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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 Aliases 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.

rs121913507

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr4:54733155 (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
A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
KIT : Missense Variant
Publications
21 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 4 NC_000004.12:g.54733155A>T
GRCh37.p13 chr 4 NC_000004.11:g.55599321A>T
KIT RefSeqGene (LRG_307) NG_007456.1:g.80161A>T
Gene: KIT, KIT proto-oncogene, receptor tyrosine kinase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
KIT transcript variant 2 NM_001093772.1:c.2435A>T D [GAC] > V [GTC] Coding Sequence Variant
mast/stem cell growth factor receptor Kit isoform 2 NP_001087241.1:p.Asp812Val D (Asp) > V (Val) Missense Variant
KIT transcript variant 1 NM_000222.2:c.2447A>T D [GAC] > V [GTC] Coding Sequence Variant
mast/stem cell growth factor receptor Kit isoform 1 NP_000213.1:p.Asp816Val D (Asp) > V (Val) Missense Variant
KIT transcript variant X1 XM_005265740.1:c.2450A>T D [GAC] > V [GTC] Coding Sequence Variant
mast/stem cell growth factor receptor Kit isoform X1 XP_005265797.1:p.Asp817Val D (Asp) > V (Val) Missense Variant
KIT transcript variant X2 XM_005265741.1:c.2447A>T D [GAC] > V [GTC] Coding Sequence Variant
mast/stem cell growth factor receptor Kit isoform X2 XP_005265798.1:p.Asp816Val D (Asp) > V (Val) Missense Variant
KIT transcript variant X3 XM_017008178.1:c.2444A>T D [GAC] > V [GTC] Coding Sequence Variant
mast/stem cell growth factor receptor Kit isoform X3 XP_016863667.1:p.Asp815Val D (Asp) > V (Val) Missense Variant
KIT transcript variant X5 XM_017008179.1:c.2435A>T D [GAC] > V [GTC] Coding Sequence Variant
mast/stem cell growth factor receptor Kit isoform X5 XP_016863668.1:p.Asp812Val D (Asp) > V (Val) Missense Variant
KIT transcript variant X6 XM_017008180.1:c.2432A>T D [GAC] > V [GTC] Coding Sequence Variant
mast/stem cell growth factor receptor Kit isoform X6 XP_016863669.1:p.Asp811Val D (Asp) > V (Val) Missense Variant
KIT transcript variant X4 XM_005265742.3:c.2438A>T D [GAC] > V [GTC] Coding Sequence Variant
mast/stem cell growth factor receptor Kit isoform X4 XP_005265799.1:p.Asp813Val D (Asp) > V (Val) Missense 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: T (allele ID: 28891 )
ClinVar Accession Disease Names Clinical Significance
RCV000014864.24 Mast cell leukemia Likely-Pathogenic
RCV000431704.3 Gastrointestinal stroma tumor Uncertain-Significance
RCV000443179.1 Hematologic neoplasm Likely-Pathogenic
RCV000444150.1 Acute myeloid leukemia Pathogenic
RCV000505554.1 Dysgerminoma Other
RCV000656673.3 MAST CELL LEUKEMIA, SOMATIC Pathogenic
RCV000656674.3 MASTOCYTOSIS WITH ASSOCIATED HEMATOLOGIC DISORDER, SOMATIC Pathogenic
RCV000656675.3 MASTOCYTOSIS, SYSTEMIC, SOMATIC Pathogenic
RCV000656676.3 Cutaneous mastocytosis 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 A= T Note
GRCh38.p12 chr 4 NC_000004.12:g.54733155= NC_000004.12:g.54733155A>T
GRCh37.p13 chr 4 NC_000004.11:g.55599321= NC_000004.11:g.55599321A>T
KIT RefSeqGene (LRG_307) NG_007456.1:g.80161= NG_007456.1:g.80161A>T
KIT transcript variant 1 NM_000222.2:c.2447= NM_000222.2:c.2447A>T
KIT transcript variant 2 NM_001093772.1:c.2435= NM_001093772.1:c.2435A>T
KIT transcript variant X4 XM_005265742.3:c.2438= XM_005265742.3:c.2438A>T
KIT transcript variant X3 XM_005265742.1:c.2438= XM_005265742.1:c.2438A>T
KIT transcript variant X1 XM_005265740.1:c.2450= XM_005265740.1:c.2450A>T
KIT transcript variant X2 XM_005265741.1:c.2447= XM_005265741.1:c.2447A>T
KIT transcript variant X3 XM_017008178.1:c.2444= XM_017008178.1:c.2444A>T
KIT transcript variant X5 XM_017008179.1:c.2435= XM_017008179.1:c.2435A>T
KIT transcript variant X6 XM_017008180.1:c.2432= XM_017008180.1:c.2432A>T
mast/stem cell growth factor receptor Kit isoform 1 NP_000213.1:p.Asp816= NP_000213.1:p.Asp816Val
mast/stem cell growth factor receptor Kit isoform 2 NP_001087241.1:p.Asp812= NP_001087241.1:p.Asp812Val
mast/stem cell growth factor receptor Kit isoform X4 XP_005265799.1:p.Asp813= XP_005265799.1:p.Asp813Val
mast/stem cell growth factor receptor Kit isoform X1 XP_005265797.1:p.Asp817= XP_005265797.1:p.Asp817Val
mast/stem cell growth factor receptor Kit isoform X2 XP_005265798.1:p.Asp816= XP_005265798.1:p.Asp816Val
mast/stem cell growth factor receptor Kit isoform X3 XP_016863667.1:p.Asp815= XP_016863667.1:p.Asp815Val
mast/stem cell growth factor receptor Kit isoform X5 XP_016863668.1:p.Asp812= XP_016863668.1:p.Asp812Val
mast/stem cell growth factor receptor Kit isoform X6 XP_016863669.1:p.Asp811= XP_016863669.1:p.Asp811Val
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#.

4 SubSNP, 9 ClinVar submissions
No Submitter Submission ID Date (Build)
1 DF-BWCC ss275515391 Nov 22, 2010 (133)
2 OMIM-CURATED-RECORDS ss275515659 Nov 24, 2010 (133)
3 GNOMAD ss2734512669 Nov 08, 2017 (151)
4 EVA_DECODE ss3712025724 Jul 13, 2019 (153)
5 ClinVar RCV000014864.24 Oct 12, 2018 (152)
6 ClinVar RCV000431704.3 Oct 12, 2018 (152)
7 ClinVar RCV000443179.1 Oct 12, 2018 (152)
8 ClinVar RCV000444150.1 Oct 12, 2018 (152)
9 ClinVar RCV000505554.1 Oct 12, 2018 (152)
10 ClinVar RCV000656673.3 Jul 13, 2019 (153)
11 ClinVar RCV000656674.3 Jul 13, 2019 (153)
12 ClinVar RCV000656675.3 Jul 13, 2019 (153)
13 ClinVar RCV000656676.3 Jul 13, 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).

Associated ID History Updated (Build)
rs121913681 May 06, 2011 (133)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss2734512669 NC_000004.11:55599320:A:T NC_000004.12:54733154:A:T (self)
RCV000014864.24, RCV000431704.3, RCV000443179.1, RCV000444150.1, RCV000505554.1, RCV000656673.3, RCV000656674.3, RCV000656675.3, RCV000656676.3, ss275515391, ss275515659, ss3712025724 NC_000004.12:54733154:A:T NC_000004.12:54733154:A:T (self)
Help

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

21 citations for rs121913507
PMID Title Author Year Journal
7479840 Identification of a point mutation in the catalytic domain of the protooncogene c-kit in peripheral blood mononuclear cells of patients who have mastocytosis with an associated hematologic disorder. Nagata H et al. 1995 Proceedings of the National Academy of Sciences of the United States of America
7691885 Identification of mutations in the coding sequence of the proto-oncogene c-kit in a human mast cell leukemia cell line causing ligand-independent activation of c-kit product. Furitsu T et al. 1993 The Journal of clinical investigation
8589724 Somatic c-KIT activating mutation in urticaria pigmentosa and aggressive mastocytosis: establishment of clonality in a human mast cell neoplasm. Longley BJ et al. 1996 Nature genetics
9827716 Clinical correlates of the presence of the Asp816Val c-kit mutation in the peripheral blood mononuclear cells of patients with mastocytosis. Worobec AS et al. 1998 Cancer
9990072 Activating and dominant inactivating c-KIT catalytic domain mutations in distinct clinical forms of human mastocytosis. Longley BJ Jr et al. 1999 Proceedings of the National Academy of Sciences of the United States of America
11380399 Mutation analysis of C-KIT in patients with myelodysplastic syndromes without mastocytosis and cases of systemic mastocytosis. Fritsche-Polanz R et al. 2001 British journal of haematology
11493470 The Kit-activating mutation D816V enhances stem cell factor--dependent chemotaxis. Taylor ML et al. 2001 Blood
15972446 Activity of the tyrosine kinase inhibitor PKC412 in a patient with mast cell leukemia with the D816V KIT mutation. Gotlib J et al. 2005 Blood
16384925 Prognostic impact of c-KIT mutations in core binding factor leukemias: an Italian retrospective study. Cairoli R et al. 2006 Blood
16731599 An update on molecular genetics of gastrointestinal stromal tumours. Tornillo L et al. 2006 Journal of clinical pathology
16912224 EXEL-0862, a novel tyrosine kinase inhibitor, induces apoptosis in vitro and ex vivo in human mast cells expressing the KIT D816V mutation. Pan J et al. 2007 Blood
17259998 Juxtamembrane-type c-kit gene mutation found in aggressive systemic mastocytosis induces imatinib-resistant constitutive KIT activation. Nakagomi N et al. 2007 Laboratory investigation; a journal of technical methods and pathology
18024392 Synergistic growth-inhibitory effects of two tyrosine kinase inhibitors, dasatinib and PKC412, on neoplastic mast cells expressing the D816V-mutated oncogenic variant of KIT. Gleixner KV et al. 2007 Haematologica
18986703 Chemotherapy and dasatinib induce long-term hematologic and molecular remission in systemic mastocytosis with acute myeloid leukemia with KIT D816V. Ustun C et al. 2009 Leukemia research
19164557 KIT kinase mutants show unique mechanisms of drug resistance to imatinib and sunitinib in gastrointestinal stromal tumor patients. Gajiwala KS et al. 2009 Proceedings of the National Academy of Sciences of the United States of America
21689725 Novel, activating KIT-N822I mutation in familial cutaneous mastocytosis. Wasag B et al. 2011 Experimental hematology
22504184 Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia. Smith CC et al. 2012 Nature
23582185 Secondary c-Kit mutations confer acquired resistance to RTK inhibitors in c-Kit mutant melanoma cells. Todd JR et al. 2013 Pigment cell & melanoma research
23714533 The role of kinase inhibitors in the treatment of patients with acute myeloid leukemia. Smith CC et al. 2013 American Society of Clinical Oncology educational book. American Society of Clinical Oncology. Annual Meeting
24045550 Hidden mastocytosis in acute myeloid leukemia with t(8;21)(q22;q22). Johnson RC et al. 2013 American journal of clinical pathology
25157968 Prospective enterprise-level molecular genotyping of a cohort of cancer patients. MacConaill LE et al. 2014 The Journal of molecular diagnostics

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.post308+0fe9b3b