Bicodon bias can determine the role of synonymous SNPs in human diseases

McCarthy, Christina; Carrea, Alejandra; Diambra, Luis

doi:10.1186/s12864-017-3609-6

BMC Genomics

Table 1 Pause propensity variation due to sSNPs linked to clinically relevant genetic diseases or traits

From: Bicodon bias can determine the role of synonymous SNPs in human diseases

Disease/trait	Gene	rsID	Bicondon change		Z-score
			from	to	bicodon	codon
Macular degeneration	CFHR5	rs34533956	GACGTG	GATGTG	0.91	0.51
Longevity	TERT	rs33954691	CACGCA	CATGCA	0.84	0.71
		rs33959226	GCAGAG	GCGGAG	0.83	0.55
Asthma	SLC6A7	rs2240794	GATAGC	GACAGC	0.11	0.51
Pul. sarcoidosis	CARD15	rs1861759	GTGCGT	GTGCGG	0.99	0.17
Tuberculosis	TIRAP	rs7932766	GCCTAC	GCTTAC	0.74	0.62
Cystic Fibrosis	CFTR	rs1800092	ATCATC	ATAATC	0.09	0.17
Coeliac disease	CD44	rs1071695	CACGTG	CATGTG	0.84	0.71
	APIP	rs1571133	ACACTT	ACCCTT	0.32	0.39
Crohn’ disease	IRGM	rs10065172	CTGATG	TTGATG	0.77	0.93
Smoking-related cancer	NBS1	rs709816	GATGCA	GACGCA	0.80	0.51
		rs1061302	AATCCA	AATCCG	0.79	0.47
Colorectal cancer	ERCC1	rs11615	AATGTG	AACGTG	0.97	0.07
Chronic myeloid leukemia	WT1	rs2229069	CGCACG	CGCACA	0.80	0.24
		rs2227985	CAGGAA	CAGGAG	0.69	0.10
Non-small-cell lung carcinoma	EGFR	rs2293347	ACAGAC	ACAGAT	0.48	0.51
Cervical & vulvar cancer	IL2	rs2069763	CTGCTG	CTTCTG	0.49	0.80
Drug resistance	ABCB1	rs1045642	ATTGTG	ATCGTG	0.94	0.55
	CHRNA4	rs1044396	CCGAGC	CCGAGT	0.26	0.74
Alzheimer	COX6B1	rs7991	AAGACC	AAGACT	0.84	0.36
	COX6C	rs1130569	TACGAT	TATGAT	0.59	0.24
	COX8A	rs61759492	ATCATG	ATAATG	0.83	0.17
ADHD	NTF3	rs6332	CAGCCG	CAGCCA	0.46	0.47
Huntington	ADORA2A	rs5751876	GGCTAT	GGCTAC	0.99	0.24
	PADI2	rs2076615	GGTGGC	GGGGGC	0.93	0.77
Schizophrenia	SYNGR1	rs74681509	ACCTTC	ACCTTT	0.84	0.36
	DRD2	rs6277	ACTCCC	ACTCCT	0.95	0.82
		rs6275	CACCAT	CACCAC	0.81	0.71
TMD	COMT	rs769223 ^∗	GCGAGG	GCAAGG	0.67	0.55
		rs1121923	GTGGCC	GTAGCC	0.89	0.13
Type III		rs248	GAGTTT	GAATTT	0.34	0.10
hyperlipidemia	LPL	rs45607438	CATGTT	CACGTT	0.89	0.71
		rs316	AAGACC	AAGACA	0.91	0.39
Chronic hepatitis C	IRF7	rs1061501	CGGGAT	CGAGAT	0.84	0.17
Osteoporosis	CD44	rs11033026	CATGAG	CATGAA	0.93	0.10

We computed the Z-score associated to the change in the pause propensity values, or to the change in the differential RSCU, as a consequence of single nucleotide mutations in a subset of 22 human diseases or traits selected from [41]. The first column lists the diseases/traits, the following columns list the affected genes, the rs IDs, the bicodon changes, and Z-scores. Only the variant associated with larger Z-score is listed, for a more complete table, please see Additional file 3: Table S1. ^∗ is validated by HapMap

Back to article page

ISSN: 1471-2164

Contact us

Submission enquiries: bmcgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com