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