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_025179
Gene Symbol:	PLXNA2
Description:	Homo sapiens plexin A2 (PLXNA2), mRNA.
Gene Location:	chr1(-):208195587-208417665
Browse Associations
Browse Pathways

Mutation			Mutation ID		Sample Name		Cancer Type
chr1:g.208022636G>A			COSN6439460		CHC205T		[liver][NS][carcinoma][hepatocellular_carcinoma]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-19a-5p	ccccaaaCAAAACagatat	0	AGUUUUGC	m6b	Created	no TS	0.008000	-0.960000
hsa-miR-19b-1-5p	ccccaaaCAAAACagatat	0	AGUUUUGC	m6b	Created	no TS	0.005000	-0.060000
hsa-miR-19b-2-5p	ccccaaaCAAAACagatat	0	AGUUUUGC	m6b	Created	no TS	0.005000	-0.750000
hsa-miR-26b-3p	ccccaaacAGAACAGatat	0	CCUGUUCU	m7b	Disrupted	-0.193000	no TS	0.660000
hsa-miR-4652-3p	ccccaAACAGAACagatat	3	GUUCUGUU	m8a	Disrupted	-0.136000	-0.131000	1.040000

Mutation			Mutation ID		Sample Name		Cancer Type
chr1:g.208023302A>T			COSN5364258		RK104_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-1205	tactgatCCTGCAGctgct	0	UCUGCAGG	m7b	Created	no TS	-0.080000	-0.010000
hsa-miR-1287	tactgATCCAGCAgctgct	1	UGCUGGAU	m8a	Disrupted	-0.139000	-0.057000	2.800000
hsa-miR-3135b	tactgaTCCAGCagctgct	1	GGCUGGAG	m6b	Disrupted	0.080000	0.090000	-0.080000
hsa-miR-3692-5p	tactgatCCAGCAGctgct	1	CCUGCUGG	m7b	Disrupted	-0.085000	0.008000	1.630000
hsa-miR-4722-5p	tactgaTCCTGCagctgct	3	GGCAGGAG	m6b	Created	-0.002000	-0.017000	-0.010000

Mutation			Mutation ID		Sample Name		Cancer Type
chr1:g.208024020A>T			COSN5364259		RK118_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-2467-3p	gtCCTCTGCTtggggtcag	2	AGCAGAGG	m8a	(m7b->m8a)	-0.019000	-0.005000	1.760000
hsa-miR-3678-3p	gtcCTCTGCAtggggtcag	2	CUGCAGAG	m7b	(m7b->m6c)	0.185000	0.079000	3.250000

Mutation			Mutation ID		Sample Name		Cancer Type
chr1:g.208024029G>A			COSN6020387		RK308_C01		[liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-2392	ctgcctcCCATCCTctgca	1	UAGGAUGG	m7b	Created	-0.180000	-0.081000	No effect
hsa-miR-30b-3p	ctgCCTCCCAtcctctgca	7	CUGGGAGG	m7b	(m6c->m7b)	0.049000	0.162000	No effect
hsa-miR-3605-5p	ctgcctccCATCCTCtgca	0	UGAGGAUG	m7b	Created	-0.247000	-0.161000	No effect
hsa-miR-3689a-3p	ctgCCTCCCAtcctctgca	7	CUGGGAGG	m7b	(m6c->m7b)	0.058000	0.152000	No effect
hsa-miR-3689b-3p	ctgCCTCCCAtcctctgca	7	CUGGGAGG	m7b	(m6c->m7b)	0.058000	0.152000	No effect
hsa-miR-3689c	ctgCCTCCCAtcctctgca	7	CUGGGAGG	m7b	(m6c->m7b)	0.058000	0.152000	No effect

Mutation			Mutation ID		Sample Name		Cancer Type
chr1:g.208024219T>G			COSN9057697		C0096T		[kidney][NS][other][neoplasm]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-135a-5p	aagAAGCCATtcatcttgg	8	UAUGGCUU	m7b	(m7b->m6c)	-0.014000	-0.090000	-0.040000
hsa-miR-135b-5p	aagAAGCCATtcatcttgg	8	UAUGGCUU	m7b	(m7b->m6c)	-0.014000	-0.090000	-0.080000
hsa-miR-892b	aagaAGCCAGTcatcttgg	5	CACUGGCU	m7b	Created	-0.311000	-0.334000	-0.060000

Mutation			Mutation ID		Sample Name		Cancer Type
chr1:g.208024603T>G			COSN14668155		8068595		[pancreas][NS][carcinoid-endocrine_tumour][NS]
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.208024637G>A			COSN6523922		ICGC_MB3		[central_nervous_system][brain][primitive_neuroectodermal_tumour-medulloblastoma][NS]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-136-5p	gtggagagcATGGAGaatg	1	ACUCCAUU	m6b	Created	0.192000	0.261000	-0.010000
hsa-miR-5581-3p	gtggagaGCATGGAgaatg	1	UUCCAUGC	m7b	Created	-0.333000	-0.339000	-0.470000

Mutation			Mutation ID		Sample Name		Cancer Type
chr1:g.208024816G>A			COSN6439461		CHC205T		[liver][NS][carcinoma][hepatocellular_carcinoma]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-4435	tttCTGGCCAcatggctgc	3	AUGGCCAG	m7b	(m6c->m7b)	0.020000	-0.046000	-0.190000
hsa-miR-663b	tttctGGCCACatggctgc	2	GGUGGCCC	m6b	Created	-0.155000	-0.187000	No effect

Mutation			Mutation ID		Sample Name		Cancer Type
chr1:g.208026656A>G			COSN15591634		C0040T		[kidney][NS][other][neoplasm]
miRNA Targets Table
miR ID	miRSite	Conservation	miRSeed	SeedClass	FuncClass	Wildtype CS+	Mutant CS+	PITA score change
hsa-miR-130b-5p	aaaaaaaaaGAAAGAGaaa	0	ACUCUUUC	m7b	(m6b->m7b)	-0.017000	-0.189000	-0.060000

**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
208022636	rs556625	G	G	hsa-miR-26b-3p hsa-miR-4652-3p	2 3	caaacAGAACAGA caAACAGAAcaga	Disrupted Disrupted	N N	-0.193 -0.005
208022636	rs556625	G	A	hsa-miR-19a-5p hsa-miR-19b-1-5p hsa-miR-19b-2-5p hsa-miR-2052	2 2 2 2	caaaCAAAACAga caaaCAAAACAga caaaCAAAACAga caaaCAAAACAga	Created Created Created Created	N N N N	0.008 0.005 0.005 0.002
208023783	rs11579035	C	C	hsa-miR-1973	1	acaGCACGGAaca	Disrupted	N	-0.111
208023783	rs11579035	C	T	hsa-miR-5581-3p hsa-miR-6872-3p	1 1	acaGCATGGAAca acaGCATGGAaca	Created Created	N N	-0.031 -0.005
208024045	rs181246669	C	C	hsa-miR-1909-3p hsa-miR-214-3p hsa-miR-3619-5p hsa-miR-4640-5p hsa-miR-4726-5p hsa-miR-6510-5p hsa-miR-6722-3p hsa-miR-6762-5p hsa-miR-6845-5p hsa-miR-761	1 4 4 2 2 1 1 1 1 4	ctggCCCCTGCtg ctggccCCTGCTG ctggccCCTGCTG CTGGCCCctgctg CTGGCCCctgctg ctggcCCCTGCTg ctggCCCCTGCtg cTGGCCCCtgctg cTGGCCCCtgctg ctggccCCTGCTG	Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted Disrupted	N N N N N N N N N N	0.047 0.124 0.077 0.028 0.009 0.081 0.028 -0.006 -0.006 0.114
208024045	rs181246669	C	T	hsa-miR-2467-3p hsa-miR-922	1 4	ctggCCTCTGCtg ctggccTCTGCTG	Created Created	N N	0.065 0.138
208024816	rs11118973	G	G	hsa-miR-1199-3p	3	ctGGCCGCAtggc	Disrupted	N	-0.141
208024816	rs11118973	G	A	hsa-miR-4435 hsa-miR-663b hsa-miR-7108-5p	3 3 3	CTGGCCAcatggc ctGGCCACAtggc ctGGCCACAtggc	Created Created Created	N N N	-0.066 -0.032 -0.036
208026566	rs73078875	G
208026566	rs73078875	G	A	hsa-miR-3692-5p hsa-miR-4731-5p hsa-miR-5589-5p hsa-miR-619-5p hsa-miR-6506-5p hsa-miR-6762-3p	2 1 1 1 1 5	tatcCCAGCAGcc tatCCCAGCAgcc tatCCCAGCAgcc tATCCCAGcagcc tATCCCAGcagcc tatcccAGCAGCC	Created Created Created Created Created Created	N N N N N N	-0.081 -0.096 -0.106 -0.113 -0.085 -0.132
208026648	rs148574660	-	-	hsa-miR-130b-5p hsa-miR-4753-3p hsa-miR-6809-3p hsa-miR-6881-3p hsa-miR-877-3p	0	aaagaGAAAGAGgag AAAGAGAAagaggag aAAGAGAAAgaggag aaagagaAAGAGGAg aaagagaAAGAGGAg	Unknown Unknown Unknown Unknown Unknown	N N N N N	-0.021 -0.051 -0.107 -0.008 -0.001
208026648	rs148574660	-	GA	hsa-miR-4768-5p hsa-miR-6817-3p hsa-miR-6833-3p hsa-miR-6873-3p hsa-miR-7110-3p	0	aaaGAGAGAAAgaggag aaAGAGAGAaagaggag aaaGAGAGAAAgaggag aaAGAGAGAAagaggag aaAGAGAGAaagaggag	Unknown Unknown Unknown Unknown Unknown	N N N N N	-0.153 -0.079 -0.181 -0.281 -0.101
208026651	rs112454240	-	-	hsa-miR-130b-5p hsa-miR-4753-3p hsa-miR-4768-5p hsa-miR-6809-3p hsa-miR-6833-3p	0	aaAAAGAGAaaga aaAAAGAGAAaga aaaaAGAGAAAga aaaAAGAGAAAga aaaaAGAGAAAga	Unknown Unknown Unknown Unknown Unknown	N N N N N	-0.023 -0.15 -0.013 -0.133 -0.027
208026651	rs112454240	-	A	hsa-miR-4659a-3p hsa-miR-4659b-3p hsa-miR-4778-3p hsa-miR-6875-3p	0	aaaaAGAAGAAAga aaaaAGAAGAAAga aaaAAGAAGAaaga aaaaaGAAGAAAga	Unknown Unknown Unknown Unknown	N N N N	-0.101 -0.11 -0.035 0.002
208026652	rs200958221	G	G	hsa-miR-130b-5p hsa-miR-4753-3p hsa-miR-4768-5p hsa-miR-6809-3p hsa-miR-6833-3p	0	aaaAAAGAGAaag aaaAAAGAGAAag aaaaaAGAGAAAg aaaaAAGAGAAAg aaaaaAGAGAAAg	Disrupted Disrupted Disrupted Disrupted Disrupted	N N N N N	-0.005 -0.15 -0.013 -0.133 -0.027
208026652	rs200958221	G
208026653	rs58631044	-	-	hsa-miR-130b-5p hsa-miR-4753-3p hsa-miR-4768-5p hsa-miR-6809-3p hsa-miR-6833-3p	8 8 8 8 8	aaaaAAAGAGAaa aaaaAAAGAGAAa aaaaaaAGAGAAA aaaaaAAGAGAAA aaaaaaAGAGAAA	Unknown Unknown Unknown Unknown Unknown	N N N N N	No Change 0.001 0.001 0.002 0.001
208026653	rs58631044	-	A
208026855	rs200556809	-	-	hsa-miR-4652-3p hsa-miR-4743-3p	21 21	aaaaaAACAGAAAta aaaaaaACAGAAAta	Unknown Unknown	N N	0.005 -0.001
208026855	rs200556809	-	AA
208026856	rs59073273	-	-	hsa-miR-4652-3p hsa-miR-4743-3p	21 21	gaaaaaAACAGAAAt gaaaaaaACAGAAAt	Unknown Unknown	N N	0.005 -0.001
208026856	rs59073273	-	AA

**Genome Browser**
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Somatic mutations that impact miRNA target sites

Germline mutations in target sites of miRNAs in somatic mutation table

Genome Browser