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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.

rs104894586

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr17:7585994 (GRCh38.p12) 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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00001 (3/246272, GnomAD)
A=0.00001 (1/125568, TOPMED)
A=0.00002 (2/121408, ExAC)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MPDU1 : Missense Variant
LOC100996842 : 2KB Upstream Variant
Publications
2 citations
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.p12 chr 17 NC_000017.11:g.7585994G>A
GRCh37.p13 chr 17 NC_000017.10:g.7489312G>A
MPDU1 RefSeqGene NG_009204.1:g.7348G>A
Gene: LOC100996842, uncharacterized LOC100996842 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC100996842 transcript variant 1 NM_001322800.1:c. N/A N/A
LOC100996842 transcript variant 4 NR_136401.1:n. N/A Upstream Transcript Variant
LOC100996842 transcript variant 3 NR_136402.1:n. N/A Upstream Transcript Variant
LOC100996842 transcript variant 2 NR_136403.1:n. N/A N/A
LOC100996842 transcript variant X1 XM_006721623.4:c. N/A N/A
Gene: MPDU1, mannose-P-dolichol utilization defect 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MPDU1 transcript variant 1 NM_004870.3:c.218G>A G [GGG] > E [GAG] Coding Sequence Variant
mannose-P-dolichol utilization defect 1 protein isoform 1 NP_004861.2:p.Gly73Glu G (Gly) > E (Glu) Missense Variant
MPDU1 transcript variant 3 NM_001330073.1:c.218G>A G [GGG] > E [GAG] Coding Sequence Variant
mannose-P-dolichol utilization defect 1 protein isoform 2 NP_001317002.1:p.Gly73Glu G (Gly) > E (Glu) Missense Variant
MPDU1 transcript variant 2 NR_024603.1:n.429G>A N/A Non Coding Transcript Variant
MPDU1 transcript variant X3 XM_011524081.2:c. N/A 5 Prime UTR Variant
MPDU1 transcript variant X4 XM_024451040.1:c. N/A 5 Prime UTR Variant
MPDU1 transcript variant X1 XM_006721597.2:c.218G>A G [GGG] > E [GAG] Coding Sequence Variant
mannose-P-dolichol utilization defect 1 protein isoform X1 XP_006721660.1:p.Gly73Glu G (Gly) > E (Glu) Missense Variant
MPDU1 transcript variant X2 XM_006721598.3:c.218G>A G [GGG] > E [GAG] Coding Sequence Variant
mannose-P-dolichol utilization defect 1 protein isoform X2 XP_006721661.1:p.Gly73Glu G (Gly) > E (Glu) 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: 20906 )
ClinVar Accession Disease Names Clinical Significance
RCV000006225.6 Congenital disorder of glycosylation type 1F Likely-Pathogenic
RCV000081186.5 not specified Uncertain-Significance
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
gnomAD - Exomes Global Study-wide 246272 G=0.99999 A=0.00001
gnomAD - Exomes European Sub 134020 G=0.99998 A=0.00002
gnomAD - Exomes Asian Sub 48030 G=1.0000 A=0.0000
gnomAD - Exomes American Sub 33582 G=1.0000 A=0.0000
gnomAD - Exomes African Sub 15304 G=1.0000 A=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 9850 G=1.000 A=0.000
gnomAD - Exomes Other Sub 5486 G=1.000 A=0.000
TopMed Global Study-wide 125568 G=0.99999 A=0.00001
ExAC Global Study-wide 121408 G=0.99998 A=0.00002
ExAC Europe Sub 73350 G=1.0000 A=0.0000
ExAC Asian Sub 25166 G=1.0000 A=0.0000
ExAC American Sub 11578 G=1.0000 A=0.0000
ExAC African Sub 10406 G=1.0000 A=0.0000
ExAC Other Sub 908 G=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 G= A Note
GRCh38.p12 chr 17 NC_000017.11:g.7585994G= NC_000017.11:g.7585994G>A
GRCh37.p13 chr 17 NC_000017.10:g.7489312G= NC_000017.10:g.7489312G>A
MPDU1 RefSeqGene NG_009204.1:g.7348G= NG_009204.1:g.7348G>A
MPDU1 transcript variant 1 NM_004870.3:c.218G= NM_004870.3:c.218G>A
MPDU1 transcript variant 2 NR_024603.1:n.429G= NR_024603.1:n.429G>A
MPDU1 transcript variant 3 NM_001330073.1:c.218G= NM_001330073.1:c.218G>A
MPDU1 transcript variant X2 XM_006721598.3:c.218G= XM_006721598.3:c.218G>A
MPDU1 transcript variant X3 XM_011524081.2:c.-146G= XM_011524081.2:c.-146G>A
MPDU1 transcript variant X1 XM_006721597.2:c.218G= XM_006721597.2:c.218G>A
MPDU1 transcript variant X4 XM_024451040.1:c.-146G= XM_024451040.1:c.-146G>A
mannose-P-dolichol utilization defect 1 protein isoform 1 NP_004861.2:p.Gly73= NP_004861.2:p.Gly73Glu
mannose-P-dolichol utilization defect 1 protein isoform 2 NP_001317002.1:p.Gly73= NP_001317002.1:p.Gly73Glu
mannose-P-dolichol utilization defect 1 protein isoform X2 XP_006721661.1:p.Gly73= XP_006721661.1:p.Gly73Glu
mannose-P-dolichol utilization defect 1 protein isoform X1 XP_006721660.1:p.Gly73= XP_006721660.1:p.Gly73Glu
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, 2 ClinVar, 9 SubSNP submissions
No Submitter Submission ID Date (Build)
1 OMICIA ss244239566 May 28, 2010 (132)
2 OMIM-CURATED-RECORDS ss262857674 Sep 17, 2010 (132)
3 EVA_EXAC ss1692577717 Apr 01, 2015 (144)
4 ILLUMINA ss1959721095 Feb 12, 2016 (147)
5 TOPMED ss2380162429 Dec 20, 2016 (150)
6 GNOMAD ss2742406911 Nov 08, 2017 (151)
7 ILLUMINA ss3021752068 Nov 08, 2017 (151)
8 TOPMED ss3256670356 Nov 08, 2017 (151)
9 ILLUMINA ss3652164876 Oct 12, 2018 (152)
10 ExAC NC_000017.10 - 7489312 Oct 12, 2018 (152)
11 gnomAD - Exomes NC_000017.10 - 7489312 Oct 12, 2018 (152)
12 TopMed NC_000017.11 - 7585994 Oct 12, 2018 (152)
13 ClinVar RCV000006225.6 Oct 12, 2018 (152)
14 ClinVar RCV000081186.5 Oct 12, 2018 (152)
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
3005325, 9221410, ss1692577717, ss1959721095, ss2380162429, ss2742406911, ss3021752068, ss3652164876 NC_000017.10:7489311:G= NC_000017.11:7585993:G= (self)
152391837, ss244239566, ss262857674, ss3256670356 NC_000017.11:7585993:G= NC_000017.11:7585993:G= (self)
3005325, 9221410, ss1692577717, ss1959721095, ss2380162429, ss2742406911, ss3021752068, ss3652164876 NC_000017.10:7489311:G>A NC_000017.11:7585993:G>A (self)
RCV000006225.6, RCV000081186.5, 152391837, ss244239566, ss262857674, ss3256670356 NC_000017.11:7585993:G>A NC_000017.11:7585993:G>A (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

2 citations for rs104894586
PMID Title Author Year Journal
11733564 MPDU1 mutations underlie a novel human congenital disorder of glycosylation, designated type If. Schenk B et al. 2001 The Journal of clinical investigation
23757202 Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data. Bean LJ et al. 2013 Human mutation

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.post863+3a64c51