What can you find out about SNP: rs1136201 Useful links: https://www.pharmgkb.or
ID: 142505 • Letter: W
Question
What can you find out about SNP: rs1136201
Useful links: https://www.pharmgkb.org/ http://www.ncbi.nlm.nih.gov/genome/
6) Compare the amino acid sequence of the reference gene and the gene containing the SNP. Give the sequence of the two amino acids flanking the mutation site. Example: reference sequence: Xxx-Yyy-Zzz; SNP sequence: XxxAaa-Zzz
7) Is the gene associated with an FDA label genomic warning?
8) What does the warning require to be done?
9) Which two FDA approved therapeutic antibodies target the gene?
10)Does the rs1136201 SNP change the therapeutic response of the patient to treatment?
11)Does the rs1136201 SNP influence side effects, risks or adverse effect in patients?
12)Give the PMID of a paper to support your answer (reference)
13)Give the full citation of the journal article identified in (12)
Explanation / Answer
5) The information we get about rs1136201 is.....
rs1136201 is an A/C/T single-nucleotide variation on human chromosome 17. The protein product may be altered.
Clinical test: Clinical significance untested
NM_001005862.2(ERBB2):c.1873A>G (p.Ile625Val)
Allele ID: 28912
Variant type: single nucleotide variant
Cytogenetic location: 17q12
Genomic location: Chr17: 39723335 (on Assembly GRCh38) ,Chr17: 37879588 (on Assembly GRCh37)
Protein change: V655I, I655V, I625V, I640V HGVS:
NCBI 1000 Genomes Browser:
rs1136201
Molecular consequence:
Allele frequency:
6) Compare the amino acid:
In place of A there is Y gene
A/Y
IUPAC nucleotide code
Base
A
Adenine
C
Cytosine
G
Guanine
T (or U)
Thymine (or Uracil)
R
A or G
Y
C or T
S
G or C
W
A or T
K
G or T
M
A or C
B
C or G or T
D
A or G or T
H
A or C or T
V
A or C or G
N
any base
. or -
gap
Drug named Ado-Trastuzumab Emtansineused in oncology ( therapeutic area) named as ERBB2 (HER2) as biomarker Indications and usage, warnings and precautions, adverse Reactions, Clinical Pharmacology, Clinical Studies
7) Is the gene associated with an FDA label genomic warning?
rs1136201 [Homo sapiens]
Chromosome:
17:39723335
Gene:
ERBB2 (GeneView)
Functional Consequence:
missense,nc transcript variant
Allele Origin:
G(germline)/A(germline)
Clinical significance:
untested
Validated:
by 1000G,by cluster,by frequency
Global MAF:
G=0.1214/608
HGVS:
CM000679.2:g.39723335A>G, NC_000017.10:g.37879588A>G, NC_000017.11:g.39723335A>G, NG_007503.1:g.40196A>G, NM_001005862.2:c.1873A>G, NM_001289936.1:c.1918A>G, NM_001289937.1:c.1963A>G, NM_004448.3:c.1963A>G, NP_001005862.1:p.Ile625Val, NP_001276865.1:p.Ile640Val, NP_001276866.1:p.Ile655Val, NP_004439.2:p.Ile655Val, NR_110535.1:n.2287A>G, XP_005257196.1:p.Ile640Val, XP_005257197.1:p.Ile625Val
PubMedVarview
Select item 18012002.
rs1801200 has merged into rs1136201 [Homo sapiens]
Chromosome:
17:39723335
Gene:
ERBB2 (GeneView)
Functional Consequence:
missense,nc transcript variant
Allele Origin:
G(germline)/A(germline)
Clinical significance:
untested
Validated:
by 1000G,by cluster,by frequency
Global MAF:
G=0.1214/608
HGVS:
CM000679.2:g.39723335A>G, NC_000017.10:g.37879588A>G, NC_000017.11:g.39723335A>G, NG_007503.1:g.40196A>G, NM_001005862.2:c.1873A>G, NM_001289936.1:c.1918A>G, NM_001289937.1:c.1963A>G, NM_004448.3:c.1963A>G, NP_001005862.1:p.Ile625Val, NP_001276865.1:p.Ile640Val, NP_001276866.1:p.Ile655Val, NP_004439.2:p.Ile655Val, NR_110535.1:n.2287A>G, XP_005257196.1:p.Ile640Val, XP_005257197.1:p.Ile625Val
Varview
Select item 20064063.
rs2006406 has merged into rs1136201 [Homo sapiens]
Chromosome:
17:39723335
Gene:
ERBB2 (GeneView)
Functional Consequence:
missense,nc transcript variant
Allele Origin:
G(germline)/A(germline)
Clinical significance:
untested
Validated:
by 1000G,by cluster,by frequency
Global MAF:
G=0.1214/608
HGVS:
CM000679.2:g.39723335A>G, NC_000017.10:g.37879588A>G, NC_000017.11:g.39723335A>G, NG_007503.1:g.40196A>G, NM_001005862.2:c.1873A>G, NM_001289936.1:c.1918A>G, NM_001289937.1:c.1963A>G, NM_004448.3:c.1963A>G, NP_001005862.1:p.Ile625Val, NP_001276865.1:p.Ile640Val, NP_001276866.1:p.Ile655Val, NP_004439.2:p.Ile655Val, NR_110535.1:n.2287A>G, XP_005257196.1:p.Ile640Val, XP_005257197.1:p.Ile625Val
Varview
Select item 22306994.
rs2230699 has merged into rs1136201 [Homo sapiens]
Chromosome:
17:39723335
Gene:
ERBB2 (GeneView)
Functional Consequence:
missense,nc transcript variant
Allele Origin:
G(germline)/A(germline)
Clinical significance:
untested
Validated:
by 1000G,by cluster,by frequency
Global MAF:
G=0.1214/608
HGVS:
CM000679.2:g.39723335A>G, NC_000017.10:g.37879588A>G, NC_000017.11:g.39723335A>G, NG_007503.1:g.40196A>G, NM_001005862.2:c.1873A>G, NM_001289936.1:c.1918A>G, NM_001289937.1:c.1963A>G, NM_004448.3:c.1963A>G, NP_001005862.1:p.Ile625Val, NP_001276865.1:p.Ile640Val, NP_001276866.1:p.Ile655Val, NP_004439.2:p.Ile655Val, NR_110535.1:n.2287A>G, XP_005257196.1:p.Ile640Val, XP_005257197.1:p.Ile625Val
Varview
Select item 176068155.
rs17606815 has merged into rs1136201 [Homo sapiens]
Chromosome:
17:39723335
Gene:
ERBB2 (GeneView)
Functional Consequence:
missense,nc transcript variant
Allele Origin:
G(germline)/A(germline)
Clinical significance:
untested
Validated:
by 1000G,by cluster,by frequency
Global MAF:
G=0.1214/608
HGVS:
CM000679.2:g.39723335A>G, NC_000017.10:g.37879588A>G, NC_000017.11:g.39723335A>G, NG_007503.1:g.40196A>G, NM_001005862.2:c.1873A>G, NM_001289936.1:c.1918A>G, NM_001289937.1:c.1963A>G, NM_004448.3:c.1963A>G, NP_001005862.1:p.Ile625Val, NP_001276865.1:p.Ile640Val, NP_001276866.1:p.Ile655Val, NP_004439.2:p.Ile655Val, NR_110535.1:n.2287A>G, XP_005257196.1:p.Ile640Val, XP_005257197.1:p.Ile625Val
Varview
Select item 599559616.
rs59955961 has merged into rs1136201 [Homo sapiens]
Chromosome:
17:39723335
Gene:
ERBB2 (GeneView)
Functional Consequence:
missense,nc transcript variant
Allele Origin:
G(germline)/A(germline)
Clinical significance:
untested
Validated:
by 1000G,by cluster,by frequency
Global MAF:
G=0.1214/608
HGVS:
CM000679.2:g.39723335A>G, NC_000017.10:g.37879588A>G, NC_000017.11:g.39723335A>G, NG_007503.1:g.40196A>G, NM_001005862.2:c.1873A>G, NM_001289936.1:c.1918A>G, NM_001289937.1:c.1963A>G, NM_004448.3:c.1963A>G, NP_001005862.1:p.Ile625Val, NP_001276865.1:p.Ile640Val, NP_001276866.1:p.Ile655Val, NP_004439.2:p.Ile655Val, NR_110535.1:n.2287A>G, XP_005257196.1:p.Ile640Val, XP_005257197.1:p.Ile625Val
8) the warning require to be done is : The FDA has warnings about genetics in the drug package insert. If a medication you are concerned about is not on this list, then you can call toDNA Testing Consultants at 800-TEST-DNA (800-837-8362).
9) Rituximab and Trastuzumab are the two therapeutic monoclonal antibodies against cancer approved in the European Union or United States.
10) the rs1136201 SNP is not clinically tested .
11) clinically not tested so no.
12) PMID of a paper
IUPAC nucleotide code
Base
A
Adenine
C
Cytosine
G
Guanine
T (or U)
Thymine (or Uracil)
R
A or G
Y
C or T
S
G or C
W
A or T
K
G or T
M
A or C
B
C or G or T
D
A or G or T
H
A or C or T
V
A or C or G
N
any base
. or -
gap
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