SomamiR DB

SomamiR DB 2.0 Somatic mutations altering microRNA-ceRNA interactions
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Prediction criteria:	TargetScan sites only All 6mer or longer seed matches

PolymiRTS Database

RefSeq ID:	NM_005957
Gene Symbol:	MTHFR
Description:	Homo sapiens methylenetetrahydrofolate reductase (NAD(P)H) (MTHFR), mRNA.
Gene Location:	chr1(-):11845786-11866160
Browse Associations
Browse Pathways

Mutation			Mutation ID		Sample Name		Cancer Type
chr1:g.11786311C>G			COSN4708268		PD4086a		[breast][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-186-3p	tgccagtatCTTTGGGgct	2	GCCCAAAG	m7b	(m7b->m6b)	-0.089000	-0.043000	No effect

Mutation			Mutation ID		Sample Name		Cancer Type
chr1:g.11787276A>T			COSN7173830		8050308		[pancreas][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-149-3p	gcctcttCCTCCCattccc	0	AGGGAGGG	m6b	Created	0.096000	0.112000	-0.010000
hsa-miR-30b-3p	gcctcttCCTCCCAttccc	0	CUGGGAGG	m7b	Created	no TS	0.006000	No effect
hsa-miR-3190-3p	gcctCTTCCACccattccc	2	UGUGGAAG	m7b	Disrupted	0.015000	-0.050000	No effect
hsa-miR-363-5p	gcctctTCCACCCattccc	0	CGGGUGGA	m7b	Disrupted	-0.011000	0.051000	No effect
hsa-miR-3689a-3p	gcctcttCCTCCCAttccc	0	CUGGGAGG	m7b	Created	no TS	0.006000	-0.080000
hsa-miR-3689b-3p	gcctcttCCTCCCAttccc	0	CUGGGAGG	m7b	Created	no TS	0.006000	-0.010000
hsa-miR-3689c	gcctcttCCTCCCAttccc	0	CUGGGAGG	m7b	Created	no TS	0.006000	-0.010000
hsa-miR-4483	gcctcttCCACCCattccc	0	GGGGUGGU	m6b	Disrupted	0.027000	0.034000	0.120000
hsa-miR-4506	gcctcttccACCCATTccc	2	AAAUGGGU	m7b	(m7b->m6b)	0.088000	no TS	3.860000
hsa-miR-766-5p	gcctcTTCCTCCcattccc	2	AGGAGGAA	m7b	Created	0.038000	0.133000	No effect

Mutation			Mutation ID		Sample Name		Cancer Type
chr1:g.11787277C>T			COSN7173831		8050308		[pancreas][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-197-5p	ggcctctTCTACCCattcc	0	CGGGUAGA	m7b	Created	no TS	-0.056000	No effect
hsa-miR-3132	ggcctctTCTACCCAttcc	0	UGGGUAGA	m8a	Created	no TS	-0.056000	No effect
hsa-miR-3190-3p	ggcctCTTCCACccattcc	2	UGUGGAAG	m7b	Disrupted	0.015000	-0.050000	No effect
hsa-miR-363-5p	ggcctctTCCACCCattcc	0	CGGGUGGA	m7b	Disrupted	-0.011000	0.051000	No effect
hsa-miR-4483	ggcctcttCCACCCattcc	0	GGGGUGGU	m6b	Disrupted	0.027000	0.034000	0.120000
hsa-miR-4650-3p	ggcctcTTCTACCcattcc	0	AGGUAGAA	m7b	Created	no TS	0.054000	-2.850000
hsa-miR-5197-3p	ggcCTCTTCTacccattcc	0	AAGAAGAG	m7b	(m6c->m7b)	no TS	0.233000	-0.010000

Mutation			Mutation ID		Sample Name		Cancer Type
chr1:g.11788082C>T			COSN6504575		CHC205T		[liver][NS][carcinoma][hepatocellular_carcinoma]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change

Mutation			Mutation ID		Sample Name		Cancer Type
chr1:g.11788766G>T			COSN1087814		HCC30T		[liver][NS][carcinoma][hepatocellular_carcinoma]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-18a-3p	aagAGGGCAGTacctggga	4	ACUGCCCU	m8a	Disrupted	0.069000	0.052000	No effect
hsa-miR-324-3p	aagaGGGCAGTacctggga	1	ACUGCCCC	m7a	Disrupted	-0.234000	-0.234000	No effect
hsa-miR-365a-3p	aagaGGGCATTAcctggga	2	UAAUGCCC	m8a	Created	-0.072000	-0.055000	No effect
hsa-miR-365b-3p	aagaGGGCATTAcctggga	2	UAAUGCCC	m8a	Created	-0.072000	-0.055000	No effect
hsa-miR-18a-3p	aagAGGGCAGTacctggga	4	ACUGCCCU	m8a	Disrupted	0.069000	0.052000	No effect
hsa-miR-324-3p	aagaGGGCAGTacctggga	1	ACUGCCCC	m7a	Disrupted	-0.234000	-0.234000	No effect
hsa-miR-365a-3p	aagaGGGCATTAcctggga	2	UAAUGCCC	m8a	Created	-0.072000	-0.055000	No effect
hsa-miR-365b-3p	aagaGGGCATTAcctggga	2	UAAUGCCC	m8a	Created	-0.072000	-0.055000	No effect
hsa-miR-18a-3p	aagAGGGCAGTacctggga	0	ACUGCCCU	m8a	Disrupted	0.069	0.052	No effect
hsa-miR-324-3p	aagaGGGCAGTacctggga	0	ACUGCCCC	m7a	Disrupted	-0.234	-0.234	No effect
hsa-miR-365a-3p	aagaGGGCATTAcctggga	0	UAAUGCCC	m8a	Created	-0.072	-0.055	No effect
hsa-miR-365b-3p	aagaGGGCATTAcctggga	0	UAAUGCCC	m8a	Created	-0.072	-0.055	No effect

Mutation			Mutation ID		Sample Name		Cancer Type
chr1:g.11789450C>G			COSN7173834		8069443		[pancreas][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-2117	ctatGAGAACAagtcacag	1	UGUUCUCU	m7a	Disrupted	-0.043000	-0.046000	0.010000
hsa-miR-4273	ctatGAGAACAagtcacag	1	GUGUUCUC	m7b	Disrupted	-0.221000	-0.188000	0.580000
hsa-miR-4659a-3p	ctatgAGAAGAAgtcacag	0	UUUCUUCU	m7b	Created	no TS	0.099000	-0.040000
hsa-miR-4659b-3p	ctatgAGAAGAAgtcacag	0	UUUCUUCU	m7b	Created	no TS	0.099000	-0.010000
hsa-miR-4778-3p	ctatgaGAAGAAGtcacag	0	UCUUCUUC	m7b	Created	no TS	0.015000	-3.700000
hsa-miR-617	ctatgagaaGAAGTCacag	2	AGACUUCC	m6b	Created	-0.127000	-0.112000	No effect
hsa-miR-942	ctatGAGAAGAagtcacag	3	UCUUCUCU	m7a	Created	0.186000	0.228000	-0.050000

**Germline mutations in target sites of miRNAs in somatic mutation table**
Location	SNP ID	Ancestral Allele	Allele	miR ID	Conservation	miRSite	FuncClass	Validation	context+ score change
11786141	rs15854	T	T	hsa-miR-186-3p hsa-miR-3910 hsa-miR-548an	2 1 1	gatgcCTTTGGGt gATGCCTTtgggt gaTGCCTTTgggt	Disrupted Disrupted Disrupted	N N N	-0.081 -0.044 -0.076
11786141	rs15854	T	C	hsa-miR-4761-3p hsa-miR-6814-5p	1 2	gATGCCCTtgggt gatgcCCTTGGGt	Created Created	N N	-0.108 -0.136
11787277	rs190086595	C	C	hsa-miR-1293 hsa-miR-3190-3p hsa-miR-363-5p hsa-miR-4483 hsa-miR-6077 hsa-miR-6745 hsa-miR-6756-5p hsa-miR-6766-5p hsa-miR-7-5p	20 2 4 20 1 4 20 20 2	ctcttCCACCCAt ctCTTCCACccat ctctTCCACCCAt ctcttCCACCCAt CTCTTCCAcccat ctctTCCACCCAt ctcttCCACCCAt ctcttCCACCCAt cTCTTCCAcccat	Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted	N N N N N N N N N	-0.02 0.065 -0.062 -0.007 0.161 -0.062 -0.004 0.006 0.101
11787277	rs190086595	C	T	hsa-miR-1229-5p hsa-miR-197-5p hsa-miR-3132 hsa-miR-4650-3p hsa-miR-5197-3p	20 4 4 2 1	ctcttCTACCCAt ctctTCTACCCAt ctctTCTACCCAt ctcTTCTACCcat CTCTTCTAcccat	Created Created Created Created Created	N N N N N	-0.031 -0.056 -0.056 0.054 0.233
11787277	rs35134728	-	-	hsa-miR-1293 hsa-miR-3190-3p hsa-miR-363-5p hsa-miR-4483 hsa-miR-6077 hsa-miR-6745 hsa-miR-6756-5p hsa-miR-6766-5p hsa-miR-7-5p	20 2 4 20 1 4 20 20 2	gcctcttCCACCCAttc gcctCTTCCACccattc gcctctTCCACCCAttc gcctcttCCACCCAttc gcCTCTTCCAcccattc gcctctTCCACCCAttc gcctcttCCACCCAttc gcctcttCCACCCAttc gccTCTTCCAcccattc	Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown	N N N N N N N N N	0.013 0.033 0.007 0.005 0.052 0.028 0.013 0.012 -0.001
11787277	rs35134728	-	TTC	hsa-miR-3185 hsa-miR-5197-3p	2 1	gcctCTTCTTCcacccattc gcCTCTTCTtccacccattc	Unknown Unknown	N N	0.13 0.187
11787278	rs183631107	C	C	hsa-miR-1293 hsa-miR-3190-3p hsa-miR-363-5p hsa-miR-4483 hsa-miR-6077 hsa-miR-6745 hsa-miR-6756-5p hsa-miR-6766-5p hsa-miR-7-5p	20 2 4 20 1 4 20 20 2	cctcttCCACCCA cctCTTCCACcca cctctTCCACCCA cctcttCCACCCA cCTCTTCCAccca cctctTCCACCCA cctcttCCACCCA cctcttCCACCCA ccTCTTCCAccca	Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted	N N N N N N N N N	-0.02 0.065 -0.062 -0.007 0.161 -0.062 -0.004 0.006 0.101
11787278	rs183631107	C	G	hsa-miR-4696 hsa-miR-6741-5p	2 20	ccTCTTGCAccca cctcttGCACCCA	Created Created	N N	0.091 -0.069
11787278	rs34762557	-	-	hsa-miR-1293 hsa-miR-3190-3p hsa-miR-363-5p hsa-miR-4483 hsa-miR-6077 hsa-miR-6745 hsa-miR-6756-5p hsa-miR-6766-5p hsa-miR-7-5p	20 2 4 20 1 4 22 22 2	ggcctcttCCACCCAtt ggcctCTTCCACccatt ggcctctTCCACCCAtt ggcctcttCCACCCAtt ggcCTCTTCCAcccatt ggcctctTCCACCCAtt ggcctcttCCACCCAtt ggcctcttCCACCCAtt ggccTCTTCCAcccatt	Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown Unknown	N N N N N N N N N	0.025 0.065 -0.03 0.017 0.161 -0.027 0.158 0.137 0.101
11787278	rs34762557	-	TTC	hsa-miR-3153 hsa-miR-4668-5p hsa-miR-583 hsa-miR-6124 hsa-miR-6733-5p hsa-miR-6739-5p	4 2 0 2 4 4	ggcctctTTTCCCAcccatt ggcctcTTTTCCCAcccatt ggCCTCTTTtcccacccatt ggcctCTTTTCCcacccatt ggcctctTTTCCCAcccatt ggcctctTTTCCCAcccatt	Unknown Unknown Unknown Unknown Unknown Unknown	N N N N N N	0.117 0.212 0.194 0.143 0.131 0.127
11787281	rs72505075	-	-	hsa-miR-3190-3p hsa-miR-6077 hsa-miR-6089 hsa-miR-7-5p	2 1 0 2	cccggcctCTTCCACcc cccggcCTCTTCCAccc ccCGGCCTCttccaccc cccggccTCTTCCAccc	Unknown Unknown Unknown Unknown	N N N N	0.024 0.087 -0.009 0.017
11787281	rs72505075	-	TCT	hsa-miR-4493 hsa-miR-6770-5p	0	cccGGCCTTCtcttccaccc cccggCCTTCTCttccaccc	Unknown Unknown	N N	0.036 0.127
11787282	rs70983598	-	-	hsa-miR-6077 hsa-miR-6089 hsa-miR-7-5p	1 0 6	tcccggcCTCTTCCAcc tccCGGCCTCttccacc tcccggccTCTTCCAcc	Unknown Unknown Unknown	N N N	0.052 0.014 -0.001
11787282	rs70983598	-	TCT	hsa-miR-5197-3p	1	tcccggcCTCTTCTtccacc	Unknown	N	0.187
11787460	rs150449128	G	G	hsa-miR-184 hsa-miR-4804-5p hsa-miR-8071	2 2 5	tccTCCGTCCAcc tcctCCGTCCAcc tcctccGTCCACC	Disrupted Disrupted Disrupted	N N N	-0.078 -0.034 0.047
11787460	rs150449128	G	A	hsa-miR-1193 hsa-miR-3165 hsa-miR-3691-5p hsa-miR-432-3p hsa-miR-4534 hsa-miR-4802-5p hsa-miR-6894-5p hsa-miR-7154-3p hsa-miR-765 hsa-miR-766-5p hsa-miR-8082	2 5 2 2 1 1 1 1 1 1 1	tcctCCATCCAcc tcctccATCCACC tcctcCATCCACc tcctCCATCCAcc tcCTCCATCcacc tCCTCCATccacc TCCTCCAtccacc TCCTCCAtccacc TCCTCCAtccacc TCCTCCAtccacc tcCTCCATCcacc	Created Created Created Created Created Created Created Created Created Created Created	N N N N N N N N N N N	0.06 0.118 0.102 0.051 0.113 0.055 0.041 0.037 0.043 -0.01 0.104
11787702	rs3737966	G	G	hsa-miR-1228-5p hsa-miR-6820-5p	1 1	cctgCCGCCCAAa cCTGCCGCccaaa	Disrupted Disrupted	N N	-0.189 -0.036
11787702	rs3737966	G	A	hsa-miR-1207-5p hsa-miR-1262 hsa-miR-1293 hsa-miR-363-5p hsa-miR-4483 hsa-miR-4701-3p hsa-miR-4736 hsa-miR-4763-3p hsa-miR-6736-5p hsa-miR-6741-5p hsa-miR-6745 hsa-miR-6756-5p hsa-miR-6766-5p hsa-miR-7150	0	CCTGCCAcccaaa cctgcCACCCAAa cctgCCACCCAaa cctgCCACCCAaa cctgCCACCCAaa cctgcCACCCAAa CCTGCCAcccaaa CCTGCCAcccaaa cctgcCACCCAAa cctgcCACCCAAa cctgCCACCCAaa cctgCCACCCAaa cctgCCACCCAaa CCTGCCAcccaaa	Created Created Created Created Created Created Created Created Created Created Created Created Created Created	N N N N N N N N N N N N N N	0.023 0.027 -0.015 -0.006 -0.001 0.03 0.013 0.04 0.024 0.013 -0.009 0.008 0.005 0.032
11787952	rs35066719	-	-	hsa-miR-1913 hsa-miR-210-5p hsa-miR-324-3p hsa-miR-4749-3p hsa-miR-4763-5p	1 1 1 1 3	caGGGGCAGgcct CAGGGGCAggcct caGGGGCAGgcct cAGGGGCAggcct caggGGCAGGCct	Unknown Unknown Unknown Unknown Unknown	N N N N N	-0.026 -0.051 -0.035 0.005 0.011
11787952	rs35066719	-	G	hsa-miR-4313	1	cAGGGGGCAggcct	Unknown	N	-0.037
11789313	rs45445997	C	C	hsa-miR-4428 hsa-miR-6814-5p	2 2	ccTCTCCTTgggc cctctCCTTGGGc	Disrupted Disrupted	N N	0.165 -0.01
11789313	rs45445997	C	T	hsa-miR-186-3p hsa-miR-4311 hsa-miR-6758-5p hsa-miR-6856-5p	2 2 4 4	cctctCTTTGGGc ccTCTCTTTgggc CCTCTCTttgggc CCTCTCTttgggc	Created Created Created Created	N N N N	0.11 0.22 0.056 0.038
11790026	rs45451599	A	A	hsa-miR-4297 hsa-miR-5581-5p hsa-miR-676-5p	1 1 2	ggttGAAGGCAgt ggttGAAGGCAgt gGTTGAAGgcagt	Disrupted Disrupted Disrupted	N N N	-0.066 -0.069 0.017
11790026	rs45451599	A	G	hsa-miR-18a-3p hsa-miR-4290	3 1	ggttgAGGGCAGt ggttGAGGGCAgt	Created Created	N N	-0.109 -0.124
11790418	rs141798303	G	G	hsa-miR-3909 hsa-miR-6780a-3p hsa-miR-6852-3p	6 4 6	gcAGAGGACcaca gCAGAGGAccaca gcAGAGGACcaca	Disrupted Disrupted Disrupted	N N N	-0.093 -0.041 -0.093
11790418	rs141798303	G	A	hsa-miR-1273g-5p hsa-miR-152-5p hsa-miR-182-3p hsa-miR-2117 hsa-miR-3191-5p hsa-miR-597-3p hsa-miR-6728-3p	8 6 6 6 4 6 4	gcagagAACCACA gcagAGAACCAca gcagAGAACCAca gcAGAGAACcaca gCAGAGAAccaca gcaGAGAACCAca GCAGAGAaccaca	Created Created Created Created Created Created Created	N N N N N N N	-0.088 -0.064 -0.07 -0.055 -0.033 -0.27 -0.07

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Somatic mutations that impact miRNA target sites

Germline mutations in target sites of miRNAs in somatic mutation table

Genome Browser