Description and predicted functionality of nsSNPs showing significant association with chronic lymphocytic leukemia risk
SNP . | Substitution . | Predicted functionality* . | Gene† . | Gene description† . | Gene ontology‡ . | MIM§ . |
|---|---|---|---|---|---|---|
| rs1800056 | F858L | Possibly damaging/potentially intolerant | ATM | Ataxia telangiectasia mutated | DNA repair, transcription regulation, cell-cycle control | 607585 |
| rs1800057 | P1054R | Probably damaging/intolerant | ATM | Ataxia telangiectasia mutated | DNA repair, transcription regulation, cell-cycle control | 607585 |
| rs1801376 | Q349R | Potentially damaging | BUB1B | BUB1 budding uninhibited by benzimidazoles 1 homolog beta | Cell cycling and proliferation | 602860 |
| rs17879961 | I157T | — | CHEK2 | CHK2 checkpoint homolog | DNA damage checkpoint | 604373 |
| rs10927851 | F191S | — | FBLIM1 (FBLP-1) | Filamin-binding LIM protein-1 | Cell adhesion | 607747 |
| rs9975588 | S102L | Potentially damaging | MCM3AP | MCM3 minichromosome maintenance—deficient 3 associated protein | DNA replication | 603294 |
| rs1048201 | R209Q | Potentially damaging/potentially intolerant | NUDT6 | Nudix (nucleoside diphosphate linked moiety X) motif 6 | Growth factor | 606261 |
| rs2250889 | R574P | Possibly damaging | MMP9 | Matrix metalloproteinase 9 | Collagen catabolism | 120361 |
| rs1801265 | C29R | — | DPYD | Dihydropyrimidine dehydrogenase | Thymidine/uracil catabolism | 274270 |
| rs2293925 | R525W | Possibly damaging/intolerant | TOP1MT | DNA topoisomerase I | DNA unwinding | 606387 |
| rs4874147 | G452S | Potentially damaging | ZC3H3 (ZC3HDC 3) | Zinc finger CCCH-type domain containing 3 | Nucleic acid binding | NA |
| rs7288201 | I475V | Intolerant | GGTLA1 | Gamma-glutamyltransferase-like activity 1 | Amino acid metabolism | 137168 |
| rs10067 | H604Q | Probably damaging/intolerant | OVGP1 | Oviductal glycoprotein 1 | Chitin catabolism | 603578 |
| rs17409304 | Q306E | Intolerant | CLCA2 | Chloride channel, calcium activated, member 2 | Chloride transport | 604003 |
| rs11569017 | D784V | Possibly damaging/intolerant | EGF | Epidermal growth factor | DNA replication, receptor signaling, regulation of cell proliferation | 131530 |
| rs3206824 | G335R | Intolerant | DKK3 | Dickkopf homolog 3 | Receptor signaling | 605416 |
| rs144848 | N372H | — | BRCA2 | Breast cancer 2, early onset | DNA repair, regulation of transcription | 600185 |
| rs4619 | I253M | — | IGFBP1 | Insulin-like growth factor-binding protein 1 | Regulation of cell growth, signal transduction | 146730 |
| rs16978899 | S247P | Possibly damaging/intolerant | ZNF233 | Zinc finger protein 233 | Regulation of transcription | NA |
| rs712665 | S155G | Possibly damaging | U2AF1L1 | U2 small nuclear RNA auxillary factor 1-like 1 | Nucleotide binding | 601079 |
| rs5167 | L96R | Probably damaging | APOC4 | Apolipoprotein C-IV | Lipid metabolism | 600745 |
| rs2235006 | F582L | Possibly damaging | ATM | Ataxia telangiectasia mutated | DNA repair, transcription regulation, cell cycle control | 607585 |
| rs328 | S474X | Stop codon | LPL | Lipoprotein lipase | Fatty acid metabolism | 238600 |
| rs4150521 | S704L | Possibly damaging | ERCC3 | Excision repair cross-complementing rodent repair deficiency, complementation group 3 | Induction of apoptosis, regulation of transcription | 133510 |
| rs10494745 | G306E | Possibly damaging | CFHL4 | Complement factor H-related 4 | Lipid transporter activity | 605337 |
| rs2269429 | G2555S | Possibly damaging | TNXB | Tenascin XB | Cell-matrix adhesion | 600985 |
| rs17050550 | A85S | — | OGG1 | 8-Oxoguanine DNA glycosylase | Base-excision repair | 601982 |
| rs17293607 | G65R | Intolerant | MMP10 | Matrix metalloproteinase 10 | Collagen catabolism | 185260 |
| rs619203 | S2229C | Probably damaging | ROS1 | v-ros UR2 sarcoma virus oncogene homolog 1 | Signal transduction | 165020 |
| rs459552 | V1822D | — | APC | Adenomatosis polyposis coli | Receptor signaling, cell-cycle control | 175100 |
| rs508405 | T280A | Potentially intolerant | CAPN13 | Calpain 13 | Proteolysis and peptidolysis | NA |
| rs3136797 | P242R | Possibly damaging/intolerant | POLB | Polymerase (DNA directed), beta | DNA repair, DNA replication | 174760 |
| rs11102001 | P356S | Possibly damaging | EPS8L3 | EPS8-like 3 | Receptor activity | NA |
| rs1738023 | D215N | Possibly damaging | AKR7A3 | Aldo-keto reductase family 7, member A3 | Aldehyde metabolism | 608477 |
| rs3821979 | L146H | Possibly damaging/intolerant | SHRM (Shrml) | Shroom | Death receptor adaptor protein activity | 604570 |
| rs1805087 | D919G | — | MTR | 5-Methyltetrahydrofolate-homocysteine methyltransferase | Folic acid and derivative biosynthesis, transferase activity | 156570 |
| rs2452600 | S136F | Potentially damaging/intolerant | PDLIM5 (LIM) | PDZ and LIM domain 5 | Metal ion binding | 605904 |
| rs2278106 | P278S | Intolerant | EPHA7 | EPH receptor A7 | Receptor signalling | 602190 |
| rs204900 | S873A | Intolerant | TNXB | Tenascin XB | Cell-matrix adhesion | 600985 |
| rs16900023 | P786S | Potentially damaging | MSH5 | mutS homolog 5 | DNA repair, DNA metabolism | 603382 |
| rs1800100 | R668C | Probably damaging/intolerant | CFTR | Cystic fibrosis transmembrane conductance regulator | Ion transport | 602421 |
| rs1211554 | Y268D | Probably damaging/potentially intolerant | HUS1B | HUS1 checkpoint homolog b | Cell-cycle control | NA |
| rs2032729 | S220N | Potentially damaging | ZNF24 | Zinc finger protein 24 | Regulation of transcription | 194534 |
| rs17738527 | E211K | Possibly damaging/intolerant | SEC14L4 | SEC14-like 4 | Intracellular protein transport | NA |
| rs1799954 | R2034C | Possibly damaging/intolerant | BRCA2 | Breast cancer 2, early onset | DNA repair, regulation of transcription | 600185 |
| rs17337252 | M234T | Possibly damaging | RB1CC1 | RB1-inducible coiled-coil 1 | Kinase activity | 606837 |
| rs8207 | N699D | Potentially damaging/potentially intolerant | PPIG | Peptidyl-prolyl isomerase G | RNA splicing, protein folding | 606093 |
| rs17704912 | W1037S | Probably damaging | MYO18B | Myosin XVIIIB | Nucleotide binding | 607295 |
| rs3130618 | R41L | Possibly damaging | BAT4 | HLA-B—associated transcript 4 | Nucleic acid binding | 142610 |
SNP . | Substitution . | Predicted functionality* . | Gene† . | Gene description† . | Gene ontology‡ . | MIM§ . |
|---|---|---|---|---|---|---|
| rs1800056 | F858L | Possibly damaging/potentially intolerant | ATM | Ataxia telangiectasia mutated | DNA repair, transcription regulation, cell-cycle control | 607585 |
| rs1800057 | P1054R | Probably damaging/intolerant | ATM | Ataxia telangiectasia mutated | DNA repair, transcription regulation, cell-cycle control | 607585 |
| rs1801376 | Q349R | Potentially damaging | BUB1B | BUB1 budding uninhibited by benzimidazoles 1 homolog beta | Cell cycling and proliferation | 602860 |
| rs17879961 | I157T | — | CHEK2 | CHK2 checkpoint homolog | DNA damage checkpoint | 604373 |
| rs10927851 | F191S | — | FBLIM1 (FBLP-1) | Filamin-binding LIM protein-1 | Cell adhesion | 607747 |
| rs9975588 | S102L | Potentially damaging | MCM3AP | MCM3 minichromosome maintenance—deficient 3 associated protein | DNA replication | 603294 |
| rs1048201 | R209Q | Potentially damaging/potentially intolerant | NUDT6 | Nudix (nucleoside diphosphate linked moiety X) motif 6 | Growth factor | 606261 |
| rs2250889 | R574P | Possibly damaging | MMP9 | Matrix metalloproteinase 9 | Collagen catabolism | 120361 |
| rs1801265 | C29R | — | DPYD | Dihydropyrimidine dehydrogenase | Thymidine/uracil catabolism | 274270 |
| rs2293925 | R525W | Possibly damaging/intolerant | TOP1MT | DNA topoisomerase I | DNA unwinding | 606387 |
| rs4874147 | G452S | Potentially damaging | ZC3H3 (ZC3HDC 3) | Zinc finger CCCH-type domain containing 3 | Nucleic acid binding | NA |
| rs7288201 | I475V | Intolerant | GGTLA1 | Gamma-glutamyltransferase-like activity 1 | Amino acid metabolism | 137168 |
| rs10067 | H604Q | Probably damaging/intolerant | OVGP1 | Oviductal glycoprotein 1 | Chitin catabolism | 603578 |
| rs17409304 | Q306E | Intolerant | CLCA2 | Chloride channel, calcium activated, member 2 | Chloride transport | 604003 |
| rs11569017 | D784V | Possibly damaging/intolerant | EGF | Epidermal growth factor | DNA replication, receptor signaling, regulation of cell proliferation | 131530 |
| rs3206824 | G335R | Intolerant | DKK3 | Dickkopf homolog 3 | Receptor signaling | 605416 |
| rs144848 | N372H | — | BRCA2 | Breast cancer 2, early onset | DNA repair, regulation of transcription | 600185 |
| rs4619 | I253M | — | IGFBP1 | Insulin-like growth factor-binding protein 1 | Regulation of cell growth, signal transduction | 146730 |
| rs16978899 | S247P | Possibly damaging/intolerant | ZNF233 | Zinc finger protein 233 | Regulation of transcription | NA |
| rs712665 | S155G | Possibly damaging | U2AF1L1 | U2 small nuclear RNA auxillary factor 1-like 1 | Nucleotide binding | 601079 |
| rs5167 | L96R | Probably damaging | APOC4 | Apolipoprotein C-IV | Lipid metabolism | 600745 |
| rs2235006 | F582L | Possibly damaging | ATM | Ataxia telangiectasia mutated | DNA repair, transcription regulation, cell cycle control | 607585 |
| rs328 | S474X | Stop codon | LPL | Lipoprotein lipase | Fatty acid metabolism | 238600 |
| rs4150521 | S704L | Possibly damaging | ERCC3 | Excision repair cross-complementing rodent repair deficiency, complementation group 3 | Induction of apoptosis, regulation of transcription | 133510 |
| rs10494745 | G306E | Possibly damaging | CFHL4 | Complement factor H-related 4 | Lipid transporter activity | 605337 |
| rs2269429 | G2555S | Possibly damaging | TNXB | Tenascin XB | Cell-matrix adhesion | 600985 |
| rs17050550 | A85S | — | OGG1 | 8-Oxoguanine DNA glycosylase | Base-excision repair | 601982 |
| rs17293607 | G65R | Intolerant | MMP10 | Matrix metalloproteinase 10 | Collagen catabolism | 185260 |
| rs619203 | S2229C | Probably damaging | ROS1 | v-ros UR2 sarcoma virus oncogene homolog 1 | Signal transduction | 165020 |
| rs459552 | V1822D | — | APC | Adenomatosis polyposis coli | Receptor signaling, cell-cycle control | 175100 |
| rs508405 | T280A | Potentially intolerant | CAPN13 | Calpain 13 | Proteolysis and peptidolysis | NA |
| rs3136797 | P242R | Possibly damaging/intolerant | POLB | Polymerase (DNA directed), beta | DNA repair, DNA replication | 174760 |
| rs11102001 | P356S | Possibly damaging | EPS8L3 | EPS8-like 3 | Receptor activity | NA |
| rs1738023 | D215N | Possibly damaging | AKR7A3 | Aldo-keto reductase family 7, member A3 | Aldehyde metabolism | 608477 |
| rs3821979 | L146H | Possibly damaging/intolerant | SHRM (Shrml) | Shroom | Death receptor adaptor protein activity | 604570 |
| rs1805087 | D919G | — | MTR | 5-Methyltetrahydrofolate-homocysteine methyltransferase | Folic acid and derivative biosynthesis, transferase activity | 156570 |
| rs2452600 | S136F | Potentially damaging/intolerant | PDLIM5 (LIM) | PDZ and LIM domain 5 | Metal ion binding | 605904 |
| rs2278106 | P278S | Intolerant | EPHA7 | EPH receptor A7 | Receptor signalling | 602190 |
| rs204900 | S873A | Intolerant | TNXB | Tenascin XB | Cell-matrix adhesion | 600985 |
| rs16900023 | P786S | Potentially damaging | MSH5 | mutS homolog 5 | DNA repair, DNA metabolism | 603382 |
| rs1800100 | R668C | Probably damaging/intolerant | CFTR | Cystic fibrosis transmembrane conductance regulator | Ion transport | 602421 |
| rs1211554 | Y268D | Probably damaging/potentially intolerant | HUS1B | HUS1 checkpoint homolog b | Cell-cycle control | NA |
| rs2032729 | S220N | Potentially damaging | ZNF24 | Zinc finger protein 24 | Regulation of transcription | 194534 |
| rs17738527 | E211K | Possibly damaging/intolerant | SEC14L4 | SEC14-like 4 | Intracellular protein transport | NA |
| rs1799954 | R2034C | Possibly damaging/intolerant | BRCA2 | Breast cancer 2, early onset | DNA repair, regulation of transcription | 600185 |
| rs17337252 | M234T | Possibly damaging | RB1CC1 | RB1-inducible coiled-coil 1 | Kinase activity | 606837 |
| rs8207 | N699D | Potentially damaging/potentially intolerant | PPIG | Peptidyl-prolyl isomerase G | RNA splicing, protein folding | 606093 |
| rs17704912 | W1037S | Probably damaging | MYO18B | Myosin XVIIIB | Nucleotide binding | 607295 |
| rs3130618 | R41L | Possibly damaging | BAT4 | HLA-B—associated transcript 4 | Nucleic acid binding | 142610 |
— indicates prediction not possible; NA, not available.
Functional predictions based on SIFT (intolerant) and PolyPhen (probably damaging, possibly damaging).
According to NCBI Entrez Gene (see Table 1 footnote for URL); genes in brackets have been recently revised.
Gene Ontology Consortium annotation (http://www.geneontology.org).
Online Mendelian Inheritance in Man (http://www.ncbi.nih.gov/entrez/query.fcgi?db=OMIM) accession number.