SomamiR DB 2.0
Somatic mutations altering microRNA-ceRNA interactions
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PolymiRTS Database
Prediction criteria: TargetScan sites only     All 6mer or longer seed matches
RefSeq ID: NM_148918
Gene Symbol: SHMT1
Description: Homo sapiens serine hydroxymethyltransferase 1 (soluble) (SHMT1), nuclear gene encoding mitochondrial protein, transcript variant 1, mRNA.
Gene Location: chr17(-):18231186-18266856
Browse Associations
Browse Pathways

Somatic mutations that impact miRNA target sites


Mutation Mutation ID Sample Name Cancer Type
chr17:g.18327999A>G COSN1714817 RK086_C01 [liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-miR-224-3p tagatgACCATTTTtaata
 11
 AAAAUGGU m8a Disrupted -0.158000 no TS 0.090000
hsa-miR-522-3p tagatgACCATTTTtaata
 11
 AAAAUGGU m8a Disrupted -0.148000 no TS -0.070000
hsa-miR-548ac tagatgaccGTTTTTaata
 0 CAAAAACC m6b Created no TS 0.021000 2.010000
hsa-miR-548ae tagatgaccGTTTTTaata
 0 CAAAAACU m6b Created no TS 0.024000 -0.770000
hsa-miR-548ah-3p tagatgaccGTTTTTaata
 0 CAAAAACU m6b Created no TS 0.024000 -4.210000
hsa-miR-548aj-3p tagatgaccGTTTTTAata
 0 UAAAAACU m7a (m6a->m7a) no TS 0.024000 -0.770000
hsa-miR-548am-3p tagatgaccGTTTTTaata
 0 CAAAAACU m6b Created no TS 0.024000 -3.380000
hsa-miR-548aq-3p tagatgaccGTTTTTaata
 0 CAAAAACU m6b Created no TS 0.024000 -3.630000
hsa-miR-548c-3p tagatgaccATTTTTaata
 6
 CAAAAAUC m6b Disrupted 0.217000 0.136000 1.570000
hsa-miR-548d-3p tagatgaccGTTTTTaata
 0 CAAAAACC m6b Created no TS 0.018000 -0.680000
hsa-miR-548h-3p tagatgaccGTTTTTaata
 0 CAAAAACC m6b Created no TS 0.021000 -2.980000
hsa-miR-548x-3p tagatgaccGTTTTTAata
 0 UAAAAACU m7a (m6a->m7a) no TS 0.024000 -0.770000
hsa-miR-548z tagatgaccGTTTTTaata
 0 CAAAAACC m6b Created no TS 0.021000 -2.980000
hsa-miR-553 tagatgACCGTTTTtaata
 0 AAAACGGU m8a Created no TS -0.300000 -5.270000
hsa-miR-224-3p tagatgACCATTTTtaata
 11
 AAAAUGGU m8a Disrupted -0.158000 no TS 0.090000
hsa-miR-522-3p tagatgACCATTTTtaata
 11
 AAAAUGGU m8a Disrupted -0.148000 no TS -0.070000
hsa-miR-548ac tagatgaccGTTTTTaata
 0 CAAAAACC m6b Created no TS 0.021000 2.010000
hsa-miR-548ae tagatgaccGTTTTTaata
 0 CAAAAACU m6b Created no TS 0.024000 -0.770000
hsa-miR-548ah-3p tagatgaccGTTTTTaata
 0 CAAAAACU m6b Created no TS 0.024000 -4.210000
hsa-miR-548aj-3p tagatgaccGTTTTTAata
 0 UAAAAACU m7a (m6a->m7a) no TS 0.024000 -0.770000
hsa-miR-548am-3p tagatgaccGTTTTTaata
 0 CAAAAACU m6b Created no TS 0.024000 -3.380000
hsa-miR-548aq-3p tagatgaccGTTTTTaata
 0 CAAAAACU m6b Created no TS 0.024000 -3.630000
hsa-miR-548c-3p tagatgaccATTTTTaata
 6
 CAAAAAUC m6b Disrupted 0.217000 0.136000 1.570000
hsa-miR-548d-3p tagatgaccGTTTTTaata
 0 CAAAAACC m6b Created no TS 0.018000 -0.680000
hsa-miR-548h-3p tagatgaccGTTTTTaata
 0 CAAAAACC m6b Created no TS 0.021000 -2.980000
hsa-miR-548x-3p tagatgaccGTTTTTAata
 0 UAAAAACU m7a (m6a->m7a) no TS 0.024000 -0.770000
hsa-miR-548z tagatgaccGTTTTTaata
 0 CAAAAACC m6b Created no TS 0.021000 -2.980000
hsa-miR-553 tagatgACCGTTTTtaata
 0 AAAACGGU m8a Created no TS -0.300000 -5.270000
hsa-miR-224-3p tagatgACCATTTTtaata
 0 AAAAUGGU m8a Disrupted -0.158 no TS 0.09
hsa-miR-522-3p tagatgACCATTTTtaata
 0 AAAAUGGU m8a Disrupted -0.148 no TS -0.07
hsa-miR-548ac tagatgaccGTTTTTaata
 0 CAAAAACC m6b Created no TS 0.021 2.01
hsa-miR-548ae tagatgaccGTTTTTaata
 0 CAAAAACU m6b Created no TS 0.024 -0.77
hsa-miR-548ah-3p tagatgaccGTTTTTaata
 0 CAAAAACU m6b Created no TS 0.024 -4.21
hsa-miR-548aj-3p tagatgaccGTTTTTAata
 0 UAAAAACU m7a (m6a->m7a) no TS 0.024 -0.77
hsa-miR-548am-3p tagatgaccGTTTTTaata
 0 CAAAAACU m6b Created no TS 0.024 -3.38
hsa-miR-548aq-3p tagatgaccGTTTTTaata
 0 CAAAAACU m6b Created no TS 0.024 -3.63
hsa-miR-548c-3p tagatgaccATTTTTaata
 0 CAAAAAUC m6b Disrupted 0.217 0.136 1.57
hsa-miR-548d-3p tagatgaccGTTTTTaata
 0 CAAAAACC m6b Created no TS 0.018 -0.68
hsa-miR-548h-3p tagatgaccGTTTTTaata
 0 CAAAAACC m6b Created no TS 0.021 -2.98
hsa-miR-548x-3p tagatgaccGTTTTTAata
 0 UAAAAACU m7a (m6a->m7a) no TS 0.024 -0.77
hsa-miR-548z tagatgaccGTTTTTaata
 0 CAAAAACC m6b Created no TS 0.021 -2.98
hsa-miR-553 tagatgACCGTTTTtaata
 0 AAAACGGU m8a Created no TS -0.3 -5.27

Mutation Mutation ID Sample Name Cancer Type
chr17:g.18328483A>G COSN6654275 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-200a-5p ggaaaaTAAGATactatgt
 0 CAUCUUAC m6b Created no TS -0.043000 -3.090000
hsa-miR-200b-5p ggaaaaTAAGATactatgt
 0 CAUCUUAC m6b Created no TS -0.043000 No effect

Mutation Mutation ID Sample Name Cancer Type
chr17:g.18328557T>A COSN1193786 HCC20T [liver][NS][carcinoma][hepatocellular_carcinoma]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-miR-16-1-3p gttagtAATACTGGgacag
 0 CCAGUAUU m8a Created no TS -0.114000 -4.651000
hsa-miR-16-1-3p gttagtAATACTGGgacag
 0 CCAGUAUU m8a Created no TS -0.114 -4.651

Mutation Mutation ID Sample Name Cancer Type
chr17:g.18328641C>G COSN8602471 J32_T [lung][NS][carcinoma][squamous_cell_carcinoma]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-miR-199a-5p gttgACACTGGGgcccttt
 0 CCCAGUGU m8a Created no TS -0.120000 -3.060000
hsa-miR-199b-5p gttgACACTGGGgcccttt
 0 CCCAGUGU m8a Created no TS -0.120000 -2.090000
hsa-miR-296-5p gttgacactGGGGCCCTtt
 1
 AGGGCCCC m8a (m7a->m8a) 0.000000 -0.762000 0.200000

Mutation Mutation ID Sample Name Cancer Type
chr17:g.18328684C>T COSN6654276 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-125a-3p gaccccCACCTGagagatg
 0 ACAGGUGA m6b Disrupted -0.208000 -0.115000 No effect
hsa-miR-1266 gacccccaCCTGAGagatg
 0 CCUCAGGG m6b Disrupted -0.188000 -0.108000 No effect
hsa-miR-4447 gaCCCCCACCtgagagatg
 0 GGUGGGGG m8a (m8a->m7b) -0.198000 -0.225000 No effect
hsa-miR-4465 gacccccACTTGAGagatg
 0 CUCAAGUA m7a Created NA NA -1.350000
hsa-miR-4472 gaCCCCCACCtgagagatg
 0 GGUGGGGG m8a (m8a->m7b) -0.179000 -0.206000 No effect
hsa-miR-4518 gacccccaCCTGAGagatg
 0 GCUCAGGG m6b Disrupted -0.178000 -0.098000 0.010000
hsa-miR-513c-5p gacccccaCTTGAGAgatg
 0 UUCUCAAG m7b Created no TS -0.108000 -5.170000
hsa-miR-514b-5p gacccccaCTTGAGAgatg
 0 UUCUCAAG m7b Created no TS -0.089000 -3.700000
hsa-miR-764 gaccccCACCTGagagatg
 0 GCAGGUGC m6b Disrupted -0.213000 -0.111000 1.020000
hsa-miR-92a-2-5p gacCCCCACCtgagagatg
 0 GGGUGGGG m7b (m7b->m6c) -0.184000 no TS No effect

Mutation Mutation ID Sample Name Cancer Type
chr17:g.18328703C>G COSN6654277 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-4514 aggaagCTGCCTGccggag
 1
 ACAGGCAG m7b Disrupted -0.084000 no TS 4.850000
hsa-miR-4692 aggaagCTGCCTGccggag
 1
 UCAGGCAG m7b Disrupted -0.093000 no TS 16.400000

*By default, only target sites identified by TargetScan are displayed. To display all potentially impacted target sites, select "All 6mer or longer seed matches" above.



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
18328100 rs113640881 C C hsa-miR-125a-3p
hsa-miR-3934-5p
hsa-miR-6081
hsa-miR-6880-5p
hsa-miR-764
2
2
2
2
2
 ctgctcCACCTGA
ctgctcCACCTGA
CTGCTCCAcctga
ctgCTCCACCtga
ctgctcCACCTGA
 Disrupted
Disrupted
Disrupted
Disrupted
Disrupted
N
N
N
N
N
 -0.115
-0.112
-0.357
-0.185
-0.111
T hsa-miR-2278
hsa-miR-3927-3p
hsa-miR-4451
hsa-miR-4732-5p
hsa-miR-6831-5p
2
2
2
2
2
 CTGCTCTAcctga
ctgcTCTACCTga
ctgCTCTACCtga
ctGCTCTACctga
ctgcTCTACCTga
 Created
Created
Created
Created
Created
N
N
N
N
N
 -0.289
-0.116
-0.186
-0.216
-0.135
18328483 rs12952556 A
G hsa-miR-200a-5p
hsa-miR-200b-5p
4
4
 aaaTAAGATActa
aaaTAAGATActa
 Created
Created
N
N
 -0.043
-0.043
18328684 rs1979276 T C hsa-miR-125a-3p
hsa-miR-1266-5p
hsa-miR-3664-3p
hsa-miR-3934-5p
hsa-miR-4518
hsa-miR-764
hsa-miR-92a-2-5p
0 cccCACCTGAgag
ccccaCCTGAGAg
ccccaCCTGAGAg
cccCACCTGAgag
ccccaCCTGAGAg
cccCACCTGAgag
CCCCACCtgagag
 Created
Created
Created
Created
Created
Created
Created
N
N
N
N
N
N
N
 -0.093
-0.08
-0.067
-0.093
-0.08
-0.102
-0.184
T hsa-miR-1296-3p
hsa-miR-513c-5p
hsa-miR-514b-5p
hsa-miR-6513-3p
0 CCCCACTtgagag
ccccaCTTGAGAg
ccccaCTTGAGAg
cccCACTTGAgag
 Disrupted
Disrupted
Disrupted
Disrupted
N
N
N
N
 -0.182
-0.108
-0.089
-0.051
18328703 rs3783 C C hsa-miR-4514
hsa-miR-4692
1
1
 aagCTGCCTGccg
aagCTGCCTGccg
 Disrupted
Disrupted
N
N
 -0.084
-0.093
G hsa-miR-6858-3p
1
 aaGCTGGCTgccg
 Created
N
 -0.198

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