protein 6 isoform 1 NP_001162.4:p.Asp1238= NP_001162.4:p.Asp1238His
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#.

7 SubSNP, 1 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 ABCC6-LOVD ss102701546 Jun 09, 2008 (130)
2 OMIM-CURATED-RECORDS ss263193243 Oct 28, 2010 (133)
3 ILLUMINA ss1959663761 Feb 12, 2016 (147)
4 ILLUMINA ss3021689221 Nov 08, 2017 (151)
5 ILLUMINA ss3652095682 Oct 12, 2018 (152)
6 ILLUMINA ss3725548502 Jul 13, 2019 (153)
7 PAGE_CC ss3771869374 Jul 13, 2019 (153)
8 The PAGE Study NC_000016.10 - 16159505 Jul 13, 2019 (153)
9 ClinVar RCV000006959.7 Oct 17, 2022 (156)
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
ss1959663761, ss3021689221, ss3652095682 NC_000016.9:16253361:C:G NC_000016.10:16159504:C:G (self)
RCV000006959.7, 1090843, ss102701546, ss263193243, ss3725548502, ss3771869374 NC_000016.10:16159504:C:G NC_000016.10:16159504: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.

1 citation for rs63749796
PMID Title Author Year Journal
15086542 Novel ABCC6 mutations in pseudoxanthoma elasticum. Chassaing N et al. 2004 The Journal of investigative dermatology
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