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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs779241085

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr4:102305054 (GRCh38.p7) 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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00007 (16/244186, GnomAD)
A=0.00014 (17/125568, TOPMED)
A=0.00007 (8/120574, ExAC)
Clinical Significance
Reported in ClinVar
Gene : Consequence
SLC39A8 : Missense Variant
Publications
1 citation
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.p7 chr 4 NC_000004.12:g.102305054C>A
GRCh37.p13 chr 4 NC_000004.11:g.103226211C>A
Gene: SLC39A8, solute carrier family 39 member 8 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC39A8 transcript variant 1 NM_022154.5:c.610G>T G [GGT] > C [TGT] Coding Sequence Variant
zinc transporter ZIP8 isoform a precursor NP_071437.3:p.Gly...

NP_071437.3:p.Gly204Cys

G (Gly) > C (Cys) Missense Variant
SLC39A8 transcript variant 2 NM_001135146.1:c....

NM_001135146.1:c.610G>T

G [GGT] > C [TGT] Coding Sequence Variant
zinc transporter ZIP8 isoform a precursor NP_001128618.1:p....

NP_001128618.1:p.Gly204Cys

G (Gly) > C (Cys) Missense Variant
SLC39A8 transcript variant 3 NM_001135147.1:c....

NM_001135147.1:c.610G>T

G [GGT] > C [TGT] Coding Sequence Variant
zinc transporter ZIP8 isoform b precursor NP_001128619.1:p....

NP_001128619.1:p.Gly204Cys

G (Gly) > C (Cys) Missense Variant
SLC39A8 transcript variant 4 NM_001135148.1:c....

NM_001135148.1:c.409G>T

G [GGT] > C [TGT] Coding Sequence Variant
zinc transporter ZIP8 isoform c NP_001128620.1:p....

NP_001128620.1:p.Gly137Cys

G (Gly) > C (Cys) Missense Variant
SLC39A8 transcript variant X5 XM_011532182.1:c. N/A 5 Prime UTR Variant
SLC39A8 transcript variant X1 XM_005263177.1:c....

XM_005263177.1:c.610G>T

G [GGT] > C [TGT] Coding Sequence Variant
zinc transporter ZIP8 isoform X1 XP_005263234.1:p....

XP_005263234.1:p.Gly204Cys

G (Gly) > C (Cys) Missense Variant
SLC39A8 transcript variant X2 XM_017008540.1:c....

XM_017008540.1:c.610G>T

G [GGT] > C [TGT] Coding Sequence Variant
zinc transporter ZIP8 isoform X1 XP_016864029.1:p....

XP_016864029.1:p.Gly204Cys

G (Gly) > C (Cys) Missense Variant
SLC39A8 transcript variant X2 XM_017008541.1:c....

XM_017008541.1:c.409G>T

G [GGT] > C [TGT] Coding Sequence Variant
zinc transporter ZIP8 isoform X2 XP_016864030.1:p....

XP_016864030.1:p.Gly137Cys

G (Gly) > C (Cys) Missense Variant
SLC39A8 transcript variant X4 XM_011532181.2:c....

XM_011532181.2:c.610G>T

G [GGT] > C [TGT] Coding Sequence Variant
zinc transporter ZIP8 isoform X3 XP_011530483.1:p....

XP_011530483.1:p.Gly204Cys

G (Gly) > C (Cys) Missense Variant
SLC39A8 transcript variant X6 XM_017008542.1:c....

XM_017008542.1:c.610G>T

G [GGT] > C [TGT] Coding Sequence Variant
zinc transporter ZIP8 isoform X5 XP_016864031.1:p....

XP_016864031.1:p.Gly204Cys

G (Gly) > C (Cys) Missense 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: A (allele ID: 215657 )
ClinVar Accession Disease Names Clinical Significance
RCV000203248.2 CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIn Pathogenic
RCV000203267.1 SLC39A8 deficiency Pathogenic
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 Genome Aggregation Database Global Study-wide 244186 C=0.99993 A=0.00007
The Genome Aggregation Database European Sub 132882 C=0.99989 A=0.00011
The Genome Aggregation Database Asian Sub 47764 C=1.0000 A=0.0000
The Genome Aggregation Database American Sub 33164 C=1.0000 A=0.0000
The Genome Aggregation Database African Sub 15172 C=1.0000 A=0.0000
The Genome Aggregation Database Ashkenazi Jewish Sub 9786 C=1.000 A=0.000
The Genome Aggregation Database Other Sub 5418 C=1.000 A=0.000
Trans-Omics for Precision Medicine Global Study-wide 125568 C=0.99986 A=0.00014
The Exome Aggregation Consortium Global Study-wide 120574 C=0.99993 A=0.00007
The Exome Aggregation Consortium Europe Sub 72934 C=0.9999 A=0.0001
The Exome Aggregation Consortium Asian Sub 25088 C=1.0000 A=0.0000
The Exome Aggregation Consortium American Sub 11356 C=0.9999 A=0.0001
The Exome Aggregation Consortium African Sub 10294 C=1.0000 A=0.0000
The Exome Aggregation Consortium Other Sub 902 C=1.00 A=0.00
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 Note
GRCh38.p7 chr 4 NC_000004.12:g.102305054C= NC_000004.12:g.10230505...

NC_000004.12:g.102305054C>A

GRCh37.p13 chr 4 NC_000004.11:g.103226211C= NC_000004.11:g.10322621...

NC_000004.11:g.103226211C>A

SLC39A8 transcript variant 1 NM_022154.5:c.610G= NM_022154.5:c.610G>T
SLC39A8 transcript variant X4 XM_011532181.2:c.610G= XM_011532181.2:c.610G>T
SLC39A8 transcript variant 3 NM_001135147.1:c.610G= NM_001135147.1:c.610G>T
SLC39A8 transcript variant X2 XM_017008541.1:c.409G= XM_017008541.1:c.409G>T
SLC39A8 transcript variant 2 NM_001135146.1:c.610G= NM_001135146.1:c.610G>T
SLC39A8 transcript variant X5 XM_011532182.1:c.-33G= XM_011532182.1:c.-33G>T
SLC39A8 transcript variant X2 XM_017008540.1:c.610G= XM_017008540.1:c.610G>T
SLC39A8 transcript variant X1 XM_005263177.1:c.610G= XM_005263177.1:c.610G>T
SLC39A8 transcript variant 4 NM_001135148.1:c.409G= NM_001135148.1:c.409G>T
SLC39A8 transcript variant X6 XM_017008542.1:c.610G= XM_017008542.1:c.610G>T
zinc transporter ZIP8 isoform a precursor NP_071437.3:p.Gly204= NP_071437.3:p.Gly204Cys
zinc transporter ZIP8 isoform X3 XP_011530483.1:p.Gly204= XP_011530483.1:p.Gly204Cys
zinc transporter ZIP8 isoform b precursor NP_001128619.1:p.Gly204= NP_001128619.1:p.Gly204Cys
zinc transporter ZIP8 isoform X2 XP_016864030.1:p.Gly137= XP_016864030.1:p.Gly137Cys
zinc transporter ZIP8 isoform a precursor NP_001128618.1:p.Gly204= NP_001128618.1:p.Gly204Cys
zinc transporter ZIP8 isoform X1 XP_016864029.1:p.Gly204= XP_016864029.1:p.Gly204Cys
zinc transporter ZIP8 isoform X1 XP_005263234.1:p.Gly204= XP_005263234.1:p.Gly204Cys
zinc transporter ZIP8 isoform c NP_001128620.1:p.Gly137= NP_001128620.1:p.Gly137Cys
zinc transporter ZIP8 isoform X5 XP_016864031.1:p.Gly204= XP_016864031.1:p.Gly204Cys
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#.

3 Frequency, 5 SubSNP, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1687589119 Apr 01, 2015 (144)
2 HUMAN_LONGEVITY ss2265599998 Dec 20, 2016 (150)
3 TOPMED ss2433421085 Dec 20, 2016 (150)
4 GNOMAD ss2734658029 Nov 08, 2017 (151)
5 TOPMED ss3437783981 Nov 08, 2017 (151)
6 The Exome Aggregation Consortium NC_000004.11 - 103226211 Jul 20, 2018 (151)
7 The Genome Aggregation Database NC_000004.11 - 103226211 Jul 20, 2018 (151)
8 Trans-Omics for Precision Medicine NC_000004.12 - 102305054 Jul 20, 2018 (151)
9 ClinVar RCV000203248.2 Jul 20, 2018 (151)
10 ClinVar RCV000203267.1 Jul 20, 2018 (151)
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
7561623, 3672764, ss1687589119, ss2433421085, ss2734658029 NC_000004.11:103226210:C= NC_000004.12:102305053:C= (self)
289266296, ss2265599998, ss3437783981 NC_000004.12:102305053:C= NC_000004.12:102305053:C= (self)
7561623, 3672764, ss1687589119, ss2433421085, ss2734658029 NC_000004.11:103226210:C>A NC_000004.12:102305053:C>A (self)
RCV000203248.2, RCV000203267.1, 289266296, ss2265599998, ss3437783981 NC_000004.12:102305053:C>A NC_000004.12:102305053:C>A (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 rs779241085
PMID Title Author Year Journal
26637979 SLC39A8 Deficiency: A Disorder of Manganese Transport and Glycosylation. Park JH et al. 2015 American journal of human genetics

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: 0.1.4.post833+d3ba21e