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_024993
Gene Symbol: LRRTM4
Description: Homo sapiens leucine rich repeat transmembrane neuronal 4 (LRRTM4), transcript variant 1, mRNA.
Gene Location: chr2(-):77743786-77749502
Browse Associations

Somatic mutations that impact miRNA target sites


Mutation Mutation ID Sample Name Cancer Type
chr2:g.77516709G>C COSN7084875 8067246 [pancreas][NS][carcinoma][NS]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-miR-302f actgtataAGCAATTgccc
 11
 UAAUUGCU m7b Disrupted -0.331000 -0.119000 0.030000

Mutation Mutation ID Sample Name Cancer Type
chr2:g.77517038T>C COSN1855787 RK050_C01 [liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-miR-4528 ctggcaaTATAATGtttta
 2
 UCAUUAUA m7b Disrupted -0.096000 no TS No effect
hsa-miR-4528 ctggcaaTATAATGtttta
 2
 UCAUUAUA m7b Disrupted -0.096000 no TS No effect
hsa-miR-4528 ctggcaaTATAATGtttta
 0 UCAUUAUA m7b Disrupted -0.096 no TS No effect

Mutation Mutation ID Sample Name Cancer Type
chr2:g.77517283G>T COSN7993585 ASHPC_0001_Pa_P_2 [pancreas][NS][carcinoma][NS]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-miR-224-3p accttCCATTTTatattat
 0 AAAAUGGU m7a Created -0.020000 -0.020000 -0.100000
hsa-miR-3143 accttccATGTTATattat
 12
 AUAACAUU m7a Disrupted -0.014000 -0.014000 0.210000
hsa-miR-3163 accttccATTTTATAttat
 0 UAUAAAAU m8a Created 0.110000 0.237000 -2.030000
hsa-miR-3662 accttcCATTTTatattat
 6
 GAAAAUGA m6b Created -0.085000 -0.035000 0.350000
hsa-miR-410 accttccatGTTATATTat
 0 AAUAUAAC m8a (m8a->m7a) -0.086000 no TS 1.950000
hsa-miR-4694-3p acctTCCATTTtatattat
 0 CAAAUGGA m7b Created -0.026000 -0.154000 -4.270000
hsa-miR-4802-3p acctTCCATGTtatattat
 0 UACAUGGA m7b Disrupted -0.223000 no TS 9.820000
hsa-miR-522-3p accttCCATTTTatattat
 0 AAAAUGGU m7a Created -0.017000 -0.017000 -0.190000

Mutation Mutation ID Sample Name Cancer Type
chr2:g.77517355A>G COSN5957594 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-4729 tttATAAATGAaaggagag
 0 UCAUUUAU m8a Created no TS -0.022000 -0.010000
hsa-miR-5696 tttaTAAATGAaaggagag
 0 CUCAUUUA m7b Created no TS -0.018000 No effect
hsa-miR-579 tttatAAATGAAaggagag
 0 UUCAUUUG m7a Created no TS 0.032000 -0.010000
hsa-miR-644b-3p tttatAAATGAAaggagag
 0 UUCAUUUG m7a Created no TS 0.049000 No effect

Mutation Mutation ID Sample Name Cancer Type
chr2:g.77517409A>G COSN5957595 RK187_C01 [liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-miR-382-3p aaagaAATGATatgtattc
 3
 AAUCAUUC m6b Disrupted 0.028000 no TS No effect
hsa-miR-5580-3p aaagaaatgATATGTattc
 4
 CACAUAUG m6b Disrupted 0.016000 no TS -0.310000

Mutation Mutation ID Sample Name Cancer Type
chr2:g.77517729C>A COSN5957596 RK217_C01 [liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-let-7a-3p taaTTGTATAaggctccta
 12
 CUAUACAA m7b (m6c->m7b) -0.136000 -0.165000 -0.400000
hsa-let-7b-3p taaTTGTATAaggctccta
 12
 CUAUACAA m7b (m6c->m7b) -0.117000 -0.146000 -0.400000
hsa-let-7f-1-3p taaTTGTATAaggctccta
 12
 CUAUACAA m7b (m6c->m7b) -0.145000 -0.164000 -0.240000
hsa-let-7f-2-3p taatTGTATAaggctccta
 4
 CUAUACAG m6b Created -0.282000 -0.254000 -0.040000
hsa-miR-1185-1-3p taatTGTATAaggctccta
 4
 AUAUACAG m6b Created -0.261000 -0.233000 No effect
hsa-miR-1185-2-3p taatTGTATAaggctccta
 4
 AUAUACAG m6b Created -0.261000 -0.233000 -0.010000
hsa-miR-300 taaTTGTATAaggctccta
 12
 UAUACAAG m7a (m6b->m7a) 0.005000 0.038000 -0.430000
hsa-miR-381 taaTTGTATAaggctccta
 12
 UAUACAAG m7a (m6b->m7a) -0.009000 0.024000 -0.430000
hsa-miR-4293 taattgtaTCAGGCTccta
 3
 CAGCCUGA m7b Disrupted -0.205000 no TS 0.130000
hsa-miR-4789-5p taatTGTATAaggctccta
 7
 GUAUACAC m6b Created -0.051000 -0.019000 -0.360000

Mutation Mutation ID Sample Name Cancer Type
chr2:g.77517846T>C COSN7993586 PCSI_0083_Pa_P_526 [pancreas][NS][carcinoma][NS]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-miR-3065-5p ggttgatTTTGTTGtaaat
 7
 UCAACAAA m7b Disrupted -0.114000 no TS 0.020000
hsa-miR-3529-3p ggttgattTTGTTGTaaat
 6
 AACAACAA m7b Disrupted -0.285000 -0.054000 3.390000
hsa-miR-551b-5p ggTTGATTTCgttgtaaat
 12
 GAAAUCAA m8a (m7b->m8a) 0.081000 0.109000 0.120000

Mutation Mutation ID Sample Name Cancer Type
chr2:g.77517974T>G COSN7084876 8030353 [pancreas][NS][carcinoma][NS]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-miR-548b-3p gtctGGTTCTTGgtgtttg
 12
 CAAGAACC m8a Disrupted -0.126000 no TS 0.330000


Mutation Mutation ID Sample Name Cancer Type
chr2:g.77518029T>A COSN6684661 CHC433T [liver][NS][carcinoma][hepatocellular_carcinoma]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
No TargetScan sites are altered. To display all potentially impacted target sites, select "All 6mer or longer seed matches" above.


Mutation Mutation ID Sample Name Cancer Type
chr2:g.77518036G>T COSN8561360 tumor_4120193 [haematopoietic_and_lymphoid_tissue][NS][lymphoid_neoplasm][NS]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
hsa-miR-10a-5p tatACAGGGTttggactta
 0 UACCCUGU m7b (m6c->m7b) no TS -0.302000 -0.010000
hsa-miR-10b-5p tatACAGGGTttggactta
 0 UACCCUGU m7b (m6c->m7b) no TS -0.302000 No effect


Mutation Mutation ID Sample Name Cancer Type
chr2:g.77518130T>- ICGC_ssm_v3_139628 HCC74T [liver][NS][carcinoma][NS]
miRNA Targets Table
miR ID miRSite Conservation miRSeed SeedClass FuncClass Wildtype CS+ Mutant CS+ PITA score change
No TargetScan sites are altered. To display all potentially impacted target sites, select "All 6mer or longer seed matches" above.


Mutation Mutation ID Sample Name Cancer Type
chr2:g.77518232T>C COSN8609610 522_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-1245a tctaATCACTagaaagatt
 1
 AAGUGAUC m6b Disrupted -0.528000 -0.416000 0.070000
hsa-miR-4299 tctaaTCACCAGaaagatt
 0 GCUGGUGA m7b Created no TS -0.496000 -2.190000
hsa-miR-4456 tctaatCACCAGaaagatt
 15
 CCUGGUGG m6b Created -0.334000 -0.505000 0.420000
hsa-miR-548q tctaatCACCAGaaagatt
 0 GCUGGUGC m6b Created no TS -0.183000 No effect
hsa-miR-921 tctaaTCACTAGaaagatt
 0 CUAGUGAG m7a Disrupted NA NA 2.990000

*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
77516704 rs181059905 T T hsa-miR-302f
6
 AGCAATTgccctt
 Disrupted
N
 -0.212
C hsa-miR-8053
5
 agcAATCGCCctt
 Created
N
 -0.336
77516713 rs185545008 A A hsa-let-7a-3p
hsa-let-7b-3p
hsa-let-7f-1-3p
hsa-let-7f-2-3p
hsa-miR-1185-1-3p
hsa-miR-1185-2-3p
hsa-miR-4789-5p
hsa-miR-582-5p
hsa-miR-98-3p
7
7
7
7
7
7
7
2
7
 aacTGTATAAgca
aacTGTATAAgca
aacTGTATAAgca
aaCTGTATAAgca
aaCTGTATAAgca
aaCTGTATAAgca
aacTGTATAAgca
AACTGTAtaagca
aacTGTATAAgca
 Disrupted
Disrupted
Disrupted
Disrupted
Disrupted
Disrupted
Disrupted
Disrupted
Disrupted
N
N
N
N
N
N
N
N
N
 -0.051
-0.051
-0.051
-0.282
-0.261
-0.261
-0.051
-0.165
-0.051
G hsa-miR-3941
hsa-miR-466
hsa-miR-4672
hsa-miR-6768-5p
7
7
7
8
 aacTGTGTAAgca
aacTGTGTAAgca
aaCTGTGTAAgca
aaCTGTGTAagca
 Created
Created
Created
Created
N
N
N
N
 -0.102
-0.084
-0.339
-0.127

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