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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.

rs121434616

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chrX:120544179 (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
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
CUL4B : Stop Gained
Publications
4 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 X NC_000023.11:g.120544179G>A
GRCh37.p13 chr X NC_000023.10:g.119678034G>A
CUL4B RefSeqGene NG_009388.1:g.36651C>T
Gene: CUL4B, cullin 4B (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CUL4B transcript variant 1 NM_003588.3:c.1162C>T R [CGA] > * [TGA] Coding Sequence Variant
cullin-4B isoform 1 NP_003579.3:p.Arg388Ter R (Arg) > * (Ter) Stop Gained
CUL4B transcript variant 2 NM_001079872.1:c.1108C>T R [CGA] > * [TGA] Coding Sequence Variant
cullin-4B isoform 2 NP_001073341.1:p.Arg370Ter R (Arg) > * (Ter) Stop Gained
CUL4B transcript variant 3 NM_001330624.1:c.1123C>T R [CGA] > * [TGA] Coding Sequence Variant
cullin-4B isoform 3 NP_001317553.1:p.Arg375Ter R (Arg) > * (Ter) Stop Gained
CUL4B transcript variant X1 XM_005262481.1:c.1162C>T R [CGA] > * [TGA] Coding Sequence Variant
cullin-4B isoform X1 XP_005262538.1:p.Arg388Ter R (Arg) > * (Ter) Stop Gained
CUL4B transcript variant X2 XM_006724784.1:c.1123C>T R [CGA] > * [TGA] Coding Sequence Variant
cullin-4B isoform X2 XP_006724847.1:p.Arg375Ter R (Arg) > * (Ter) Stop Gained
CUL4B transcript variant X5 XM_011531401.1:c.520C>T R [CGA] > * [TGA] Coding Sequence Variant
cullin-4B isoform X5 XP_011529703.1:p.Arg174Ter R (Arg) > * (Ter) Stop Gained
CUL4B transcript variant X3 XM_011531399.2:c.574C>T R [CGA] > * [TGA] Coding Sequence Variant
cullin-4B isoform X3 XP_011529701.1:p.Arg192Ter R (Arg) > * (Ter) Stop Gained
CUL4B transcript variant X4 XM_011531400.2:c.574C>T R [CGA] > * [TGA] Coding Sequence Variant
cullin-4B isoform X4 XP_011529702.1:p.Arg192Ter R (Arg) > * (Ter) Stop Gained
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: 26378 )
ClinVar Accession Disease Names Clinical Significance
RCV000012092.13 Syndromic X-linked mental retardation, Cabezas type Pathogenic
RCV000415116.1 Abnormal facial shape,Global developmental delay,Intellectual disability,Seizures,Short stature 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").

None
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 X NC_000023.11:g.120544179G= NC_000023.11:g.12054417...

NC_000023.11:g.120544179G>A

GRCh37.p13 chr X NC_000023.10:g.119678034G= NC_000023.10:g.11967803...

NC_000023.10:g.119678034G>A

CUL4B RefSeqGene NG_009388.1:g.36651C= NG_009388.1:g.36651C>T
CUL4B transcript variant 1 NM_003588.3:c.1162C= NM_003588.3:c.1162C>T
CUL4B transcript variant 2 NM_001079872.1:c.1108C= NM_001079872.1:c.1108C>T
CUL4B transcript variant 3 NM_001330624.1:c.1123C= NM_001330624.1:c.1123C>T
CUL4B transcript variant X4 XM_011531400.2:c.574C= XM_011531400.2:c.574C>T
CUL4B transcript variant X3 XM_011531399.2:c.574C= XM_011531399.2:c.574C>T
CUL4B transcript variant X1 XM_005262481.1:c.1162C= XM_005262481.1:c.1162C>T
CUL4B transcript variant X2 XM_006724784.1:c.1123C= XM_006724784.1:c.1123C>T
CUL4B transcript variant X5 XM_011531401.1:c.520C= XM_011531401.1:c.520C>T
cullin-4B isoform 1 NP_003579.3:p.Arg388= NP_003579.3:p.Arg388Ter
cullin-4B isoform 2 NP_001073341.1:p.Arg370= NP_001073341.1:p.Arg370Ter
cullin-4B isoform 3 NP_001317553.1:p.Arg375= NP_001317553.1:p.Arg375Ter
cullin-4B isoform X4 XP_011529702.1:p.Arg192= XP_011529702.1:p.Arg192Ter
cullin-4B isoform X3 XP_011529701.1:p.Arg192= XP_011529701.1:p.Arg192Ter
cullin-4B isoform X1 XP_005262538.1:p.Arg388= XP_005262538.1:p.Arg388Ter
cullin-4B isoform X2 XP_006724847.1:p.Arg375= XP_006724847.1:p.Arg375Ter
cullin-4B isoform X5 XP_011529703.1:p.Arg174= XP_011529703.1:p.Arg174Ter
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#.

2 SubSNP, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss256302387 Aug 26, 2010 (132)
2 OMIM-CURATED-RECORDS ss256302388 Aug 26, 2010 (132)
3 ClinVar RCV000012092.13 Oct 12, 2018 (152)
4 ClinVar RCV000415116.1 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).

Associated ID History Updated (Build)
rs121434617 Oct 26, 2010 (133)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
RCV000012092.13, RCV000415116.1, ss256302387, ss256302388 NC_000023.11:120544178:G:A NC_000023.11:120544178: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.

4 citations for rs121434616
PMID Title Author Year Journal
8135271 Smith-Fineman-Myers syndrome: report on a large family. Wei J et al. 1993 American journal of medical genetics
17236139 Mutations in CUL4B, which encodes a ubiquitin E3 ligase subunit, cause an X-linked mental retardation syndrome associated with aggressive outbursts, seizures, relative macrocephaly, central obesity, hypogonadism, pes cavus, and tremor. Tarpey PS et al. 2007 American journal of human genetics
17273978 Mutation in CUL4B, which encodes a member of cullin-RING ubiquitin ligase complex, causes X-linked mental retardation. Zou Y et al. 2007 American journal of human genetics
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine

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