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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.

rs199476125

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chrMT:3733 (GRCh38.p13) 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
G=0.000 (0/792, PRJEB37584)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MT-ND1 : Missense Variant
MT-ND2 : 2KB Upstream Variant
Publications
2 citations
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").

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Study Population Group Sample Size Ref Allele Alt Allele
CNV burdens in cranial meningiomas Global Study-wide 792 G=0.000 A=1.000
CNV burdens in cranial meningiomas CRM Sub 792 G=0.000 A=1.000
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.

Gene: MT-ND2, mitochondrially encoded NADH dehydrogenase 2 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.3733G>A E [GAA] > K [AAA] Coding Sequence Variant
NADH dehydrogenase subunit 1 YP_003024026.1:p.Glu143Lys E (Glu) > K (Lys) Missense Variant
MT NC_012920.1:m.3733G>A N/A N/A
Gene: MT-ND1, mitochondrially encoded NADH dehydrogenase 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.3733G>A E [GAA] > K [AAA] Coding Sequence Variant
NADH dehydrogenase subunit 1 YP_003024026.1:p.Glu143Lys E (Glu) > K (Lys) Missense Variant
MT NC_012920.1:m.3733G>A N/A N/A
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: 24775 )
ClinVar Accession Disease Names Clinical Significance
RCV000010389.4 Leber's optic atrophy Pathogenic
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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
MT NC_012920.1:m.3733= NC_012920.1:m.3733G>A
NADH dehydrogenase subunit 1 YP_003024026.1:p.Glu143= YP_003024026.1:p.Glu143Lys
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 SubSNP, 1 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss510085606 Apr 11, 2012 (136)
2 AFFY ss2986125512 Oct 12, 2018 (152)
3 EVA ss3984773708 Apr 27, 2021 (155)
4 CNV burdens in cranial meningiomas NC_012920.1 - 3733 Apr 27, 2021 (155)
5 ClinVar RCV000010389.4 Jul 14, 2019 (153)
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
RCV000010389.4, 312408, ss510085606, ss2986125512, ss3984773708 NC_012920.1:3732:G:A NC_012920.1:3732: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 rs199476125
PMID Title Author Year Journal
15505787 The ND1 gene of complex I is a mutational hot spot for Leber's hereditary optic neuropathy. Valentino ML et al. 2004 Annals of neurology
20301353 Leber Hereditary Optic Neuropathy Yu-Wai-Man P et al. 1993 GeneReviews®
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The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

No flank sequence available

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.post676+237644a