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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.

rs200613617

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrMT:9804 (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
G>A / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00443 (347/78260, ALFA)
A=0.00439 (62/14129, 14KJPN)
A=0.0044 (37/8380, 8.3KJPN) (+ 4 more)
A=0.0048 (14/2922, KOREAN)
A=0.003 (2/790, PRJEB37584)
A=0.004 (2/534, MGP)
G=0.2 (1/4, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MT-CO3 : Missense Variant
MT-ND3 : 2KB Upstream Variant
MT-ND4 : 2KB Upstream Variant (+ 1 more)
MT-ND4L : 2KB Upstream Variant
Publications
2 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 78260 G=0.99557 A=0.00443
European Sub 67912 G=0.99552 A=0.00448
African Sub 1466 G=0.9945 A=0.0055
African Others Sub 60 G=1.00 A=0.00
African American Sub 1406 G=0.9943 A=0.0057
Asian Sub 3236 G=0.9944 A=0.0056
East Asian Sub 2582 G=0.9938 A=0.0062
Other Asian Sub 654 G=0.997 A=0.003
Latin American 1 Sub 290 G=1.000 A=0.000
Latin American 2 Sub 318 G=1.000 A=0.000
South Asian Sub 176 G=1.000 A=0.000
Other Sub 4862 G=0.9965 A=0.0035


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
Allele Frequency Aggregator Total Global 78260 G=0.99557 A=0.00443
Allele Frequency Aggregator European Sub 67912 G=0.99552 A=0.00448
Allele Frequency Aggregator Other Sub 4862 G=0.9965 A=0.0035
Allele Frequency Aggregator Asian Sub 3236 G=0.9944 A=0.0056
Allele Frequency Aggregator African Sub 1466 G=0.9945 A=0.0055
Allele Frequency Aggregator Latin American 2 Sub 318 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 290 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 176 G=1.000 A=0.000
14KJPN JAPANESE Study-wide 14129 G=0.99561 A=0.00439
8.3KJPN JAPANESE Study-wide 8380 G=0.9956 A=0.0044
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9952 A=0.0048
CNV burdens in cranial meningiomas Global Study-wide 790 G=0.997 A=0.003
CNV burdens in cranial meningiomas CRM Sub 790 G=0.997 A=0.003
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.996 A=0.004
SGDP_PRJ Global Study-wide 4 G=0.2 A=0.8
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-ND3, mitochondrially encoded NADH dehydrogenase 3 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.9804G>A A [GCC] > T [ACC] Coding Sequence Variant
cytochrome c oxidase subunit III YP_003024032.1:p.Ala200Thr A (Ala) > T (Thr) Missense Variant
MT NC_012920.1:m.9804G>A N/A N/A
MT NC_012920.1:m.9804G>A N/A N/A
MT NC_012920.1:m.9804G>A N/A N/A
MT NC_012920.1:m.9804G>C A [GCC] > P [CCC] Coding Sequence Variant
cytochrome c oxidase subunit III YP_003024032.1:p.Ala200Pro A (Ala) > P (Pro) Missense Variant
MT NC_012920.1:m.9804G>C N/A N/A
MT NC_012920.1:m.9804G>C N/A N/A
MT NC_012920.1:m.9804G>C N/A N/A
MT NC_012920.1:m.9804G>T A [GCC] > S [TCC] Coding Sequence Variant
cytochrome c oxidase subunit III YP_003024032.1:p.Ala200Ser A (Ala) > S (Ser) Missense Variant
MT NC_012920.1:m.9804G>T N/A N/A
MT NC_012920.1:m.9804G>T N/A N/A
MT NC_012920.1:m.9804G>T N/A N/A
Gene: MT-ND4, mitochondrially encoded NADH dehydrogenase 4 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.9804G>A A [GCC] > T [ACC] Coding Sequence Variant
cytochrome c oxidase subunit III YP_003024032.1:p.Ala200Thr A (Ala) > T (Thr) Missense Variant
MT NC_012920.1:m.9804G>A N/A N/A
MT NC_012920.1:m.9804G>A N/A N/A
MT NC_012920.1:m.9804G>A N/A N/A
MT NC_012920.1:m.9804G>C A [GCC] > P [CCC] Coding Sequence Variant
cytochrome c oxidase subunit III YP_003024032.1:p.Ala200Pro A (Ala) > P (Pro) Missense Variant
MT NC_012920.1:m.9804G>C N/A N/A
MT NC_012920.1:m.9804G>C N/A N/A
MT NC_012920.1:m.9804G>C N/A N/A
MT NC_012920.1:m.9804G>T A [GCC] > S [TCC] Coding Sequence Variant
cytochrome c oxidase subunit III YP_003024032.1:p.Ala200Ser A (Ala) > S (Ser) Missense Variant
MT NC_012920.1:m.9804G>T N/A N/A
MT NC_012920.1:m.9804G>T N/A N/A
MT NC_012920.1:m.9804G>T N/A N/A
Gene: MT-ND4L, mitochondrially encoded NADH 4L dehydrogenase (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.9804G>A A [GCC] > T [ACC] Coding Sequence Variant
cytochrome c oxidase subunit III YP_003024032.1:p.Ala200Thr A (Ala) > T (Thr) Missense Variant
MT NC_012920.1:m.9804G>A N/A N/A
MT NC_012920.1:m.9804G>A N/A N/A
MT NC_012920.1:m.9804G>A N/A N/A
MT NC_012920.1:m.9804G>C A [GCC] > P [CCC] Coding Sequence Variant
cytochrome c oxidase subunit III YP_003024032.1:p.Ala200Pro A (Ala) > P (Pro) Missense Variant
MT NC_012920.1:m.9804G>C N/A N/A
MT NC_012920.1:m.9804G>C N/A N/A
MT NC_012920.1:m.9804G>C N/A N/A
MT NC_012920.1:m.9804G>T A [GCC] > S [TCC] Coding Sequence Variant
cytochrome c oxidase subunit III YP_003024032.1:p.Ala200Ser A (Ala) > S (Ser) Missense Variant
MT NC_012920.1:m.9804G>T N/A N/A
MT NC_012920.1:m.9804G>T N/A N/A
MT NC_012920.1:m.9804G>T N/A N/A
Gene: MT-CO3, mitochondrially encoded cytochrome c oxidase III (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MT NC_012920.1:m.9804G>A A [GCC] > T [ACC] Coding Sequence Variant
cytochrome c oxidase subunit III YP_003024032.1:p.Ala200Thr A (Ala) > T (Thr) Missense Variant
MT NC_012920.1:m.9804G>A N/A N/A
MT NC_012920.1:m.9804G>A N/A N/A
MT NC_012920.1:m.9804G>A N/A N/A
MT NC_012920.1:m.9804G>C A [GCC] > P [CCC] Coding Sequence Variant
cytochrome c oxidase subunit III YP_003024032.1:p.Ala200Pro A (Ala) > P (Pro) Missense Variant
MT NC_012920.1:m.9804G>C N/A N/A
MT NC_012920.1:m.9804G>C N/A N/A
MT NC_012920.1:m.9804G>C N/A N/A
MT NC_012920.1:m.9804G>T A [GCC] > S [TCC] Coding Sequence Variant
cytochrome c oxidase subunit III YP_003024032.1:p.Ala200Ser A (Ala) > S (Ser) Missense Variant
MT NC_012920.1:m.9804G>T N/A N/A
MT NC_012920.1:m.9804G>T N/A N/A
MT NC_012920.1:m.9804G>T 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: 24691 )
ClinVar Accession Disease Names Clinical Significance
RCV000010287.5 Leber optic atrophy Pathogenic
RCV000756352.5 not provided Uncertain-Significance
RCV000854582.1 Leigh syndrome Benign
RCV001196020.1 See cases Uncertain-Significance
Allele: C (allele ID: 681765 )
ClinVar Accession Disease Names Clinical Significance
RCV000854583.1 Leigh syndrome Uncertain-Significance
Allele: T (allele ID: 681766 )
ClinVar Accession Disease Names Clinical Significance
RCV000854584.1 Leigh syndrome Uncertain-Significance
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 C T
MT NC_012920.1:m.9804= NC_012920.1:m.9804G>A NC_012920.1:m.9804G>C NC_012920.1:m.9804G>T
cytochrome c oxidase subunit III YP_003024032.1:p.Ala200= YP_003024032.1:p.Ala200Thr YP_003024032.1:p.Ala200Pro YP_003024032.1:p.Ala200Ser
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#.

24 SubSNP, 7 Frequency, 6 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EXOME_CHIP ss491581417 May 04, 2012 (137)
2 OMIM-CURATED-RECORDS ss537712847 Jul 19, 2012 (137)
3 ILLUMINA ss780796944 Jul 19, 2016 (147)
4 ILLUMINA ss783478206 Jul 19, 2016 (147)
5 EVA_MGP ss1711594842 Jul 19, 2016 (147)
6 ILLUMINA ss1752791319 Jul 19, 2016 (147)
7 ILLUMINA ss1917715440 Jul 19, 2016 (147)
8 ILLUMINA ss1945966483 Jul 19, 2016 (147)
9 ILLUMINA ss1958161314 Jul 19, 2016 (147)
10 SWEGEN ss3020999115 Oct 12, 2018 (152)
11 ILLUMINA ss3022981571 Oct 12, 2018 (152)
12 ILLUMINA ss3640947778 Oct 12, 2018 (152)
13 ILLUMINA ss3645007191 Oct 12, 2018 (152)
14 ILLUMINA ss3653538987 Oct 12, 2018 (152)
15 ILLUMINA ss3726656281 Jul 14, 2019 (153)
16 ILLUMINA ss3745540357 Jul 14, 2019 (153)
17 ILLUMINA ss3773032077 Jul 14, 2019 (153)
18 SGDP_PRJ ss3892819500 Apr 27, 2020 (154)
19 KRGDB ss3892821546 Apr 27, 2020 (154)
20 EVA ss3984773784 Apr 27, 2021 (155)
21 TOMMO_GENOMICS ss5236851803 Apr 27, 2021 (155)
22 SANFORD_IMAGENETICS ss5666160594 Oct 13, 2022 (156)
23 TOMMO_GENOMICS ss5799399757 Oct 13, 2022 (156)
24 EVA ss5848225848 Oct 13, 2022 (156)
25 KOREAN population from KRGDB NC_001807.4 - 9805 Apr 27, 2020 (154)
26 Medical Genome Project healthy controls from Spanish population NC_012920.1 - 9804 Apr 27, 2020 (154)
27 CNV burdens in cranial meningiomas NC_012920.1 - 9804 Apr 27, 2021 (155)
28 SGDP_PRJ NC_012920.1 - 9804 Apr 27, 2020 (154)
29 8.3KJPN NC_012920.1 - 9804 Apr 27, 2021 (155)
30 14KJPN NC_012920.1 - 9804 Oct 13, 2022 (156)
31 ALFA NC_012920.1 - 9804 Apr 27, 2021 (155)
32 ClinVar RCV000010287.5 Oct 13, 2022 (156)
33 ClinVar RCV000756352.5 Oct 13, 2022 (156)
34 ClinVar RCV000854582.1 Apr 27, 2020 (154)
35 ClinVar RCV000854583.1 Apr 27, 2020 (154)
36 ClinVar RCV000854584.1 Apr 27, 2020 (154)
37 ClinVar RCV001196020.1 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
50800596, ss3892821546 NC_001807.4:9804:G:A NC_012920.1:9803:G:A (self)
RCV000010287.5, RCV000756352.5, RCV000854582.1, RCV001196020.1, 710602, 312485, 44836480, 94821110, 133236861, 8758009300, ss491581417, ss537712847, ss780796944, ss783478206, ss1711594842, ss1752791319, ss1917715440, ss1945966483, ss1958161314, ss3020999115, ss3022981571, ss3640947778, ss3645007191, ss3653538987, ss3726656281, ss3745540357, ss3773032077, ss3892819500, ss3984773784, ss5236851803, ss5666160594, ss5799399757, ss5848225848 NC_012920.1:9803:G:A NC_012920.1:9803:G:A (self)
RCV000854583.1 NC_012920.1:9803:G:C NC_012920.1:9803:G:C (self)
RCV000854584.1 NC_012920.1:9803:G:T NC_012920.1:9803:G:T (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 rs200613617
PMID Title Author Year Journal
8240356 Cytochrome c oxidase mutations in Leber hereditary optic neuropathy. Johns DR et al. 1993 Biochemical and biophysical research communications
20301353 Leber Hereditary Optic Neuropathy. Yu-Wai-Man P et al. 1993 GeneReviews(®)
Help

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.post761+d5e8e07