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dbSNP Short Genetic Variations

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.


Current Build 152

Released October 2, 2018

Homo sapiens
chrX:38401332 (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.

G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Clinical Significance
Reported in ClinVar
Gene : Consequence
OTC : Missense Variant
2 citations
Genomic View
See rs on genome

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 X NC_000023.11:g.38401332G>C
GRCh38.p12 chr X NC_000023.11:g.38401332G>T
GRCh37.p13 chr X NC_000023.10:g.38260585G>C
GRCh37.p13 chr X NC_000023.10:g.38260585G>T
OTC RefSeqGene NG_008471.1:g.53850G>C
OTC RefSeqGene NG_008471.1:g.53850G>T
Gene: OTC, ornithine carbamoyltransferase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
OTC transcript NM_000531.5:c.444G>C L [TTG] > F [TTC] Coding Sequence Variant
ornithine carbamoyltransferase, mitochondrial precursor NP_000522.3:p.Leu148Phe L (Leu) > F (Phe) Missense Variant
OTC transcript NM_000531.5:c.444G>T L [TTG] > F [TTT] Coding Sequence Variant
ornithine carbamoyltransferase, mitochondrial precursor NP_000522.3:p.Leu148Phe L (Leu) > F (Phe) Missense Variant
OTC transcript variant X1 XM_017029556.1:c.444G>C L [TTG] > F [TTC] Coding Sequence Variant
ornithine carbamoyltransferase, mitochondrial isoform X1 XP_016885045.1:p.Leu148Phe L (Leu) > F (Phe) Missense Variant
OTC transcript variant X1 XM_017029556.1:c.444G>T L [TTG] > F [TTT] Coding Sequence Variant
ornithine carbamoyltransferase, mitochondrial isoform X1 XP_016885045.1:p.Leu148Phe L (Leu) > F (Phe) Missense Variant

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: C (allele ID: 26050 )
ClinVar Accession Disease Names Clinical Significance
RCV000011758.6 Ornithine carbamoyltransferase deficiency Pathogenic
RCV000083441.1 not provided Pathogenic
Allele: T (allele ID: 103096 )
ClinVar Accession Disease Names Clinical Significance
RCV000083442.1 not provided Pathogenic

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").


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= C T Note
GRCh38.p12 chr X NC_000023.11:g.38...






GRCh37.p13 chr X NC_000023.10:g.38...






OTC RefSeqGene NG_008471.1:g.538...






OTC transcript NM_000531.5:c.444G= NM_000531.5:c.444G>C NM_000531.5:c.444G>T
OTC transcript variant X1 XM_017029556.1:c....






ornithine carbamoyltransferase, mitochondrial precursor NP_000522.3:p.Leu...






ornithine carbamoyltransferase, mitochondrial isoform X1 XP_016885045.1:p....







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#.

6 SubSNP, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 GENMED_METABOLISM ss105441876 Feb 04, 2009 (130)
2 GENMED_METABOLISM ss105441877 Feb 04, 2009 (131)
3 OMIM-CURATED-RECORDS ss289354256 Dec 29, 2010 (133)
4 ILLUMINA ss1958188632 Feb 12, 2016 (147)
5 ILLUMINA ss3023002346 Nov 08, 2017 (151)
6 ILLUMINA ss3653560823 Oct 12, 2018 (152)
7 ClinVar RCV000011758.6 Oct 12, 2018 (152)
8 ClinVar RCV000083441.1 Oct 12, 2018 (152)
9 ClinVar RCV000083442.1 Oct 12, 2018 (152)

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).

Associated ID History Updated (Build)
rs66741319 Dec 07, 2009 (131)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss1958188632, ss3023002346, ss3653560823 NC_000023.10:38260584:G:C NC_000023.11:38401331:G:C (self)
RCV000011758.6, RCV000083441.1, ss105441876, ss289354256 NC_000023.11:38401331:G:C NC_000023.11:38401331:G:C (self)
RCV000083442.1, ss105441877 NC_000023.11:38401331:G:T NC_000023.11:38401331:G:T (self)

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

2 citations for rs66741318
PMID Title Author Year Journal
9056557 Familial lethal inheritance of a mutated paternal gene in females causing X-linked ornithine transcarbamylase (OTC) deficiency. Komaki S et al. 1997 American journal of medical genetics
9590019 [Ornithine transcarbamylase deficiency (OTCD)]. Matsuura T et al. 1998 Ryoikibetsu shokogun shirizu

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.post104+4a6ee9c