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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.

rs1057519565

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:687941 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
DEAF1 : Missense Variant
Publications
0 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").

None
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.p14 chr 11 NC_000011.10:g.687941C>A
GRCh38.p14 chr 11 NC_000011.10:g.687941C>T
GRCh37.p13 chr 11 NC_000011.9:g.687941C>A
GRCh37.p13 chr 11 NC_000011.9:g.687941C>T
DEAF1 RefSeqGene NG_034156.2:g.24143G>T
DEAF1 RefSeqGene NG_034156.2:g.24143G>A
Gene: DEAF1, DEAF1 transcription factor (minus strand)
Molecule type Change Amino acid[Codon] SO Term
DEAF1 transcript variant 3 NM_001367390.1:c.-93= N/A 5 Prime UTR Variant
DEAF1 transcript variant 2 NM_001293634.1:c.634G>T G [GGC] > C [TGC] Coding Sequence Variant
deformed epidermal autoregulatory factor 1 homolog isoform b NP_001280563.1:p.Gly212Cys G (Gly) > C (Cys) Missense Variant
DEAF1 transcript variant 2 NM_001293634.1:c.634G>A G [GGC] > S [AGC] Coding Sequence Variant
deformed epidermal autoregulatory factor 1 homolog isoform b NP_001280563.1:p.Gly212Ser G (Gly) > S (Ser) Missense Variant
DEAF1 transcript variant 1 NM_021008.4:c.634G>T G [GGC] > C [TGC] Coding Sequence Variant
deformed epidermal autoregulatory factor 1 homolog isoform a NP_066288.2:p.Gly212Cys G (Gly) > C (Cys) Missense Variant
DEAF1 transcript variant 1 NM_021008.4:c.634G>A G [GGC] > S [AGC] Coding Sequence Variant
deformed epidermal autoregulatory factor 1 homolog isoform a NP_066288.2:p.Gly212Ser G (Gly) > S (Ser) Missense Variant
DEAF1 transcript variant X6 XM_047426250.1:c.-93= N/A 5 Prime UTR Variant
DEAF1 transcript variant X7 XM_047426251.1:c.-93= N/A 5 Prime UTR Variant
DEAF1 transcript variant X1 XM_047426248.1:c.634G>T G [GGC] > C [TGC] Coding Sequence Variant
deformed epidermal autoregulatory factor 1 homolog isoform X1 XP_047282204.1:p.Gly212Cys G (Gly) > C (Cys) Missense Variant
DEAF1 transcript variant X1 XM_047426248.1:c.634G>A G [GGC] > S [AGC] Coding Sequence Variant
deformed epidermal autoregulatory factor 1 homolog isoform X1 XP_047282204.1:p.Gly212Ser G (Gly) > S (Ser) Missense Variant
DEAF1 transcript variant X2 XM_011519842.4:c.634G>T G [GGC] > C [TGC] Coding Sequence Variant
deformed epidermal autoregulatory factor 1 homolog isoform X2 XP_011518144.1:p.Gly212Cys G (Gly) > C (Cys) Missense Variant
DEAF1 transcript variant X2 XM_011519842.4:c.634G>A G [GGC] > S [AGC] Coding Sequence Variant
deformed epidermal autoregulatory factor 1 homolog isoform X2 XP_011518144.1:p.Gly212Ser G (Gly) > S (Ser) Missense Variant
DEAF1 transcript variant X3 XM_047426249.1:c.634G>T G [GGC] > C [TGC] Coding Sequence Variant
deformed epidermal autoregulatory factor 1 homolog isoform X3 XP_047282205.1:p.Gly212Cys G (Gly) > C (Cys) Missense Variant
DEAF1 transcript variant X3 XM_047426249.1:c.634G>A G [GGC] > S [AGC] Coding Sequence Variant
deformed epidermal autoregulatory factor 1 homolog isoform X3 XP_047282205.1:p.Gly212Ser G (Gly) > S (Ser) Missense Variant
DEAF1 transcript variant X4 XR_007062436.1:n.809G>T N/A Non Coding Transcript Variant
DEAF1 transcript variant X4 XR_007062436.1:n.809G>A N/A Non Coding Transcript Variant
DEAF1 transcript variant X5 XR_007062437.1:n.575G>T N/A Non Coding Transcript Variant
DEAF1 transcript variant X5 XR_007062437.1:n.575G>A N/A Non Coding Transcript 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: 1087073 )
ClinVar Accession Disease Names Clinical Significance
RCV001420245.1 See cases Pathogenic
Allele: T (allele ID: 362364 )
ClinVar Accession Disease Names Clinical Significance
RCV000417021.3 Intellectual disability, autosomal dominant 24 Pathogenic-Likely-Pathogenic
RCV000493974.2 not provided Pathogenic
RCV001788214.1 Intellectual disability, autosomal dominant 24,Intellectual disability-epilepsy-extrapyramidal syndrome Not-Provided
RCV002274025.1 Neurodevelopmental delay Pathogenic
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 C= A T
GRCh38.p14 chr 11 NC_000011.10:g.687941= NC_000011.10:g.687941C>A NC_000011.10:g.687941C>T
GRCh37.p13 chr 11 NC_000011.9:g.687941= NC_000011.9:g.687941C>A NC_000011.9:g.687941C>T
DEAF1 RefSeqGene NG_034156.2:g.24143= NG_034156.2:g.24143G>T NG_034156.2:g.24143G>A
DEAF1 transcript variant 1 NM_021008.4:c.634= NM_021008.4:c.634G>T NM_021008.4:c.634G>A
DEAF1 transcript variant 1 NM_021008.3:c.634= NM_021008.3:c.634G>T NM_021008.3:c.634G>A
DEAF1 transcript NM_021008.2:c.634= NM_021008.2:c.634G>T NM_021008.2:c.634G>A
DEAF1 transcript variant 2 NM_001293634.1:c.634= NM_001293634.1:c.634G>T NM_001293634.1:c.634G>A
DEAF1 transcript variant 3 NM_001367390.1:c.-93= NM_001367390.1:c.-93G>T NM_001367390.1:c.-93G>A
DEAF1 transcript variant X2 XM_011519842.4:c.634= XM_011519842.4:c.634G>T XM_011519842.4:c.634G>A
DEAF1 transcript variant X2 XM_011519842.3:c.634= XM_011519842.3:c.634G>T XM_011519842.3:c.634G>A
DEAF1 transcript variant X2 XM_011519842.2:c.634= XM_011519842.2:c.634G>T XM_011519842.2:c.634G>A
DEAF1 transcript variant X2 XM_011519842.1:c.634= XM_011519842.1:c.634G>T XM_011519842.1:c.634G>A
DEAF1 transcript variant X4 XR_007062436.1:n.809= XR_007062436.1:n.809G>T XR_007062436.1:n.809G>A
DEAF1 transcript variant X6 XM_047426250.1:c.-93= XM_047426250.1:c.-93G>T XM_047426250.1:c.-93G>A
DEAF1 transcript variant X7 XM_047426251.1:c.-93= XM_047426251.1:c.-93G>T XM_047426251.1:c.-93G>A
DEAF1 transcript variant X1 XM_047426248.1:c.634= XM_047426248.1:c.634G>T XM_047426248.1:c.634G>A
DEAF1 transcript variant X3 XM_047426249.1:c.634= XM_047426249.1:c.634G>T XM_047426249.1:c.634G>A
DEAF1 transcript variant X5 XR_007062437.1:n.575= XR_007062437.1:n.575G>T XR_007062437.1:n.575G>A
deformed epidermal autoregulatory factor 1 homolog isoform a NP_066288.2:p.Gly212= NP_066288.2:p.Gly212Cys NP_066288.2:p.Gly212Ser
deformed epidermal autoregulatory factor 1 homolog isoform b NP_001280563.1:p.Gly212= NP_001280563.1:p.Gly212Cys NP_001280563.1:p.Gly212Ser
deformed epidermal autoregulatory factor 1 homolog isoform X2 XP_011518144.1:p.Gly212= XP_011518144.1:p.Gly212Cys XP_011518144.1:p.Gly212Ser
deformed epidermal autoregulatory factor 1 homolog isoform X1 XP_047282204.1:p.Gly212= XP_047282204.1:p.Gly212Cys XP_047282204.1:p.Gly212Ser
deformed epidermal autoregulatory factor 1 homolog isoform X3 XP_047282205.1:p.Gly212= XP_047282205.1:p.Gly212Cys XP_047282205.1:p.Gly212Ser
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, 5 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CLINVAR ss2137497417 Feb 23, 2017 (149)
2 HUMAN_LONGEVITY ss2179552366 Dec 20, 2016 (136)
3 ClinVar RCV000417021.3 Apr 26, 2021 (155)
4 ClinVar RCV000493974.2 Jul 13, 2019 (153)
5 ClinVar RCV001420245.1 Oct 16, 2022 (156)
6 ClinVar RCV001788214.1 Oct 16, 2022 (156)
7 ClinVar RCV002274025.1 Oct 16, 2022 (156)
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)
rs1056249892 Apr 07, 2017 (136)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
RCV001420245.1 NC_000011.10:687940:C:A NC_000011.10:687940:C:A
RCV000417021.3, RCV000493974.2, RCV001788214.1, RCV002274025.1, ss2137497417, ss2179552366 NC_000011.10:687940:C:T NC_000011.10:687940:C:T (self)
Help

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

No publications for rs1057519565

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

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