Human SNPs resulting in premature stop codons and protein truncation

Savas, Sevtap; Tuzmen, Sukru; Ozcelik, Hilmi

doi:10.1186/1479-7364-2-5-274

Human Genomics

Table 1 Validated X-SNPs in the human genome.

From: Human SNPs resulting in premature stop codons and protein truncation

Gene	^aGene function	^bAccession #	Location	^cSNP ID	^dFrequency	^eHomozygosity	X-SNP	^fProtein length (truncation)	gNMD	^hCpG
AGT	Cell signalling; hypertension	NM_000029.1	1q42-q43	rs5039	CEPH-MULTI-NATIONAL 184 chr. G = 1.000 A = 0.000 HYP1-MULTI-NATIONAL 80 chr. G = 0.950 A = 0.050	n/a	Q53X	485 (89%)	+	+
APOC4	Lipid metabolism	NM_001646.1	19q13.2	rs5164	CEPH-MULTI-NATIONAL 184 chr. G = 1.000 A = 0.000 HYP1-MULTI-NATIONAL 80 chr. G = 0.950 A = 0.050	-	W47X	127 (63%)	+	-
CDH15	Cell adhesion; morphogenetic processes	NM_004933.2	16q24.3	rs2270416	JBIC-allele-EAST ASIA 1500 chr. G = 0.826 T = 0.174	n/a	Y788X	814 (3.2%)	-	+
CLCA3	Transport	NM_004921.1	1p31-p22	rs2292830	JBIC-allele -EAST ASIA 1462 chr. G = 0.569 C = 0.431	n/a	Y84X	262 (67.3%)	-	-
CYP2C19	Transport; drug metabolism and synthesis of lipids	NM_000769.1	10q24. 1-q24.3	rs4986893	PAC1-EAST ASIA 46 chr. G = 0.913 A = 0.087 CAUC1-MULTI-NATIONAL 60 chr. G = 1.000 A = 0.000 AFR1-MULTI-NATIONAL 48 chr. G = 0.979 A = 0.021 HISP1-CENTRAL/SOUTH AMERICA 44 chr. G = 1.000 A = 0.000 P1-MULTI-NATIONAL 198 chr. G = 0.975 A = 0.025	n/a	W212X	446 (52.5%)	-	-
DSCR8	Unknown	NM_032589.2	21q22.2	rs2836172	NCBI\|NIHPDR-NORTH AMERICA 20 chr. A = 0.900 T = 0.100 AFD_EUR_PANEL-NORTH AMERICA 48 chr. A = 1.000 AFD_AFR_PANEL-NORTH AMERICA 46 chr. A = 0.783 T = 0.217 AFD_CHN_PANEL-NORTH AMERICA 48 chr. A = 0.854 T = 0.146	+	K79X	91 (13.2%)	-	-
EPHX1	Aromatic compound catabolism; xenobiotic metabolism	NM_000120.2	1q42.1	rs4986931	PAC1-EAST ASIA 46 chr. A = 0.978 G = 0.022 P1-MULTI-NATIONAL 202 chr. A = 0.990 G = 0.010 CAUC1-MULTI-NATIONAL 62 chr. A = 1.000 G = 0.000 AFR1-MULTI-NATIONAL 48 chr. A = 1.000 G = 0.000 HISP1-CENTRAL/SOUTH AMERICA 46 chr. A = 0.978 G = 0.022	-	W97X	455 (78.7%)	+	-
FUT2	Carbohydrate metabolism; protein glycosylation	NM_000511.1	19q\|3.3	rs1800030	PAC1-EAST ASIA 48 chr. G = 0.979 A = 0.021 P1-MULTI-NATIONAL 202 chr. G = 0.995 A = 0.005 CAUC1-MULTI-NATIONAL 60 chr. G = 1.000 A = 0.000 AFR1-MULTI-NATIONAL 48 chr. G = 1.000 A = 0.000 HISP1-CENTRAL/SOUTH AMERICA 46 chr. G = 1.000 A = 0.000	-	W297X	346 (14.2%)	-	-
HPS4	Organelle biogenesis; protein stabilisation/targeting	NM_152843.1	22cen--q\|2.3	rs3747129	JBIC-allele-EAST ASIA 1492 chr. G = 0.798 A = 0.202 AFD_EUR_PANEL-NORTH AMERICA 48 chr. G = 0.812 A = 0.188 AFD_AFR_PANEL-NORTH AMERICA 46 chr. G = 0.978 A = 0.022 AFD_CHN_PANEL-NORTH AMERICA 48 chr. G = 0.750 A = 0.250 HapMap-CEU-EUROPE 120 chr. G = 0.825 A = 0.175	+	R246X	528 (53.4%)	-	+
IL17RB	Immuno-regulatory activity; regulation of cell growth	NM_018725.2	3p2\|.1	rs1043261	JBIC-allele-EAST ASIA 1476 chr. C = 0.902 T = 0.098 HapMap-CEU-EUROPE 120 chr. C = 0.908 T = 0.092 AFD_EUR_PANEL-NORTH AMERICA 48 chr. C = 0.938 T = 0.062 AFD_AFR_PANEL-NORTH AMERICA 46 chr. C = 0.978 T = 0.022 AFD_CHN_PANEL-NORTH AMERICA 48 chr. C = 0.792 T = 0.208	+	Q484X	502 (3.6%)	-	+
KRTAP1-1	Cytoskeleton; intermediate filaments	NM_030967.2	17q12-q21	rs3213755	JBIC-allele-EAST ASIA 708 chr. C = 0.617 T = 0.383 HapMap-CEU-EUROPE 120 chr. G = 0.800 A = 0.200	+	Q51X	177 (71.2%)	-	-
LCE5A	Unknown	NM_178438.1	1q21.3	rs2282298	JBIC-allele-EAST ASIA 1504 chr. G = 0.979 A = 0.021 AFD_EUR_PANEL-NORTH AMERICA 48 chr. C = 1.000 AFD_AFR_PANEL-NORTH AMERICA 46 chr. C = 1.000 AFD_CHN_PANEL-NORTH AMERICA 48 chr. C = 0.896 T = 0.104	-	R79X	118 (33.1%)	-	+
LIG4	DNA repair; cell cycle	NM_206937.1	13q33-q34	rs2232636	PAC1-EAST ASIA 46 chr. G = 1.000 A = 0.000 P1-MULTI-NATIONAL 202 chr. G = 0.995 A = 0.005 CAUC1-MULTI-NATIONAL 62 chr. G = 1.000 A = 0.000 AFR1-MULTI-NATIONAL 48 chr. G = 0.979 A = 0.021 HISP1-CENTRAL/SOUTH AMERICA 46 chr. G = 1.000 A = 0.000	-	W46X	911 (95%)	-	-
LPL	Lipoprotein metabolism	NM_000237.1	8p22	rs328	WIAF-CSNP-MITOGPOP5-MULTI-NATI-ONAL 112 chr. C = 0.982 G = 0.018 JBIC-allele-EAST ASIA 1458 chr. C = 0.860 G = 0.140 CEPH-MULTI-NATIONAL 184 chr. C = 0.640G = 0.360 AFD_EUR_PANEL-NORTH AMERICA 44 chr. C = 0.727 G = 0.273 AFD_AFR_PANEL-NORTH AMERICA 42 chr. C = 0.952 G = 0.048 AFD_CHN_PANEL-NORTH AMERICA 46 chr. C = 0.935 G = 0.065	+	S474X	475 (0.2%)	-	-
MAGEE2	Unknown	NM_138703.2	Xq13.3	rs1343879	TSC_42_C-NORTH AMERICA 84 chr. C = 0.950 A = 0.050 C_42_A-EAST ASIA 84 chr. A = 0.650 C = 0.350 TSC_42_AA-NORTHAMERICA 84 chr. C = 0.950 A = 0.050 HapMap-CEU-EUROPE 120 chr. C = 0.983 A = 0.017	-	E120X	523 (77.1%)	-	-
MS4A12	Signal transduction	NM_017716.1	11q12	rs2298553	JBIC-allele-EAST ASIA 726 chr. C = 0.585 T = 0.415 AFD_EUR_PANEL-NORTH AMERICA 48 chr. C = 0.583 T = 0.417 AFD_AFR_PANEL-NORTH AMERICA 42 chr. C = 0.548 T = 0.452 AFD_CHN_PANEL-NORTH AMERICA 48 chr. C = 0.542 T = 0.458	+	Q71X	267 (73.4%)	+	-
OAS2	Immune response	NM_016817.1	12q24.2	rs15895	POOLED_CEPH-MULTI-NATIONAL 188 chr. A = 0.668 G = 0.332 CEPH-MULTI-NATIONAL 184 chr. C = 0.670 T = 0.330 SC_12_A-EAST ASIA 20 chr. G = 1.000 SC_12_AA-NORTH AMERICA 24 chr. G = 0.830 A = 0.170 SC_12_C-NORTH AMERICA 24 chr. G = 0.710 A = 0.290 SC_95_C-NORTH AMERICA 184 chr. C = 0.590 T = 0.410 AFD_EUR_PANEL-NORTH AMERICA 48 chr. G = 0.562 A = 0.438 AFD_AFR_PANEL-NORTH AMERICA 46 chr. G = 0.913 A = 0.087 AFD_CHN_PANEL-NORTH AMERICA 48 chr. G = 1.000	+	W720X	727 (1%)	-	-
OVCH2	Proteolysis	NM_198185.1	11p15.4	rs4509745	HapMap-CEU-EUROPE chr.120 T = 0.658 C = 0.342 HapMap-HCB-EAST ASIA 88 chr. T = 0.705 C = 0.295 HapMap-JPT-EAST ASIA 88 chr. T = 0.614 C = 0.386 HapMap-YRI-WEST AFRICA 120 chr. C = 0.783 T = 0.217 AFD_EUR_PANEL-NORTH AMERICA 44 chr. T = 0.568 C = 0.432 AFD_AFR_PANEL-NORTH AMERICA 46 chr. C = 0.609 T = 0.391 AFD_CHN_PANEL-NORTH AMERICA 48 chr. T = 0.583 C = 0.417	+	W556X	564 (1.4%)	-	-
POLE2	DNA repair	NM_002692.2	14q21- q22	rs3218790	NIHPDR-NORTH AMERICA 170 chr. A = 0.988 T = 0.012 HapMap-CEU-EUROPE 120 chr. A = 1.000 HapMap-HCB-EAST ASIA 90 chr. A = 1.000 HapMap-JPT-EAST ASIA 88 chr. A = 1.000 HapMap-YRI-WEST AFRICA 120 chr. A = 1.000	-	K443X	527 (15.9%)	+	-
SER-PINB11	Serine-type endopeptidase inhibitor activity	NM_080475.1	18	rs4940595	AfAm 12 chr. C = 0.667 A = 0.333 Caucasian 24 chr. A = 0.667 C = 0.333 Asian 12 chr. C = 0.667 A = 0.333 CEPH 12 chr. C = 0.667 A = 0.333 PDpanel 48 chr. A = 0.521 C = 0.479 AFD_EUR_PANEL-NORTH AMERICA 48 chr. T = 0.625 G = 0.375 AFD_AFR_PANEL-NORTH AMERICA 44 chr. G = 0.545 T = 0.455 AFD_CHN_PANEL-NORTH AMERICA 48 chr. G = 0.771 T = 0.229	+	E90X	392 (77%)	+	-
SMUG1	DNA repair	NM_014311.1	12q13.11-q13.3	rs2233919	NIHPDR-NORTH AMERICA 574 chr. C = 0.986 T = 0.014 PDR90 166 chr. C = 0.988 T = 0.012	-	Q3X	270 (98.9%)	+	-
SPTBN5	Actin cytoskeleton organisation and biogenesis	NM_016642.1	15q21	rs2271286	JBIC-allele-EAST ASIA 1482 chr. G = 0.951 A = 0.049	-	Q72X	3674 (98%)	-	-
TAP2	Immune response; protein transport and assembly	NM_000544.2	6p21.3	rs241448	CEPH-MULTI-NATIONAL 184 T = 0.700 C = 0.300 WIAF-CSNP-MITOGPOP5-MULTI-NATI-ONAL 48 chr. T = 0.812 C = 0.188	+	Q687X	703 (2.3%)	-	-
TAAR9	Signal transduction	NM_175057.1	6q23.2	rs2842899	HapMap-CEU-EUROPE 120 chr. T = 0.708 A = 0.292 HapMap-YRI-WEST AFRICA 120 chr. T = 0.883 A = 0.117 AFD_EUR_PANEL-NORTH AMERICA 48 chr. A = 0.812 T = 0.188 AFD_AFR_PANEL-NORTH AMERICA 46 chr. A = 0.783 T = 0.217 AFD_CHN_PANEL-NORTH AMERICA 48 chr. A = 0.854 T = 0.146	+	Q61X	348 (82.5%)	-	-
TLR5	Immune response	NM_003268.3	1q41-q42	rs5744168	D-0-NORTH AMERICA 48 chr.C = 0.938 T = 0.062 E-0-NORTH AMERICA 40 chr. C = 0.925 T = 0.075 E-1-EUROPE 6 chr. C = 1.000	-	R392X	858 (54.3%)	-	+
TRPM1	Cation transport	NM_002420.3	15q13-q14	rs3784589	JBIC-allele-EAST ASIA 1502 chr. C = 0.965 A = 0.035 HapMap-CEU-EUROPE 120 chr. C = 0.942 A = 0.058 HapMap-HCB-EAST ASIA 90 chr. C = 1.000 HapMap-JPT-EAST ASIA 88 chr. C = 0.955 A = 0.045 HapMap-YRI-WEST AFRICA 118 chr. C = 0.958 A = 0.042 AFD_EUR_PANEL-NORTH AMERICA 48 chr C = 0.917 A = 0.083 AFD_AFR_PANEL-NORTH AMERICA 46 chr. C = 0.913 A = 0.087 AFD_CHN_PANEL-NORTH AMERICA 48 chr. C = 1.000	+	E1305X	1533 (14.9%)	-	-
UNC93A	Unknown	NM_018974.2	6q27	rs2235197	JBIC-allele-EAST ASIA 1484 chr. G = 0.852 A = 0.148	n/a	W151X	456 (66.9%)	-	-
ZNF34	Gene expression	NM_030580.2	8q24.3	rs2294120	JBIC-allele-EAST ASIA 1494 chr. C = 0.729 T = 0.271	n/a	Q56X	549 (89.8%)	+	+

Abbreviation: SNP = single nucleotide polymorphism.
^aGene functions are retrieved from the Entrez Gene database of NCBI [30].
^bThe accession numbers onto which the SNP-flanking sequences have been located.
^cSNP ID corresponds to the dbSNP database SNP identifiers.
^dThe frequency information is as posted in dbSNP build 124.
^eThis information indicates whether or not a homozygous sample in a sample set was reported for the corresponding X-SNP and was collected from the dbSNP database 'summary of genotypes' section: 'n/a': no information was available, ' + ': homozygous genotype was reported, ' 2 ': no homozygous was reported.
^fLength of the wild-type protein products. In parentheses are the percentages of the protein truncation at the C-terminus caused by the X-SNP.
^gSNPs that may lead to nonsense-mediated mRNA decay are annotated by ' + '.
^hSNPs occurring at CpG dinucleotides and thus can be hot spot mutations are annotated by ' + '.

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ISSN: 1479-7364

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