PMID: 25151476

Genome resequencing and bioinformatic analysis of SNP containing candidate genes in the autoimmune vitiligo Smyth line chicken model.

BMC genomics
HM Jang, GF Erf, KC Rowland, BW Kong
2014-08-23

209 variants were identified in this publication


Variant ID Gene cDNA Protein Consequence Exon Intron
7-12443306-T-C VWDE c.37A>G p.Met13Val Missense 1/29 -
8-48849042-G-A PRKDC c.1149C>T p.Phe383Phe Synonymous 12/86 -
21-40778329-G-T LCA5L c.1492C>A p.Gln498Lys Missense 10/10 -
18-13056526-T-A CEP192 c.3937T>A p.Cys1313Ser Missense 19/45 -
9-136298781-C-T ADAMTS13 c.1265C>T p.Ala422Val Missense 11/29 -
13-32899251-A-G BRCA2 c.355A>G p.Thr119Ala Missense 4/27 -
3-196199632-A-C RNF168 c.774T>G p.Ser258Arg Missense 6/6 -
12-66698520-G-T HELB c.197G>T p.Cys66Phe Missense 2/14 -
6-152765608-C-T SYNE1 c.3775G>A p.Ala1259Thr Missense 30/146 -
6-75904586-G-A COL12A1 c.151C>T p.Pro51Ser Missense 3/66 -
X-134711299-C-T INTS6L c.1955C>T p.Ala652Val Missense 14/17 -
3-183469952-C-T YEATS2 c.1061C>T p.Ser354Phe Missense 10/31 -
13-32910533-G-T BRCA2 c.2041G>T p.Val681Leu Missense 11/27 -
12-124239084-C-T ATP6V0A2 c.2293C>T p.Gln765* Nonsense 18/20 -
12-65222236-C-T TBC1D30 c.229C>T p.Leu77Phe Missense 3/12 -
6-75904655-G-A COL12A1 c.82C>T p.Pro28Ser Missense 3/66 -
6-152765606-A-T SYNE1 c.3777T>A p.Ala1259Ala Synonymous 30/146 -
6-152765606-A-C SYNE1 c.3777T>G p.Ala1259Ala Synonymous 30/146 -
14-94046679-A-T UNC79 c.2087A>T p.Glu696Val Missense 19/50 -
6-152765606-A-G SYNE1 c.3777T>C p.Ala1259Ala Synonymous 30/146 -
12-66704300-C-T HELB c.1592C>T p.Ala531Val Missense 4/14 -
8-68028179-C-A CSPP1 c.1303C>A p.Pro435Thr Missense 11/29 -
13-22084231-C-T MICU2 c.673G>A p.Val225Met Missense 8/12 -
7-99758206-T-C GAL3ST4 c.806A>G p.His269Arg Missense 4/4 -
3-39228593-G-A XIRP1 c.2344C>T p.Pro782Ser Missense 2/2 -
7-12420144-G-A VWDE c.757C>T p.Leu253Phe Missense 5/29 -
7-12420137-C-A VWDE c.764G>T p.Gly255Val Missense 5/29 -
X-14862785-G-T FANCB c.2005C>A p.Leu669Met Missense 8/9 -
7-117451036-C-A CTTNBP2 c.197G>T p.Arg66Met Missense 3/23 -
X-38271246-A-T OTC c.999A>T p.Thr333Thr Synonymous 9/10 -
X-38271246-A-C OTC c.999A>C p.Thr333Thr Synonymous 9/10 -
X-38271246-A-G OTC c.999A>G p.Thr333Thr Synonymous 9/10 -
3-128990700-A-G COPG1 c.1934A>G p.Glu645Gly Missense 19/24 -
1-214794010-A-G CENPF c.586A>G p.Thr196Ala Missense 6/20 -
6-75899421-C-T COL12A1 c.505G>A p.Ala169Thr Missense 6/66 -
16-846968-G-C CHTF18 c.2609G>C p.Gly870Ala Missense 20/22 -
6-136470240-G-T PDE7B c.334G>T p.Val112Leu Missense 5/13 -
12-109495769-T-C USP30 c.232T>C p.Phe78Leu Missense 3/13 -
18-13056527-G-C CEP192 c.3938G>C p.Cys1313Ser Missense 19/45 -
13-109562354-G-A MYO16 c.1715G>A p.Arg572Lys Missense 16/35 -
10-129910552-GA-AA MKI67 c.1813_1814delTCinsAA p.Ser605Asn Missense 9/15 -
13-51915481-A-G SERPINE3 c.254A>G p.His85Arg Missense 1/7 -
6-152751742-T-C SYNE1 c.4564A>G p.Ile1522Val Missense 35/146 -
5-7878241-T-C MTRR c.586T>C p.Phe196Leu Missense 5/15 -
7-34091526-G-A BMPER c.730G>A p.Val244Ile Missense 9/16 -
9-139283001-G-A SNAPC4 c.1018C>T p.His340Tyr Missense 10/23 -
1-197097683-A-G ASPM c.2873T>C p.Phe958Ser Missense 10/28 -
7-99764675-G-T GAL3ST4 c.44C>A p.Pro15His Missense 2/4 -
6-152629745-T-C SYNE1 c.17225A>G p.Gln5742Arg Missense 91/146 -
10-129923867-A-G MKI67 c.65T>C p.Leu22Pro Missense 2/15 -
16-817462-G-T MSLN c.1588G>T p.Ala530Ser Missense 16/18 -
9-139273670-C-G SNAPC4 c.2609G>C p.Arg870Pro Missense 21/23 -
6-75901958-C-T COL12A1 c.304G>A p.Glu102Lys Missense 4/66 -
3-183521881-G-A YEATS2 c.3689G>A p.Cys1230Tyr Missense 27/31 -
12-104067841-G-A STAB2 c.2528G>A p.Cys843Tyr Missense 23/69 -
3-44955189-C-T TGM4 c.2027C>T p.Ala676Val Missense 14/14 -
1-214830281-G-A CENPF c.8491G>A p.Val2831Ile Missense 18/20 -
3-196199632-A-G RNF168 c.774T>C p.Ser258Ser Synonymous 6/6 -
3-196199632-A-T RNF168 c.774T>A p.Ser258Arg Missense 6/6 -
1-197390648-G-A CRB1 c.1690G>A p.Asp564Asn Missense 6/12 -
7-117431550-A-T CTTNBP2 c.1700T>A p.Ile567Lys Missense 4/23 -
5-154305497-TAC-ATG GEMIN5 c.1213_1215delGTAinsATG p.Val405Met Missense 8/28 -
1-94502787-A-G ABCA4 c.3727T>C p.Tyr1243His Missense 25/50 -
9-135203882-T-C SETX c.3103A>G p.Lys1035Glu Missense 10/26 -
13-45533612-C-G NUFIP1 c.925G>C p.Val309Leu Missense 7/10 -
12-104044331-C-T STAB2 c.1232C>T p.Thr411Ile Missense 11/69 -
3-183469951-TC-AA YEATS2 c.1060_1061delTCinsAA p.Ser354Asn Missense 10/31 -
3-38080876-G-A DLEC1 c.160G>A p.Ala54Thr Missense 1/36 -
2-170066148-C-T LRP2 c.6284G>A p.Arg2095Gln Missense 38/79 -
1-197071681-G-A ASPM c.6700C>T p.Gln2234* Nonsense 18/28 -
3-196199237-T-G RNF168 c.1169A>C p.Asn390Thr Missense 6/6 -
9-139270824-C-T SNAPC4 c.4394G>A p.Arg1465Gln Missense 22/23 -
1-197112780-T-C ASPM c.602A>G p.Asn201Ser Missense 3/28 -
12-25274740-T-C CASC1 c.1186A>G p.Ile396Val Missense 11/16 -
12-104098354-T-G STAB2 c.3862T>G p.Ser1288Ala Missense 36/69 -
13-79191237-G-T RNF219 c.659C>A p.Ala220Asp Missense 6/6 -
9-139370960-C-T SEC16A c.1108G>A p.Gly370Arg Missense 3/32 -
1-197097682-A-G ASPM c.2874T>C p.Phe958Phe Synonymous 10/28 -
12-104140473-A-G STAB2 c.6235A>G p.Thr2079Ala Missense 58/69 -
1-216373041-T-C USH2A c.3739A>G p.Ser1247Gly Missense 17/21 -
6-136472355-A-G PDE7B c.440A>G p.His147Arg Missense 6/13 -
X-142718485-T-C SLITRK4 c.440A>G p.Glu147Gly Missense 2/2 -
13-23930092-G-T SACS c.659C>A p.Thr220Lys Missense 8/10 -
3-15070205-A-G NR2C2 c.968A>G p.Gln323Arg Missense 9/15 -
1-197390289-G-C CRB1 c.1331G>C p.Gly444Ala Missense 6/12 -
2-241537332-G-A CAPN10 c.1771G>A p.Ala591Thr Missense 10/12 -
10-43312059-G-A BMS1 c.2342G>A p.Gly781Asp Missense 14/23 -
3-196199082-TGTTT-T RNF168 c.1323_1326delACAA p.Gln442Lysfs*45 Frameshift 6/6 -
1-228403423-G-A OBSCN c.1988G>A p.Arg663His Missense 6/81 -
1-200818772-T-C CAMSAP2 c.2875T>C p.Ser959Pro Missense 11/17 -
1-197102540-T-C ASPM c.2359A>G p.Ile787Val Missense 6/28 -
3-15073904-A-G NR2C2 c.1186A>G p.Met396Val Missense 11/15 -
15-62276033-C-T VPS13C c.1771G>A p.Val591Ile Missense 18/83 -
7-12401144-T-C VWDE c.2902A>G p.Asn968Asp Missense 14/29 -
2-219892960-G-A CFAP65 c.1814C>T p.Ala605Val Missense 12/35 -
13-51922497-C-G SERPINE3 c.849C>G p.His283Gln Missense 4/7 -
12-103988186-G-A STAB2 c.229G>A p.Val77Ile Missense 3/69 -
16-816473-C-T MSLN c.1213C>T p.His405Tyr Missense 13/18 -
6-75892991-C-G COL12A1 c.1666G>C p.Ala556Pro Missense 10/66 -
5-154308149-G-C GEMIN5 c.849C>G p.Arg283Arg Synonymous 6/28 -
3-39230012-A-G XIRP1 c.925T>C p.Trp309Arg Missense 2/2 -
16-816701-AGG-CAT MSLN c.1264_1266delAGGinsCAT p.Arg422His Missense 14/18 -
5-7878243-C-A MTRR c.588C>A p.Phe196Leu Missense 5/15 -
2-219892628-C-T CFAP65 c.1955G>A p.Ser652Asn Missense 13/35 -
7-12409975-G-A VWDE c.1957C>T p.Leu653Phe Missense 12/29 -
9-136298502-G-A ADAMTS13 c.1097G>A p.Cys366Tyr Missense 10/29 -
3-38159491-G-A DLEC1 c.4680G>A p.Val1560Val Synonymous 33/36 -
18-13049204-T-C CEP192 c.2414T>C p.Met805Thr Missense 16/45 -
7-117417815-C-T CTTNBP2 c.2528G>A p.Gly843Asp Missense 8/23 -
12-104044332-A-G STAB2 c.1233A>G p.Thr411Thr Synonymous 11/69 -
12-104044332-A-T STAB2 c.1233A>T p.Thr411Thr Synonymous 11/69 -
12-122369748-G-A WDR66 c.844G>A p.Ala282Thr Missense 4/22 -
3-196215552-C-T RNF168 c.304G>A p.Asp102Asn Missense 2/6 -
9-136304564-CTT-C ADAMTS13 c.1783_1784delTT p.Leu595Glyfs*19 Frameshift 15/29 -
6-152712581-G-A SYNE1 c.7835C>T p.Thr2612Ile Missense 52/146 -
7-76826126-A-G FGL2 c.790T>C p.Phe264Leu Missense 2/2 -
3-38159491-G-C DLEC1 c.4680G>C p.Val1560Val Synonymous 33/36 -
3-112647880-CCT-CAT CD200R1 c.550_552delAGGinsCAT p.Arg184His Missense 5/8 -
10-112540885-C-T RBM20 c.518C>T p.Pro173Leu Missense 2/14 -
3-39230012-A-T XIRP1 c.925T>A p.Trp309Arg Missense 2/2 -
3-39228337-C-G XIRP1 c.2600G>C p.Ser867Thr Missense 2/2 -
3-38159491-G-T DLEC1 c.4680G>T p.Val1560Val Synonymous 33/36 -
1-53716438-CT-CC LRP8 c.2599_2600delAGinsCC p.Arg867Pro Missense 17/19 -
7-99757994-G-A GAL3ST4 c.1018C>T p.Leu340Phe Missense 4/4 -
5-154305520-C-T GEMIN5 c.1192G>A p.Val398Ile Missense 8/28 -
3-112648128-AC-AA CD200R1 c.428_429delGTinsAA p.Arg143Gln Missense 4/8 -
3-42751205-CAC-ATC CCDC13 c.1957_1959delGTGinsATC p.Val653Ile Missense 15/16 -
7-34085946-T-G BMPER c.605T>G p.Val202Gly Missense 8/16 -
14-94063746-T-G UNC79 c.2701T>G p.Ser901Ala Missense 24/50 -
3-88104699-G-A CGGBP1 c.428C>T p.Ser143Leu Missense 4/4 -
14-94044194-G-A UNC79 c.1687G>A p.Val563Ile Missense 18/50 -
5-7892880-A-T MTRR c.1411A>T p.Asn471Tyr Missense 11/15 -
3-183446509-G-A YEATS2 c.682G>A p.Asp228Asn Missense 7/31 -
12-124203239-C-T ATP6V0A2 c.187C>T p.Arg63* Nonsense 2/20 -
13-23985374-T-C SACS c.5A>G p.Glu2Gly Missense 2/10 -
8-79629693-T-C ZC2HC1A c.943T>C p.Cys315Arg Missense 9/9 -
1-53742664-C-G LRP8 c.583G>C p.Gly195Arg Missense 5/19 -
7-117431793-T-C CTTNBP2 c.1457A>G p.Gln486Arg Missense 4/23 -
1-197316496-G-C CRB1 c.875G>C p.Gly292Ala Missense 4/12 -
1-197113160-G-A ASPM c.368C>T p.Thr123Ile Missense 2/28 -
3-112642579-A-G CD200R1 c.992T>C p.Val331Ala Missense 8/8 -
12-124229466-G-A ATP6V0A2 c.1552G>A p.Asp518Asn Missense 13/20 -
9-139272627-G-C SNAPC4 c.3652C>G p.Pro1218Ala Missense 21/23 -
14-94046678-G-A UNC79 c.2086G>A p.Glu696Lys Missense 19/50 -
13-109777679-G-A MYO16 c.3689G>A p.Arg1230Lys Missense 30/35 -
15-62209689-G-A VPS13C c.7777C>T p.Pro2593Ser Missense 58/83 -
2-170135955-C-A LRP2 c.1492G>T p.Gly498* Nonsense 12/79 -
12-65264547-A-G TBC1D30 c.1457A>G p.Lys486Arg Missense 11/12 -
11-47612281-G-A C1QTNF4 c.82C>T p.Leu28Leu Synonymous 2/2 -
14-94046668-G-A UNC79 c.2076G>A p.Gln692Gln Synonymous 19/50 -
14-94046668-G-C UNC79 c.2076G>C p.Gln692His Missense 19/50 -
14-94046668-G-T UNC79 c.2076G>T p.Gln692His Missense 19/50 -
12-132626956-C-T DDX51 c.682G>A p.Val228Met Missense 4/15 -
12-104048411-GGG-AGC STAB2 c.1486_1488delGGGinsAGC p.Gly496Ser Missense 13/69 -
9-139273563-G-A SNAPC4 c.2716C>T p.Arg906Cys Missense 21/23 -
3-39226241-G-A XIRP1 c.4696C>T p.Pro1566Ser Missense 2/2 -
7-95039387-G-A PON2 c.521C>T p.Pro174Leu Missense 6/9 -
22-23481087-C-G RSPH14 c.242G>C p.Ser81Thr Missense 3/7 -
12-66717807-G-A HELB c.2342G>A p.Cys781Tyr Missense 10/14 -
13-23942552-G-T SACS c.334C>A p.Gln112Lys Missense 5/10 -
11-43343649-A-G API5 c.506A>G p.Lys169Arg Missense 5/14 -
5-7892882-C-T MTRR c.1413C>T p.Asn471Asn Synonymous 11/15 -
X-38271245-CA-TG OTC c.998_999delCAinsTG p.Thr333Met Missense 9/10 -
11-88242577-T-C GRM5 c.2726A>G p.Glu909Gly Missense 9/9 -
13-23928680-T-G SACS c.2071A>C p.Ile691Leu Missense 8/10 -
7-76826124-G-C FGL2 c.792C>G p.Phe264Leu Missense 2/2 -
7-76826124-G-T FGL2 c.792C>A p.Phe264Leu Missense 2/2 -
7-35872418-A-G SEPT7 c.77A>G p.Asn26Ser Missense 3/14 -
1-183532386-C-A NCF2 c.1234G>T p.Asp412Tyr Missense 13/15 -
12-109494521-G-C USP30 c.118G>C p.Gly40Arg Missense 2/13 -
6-75887457-T-C COL12A1 c.2359A>G p.Lys787Glu Missense 12/66 -
3-38159489-GTG-ATC DLEC1 c.4678_4680delGTGinsATC p.Val1560Ile Missense 33/36 -
1-197091291-T-C ASPM c.3739A>G p.Lys1247Glu Missense 15/28 -
1-220197771-G-A EPRS c.778C>T p.His260Tyr Missense 8/32 -
1-228505323-G-A OBSCN c.13720G>A p.Glu4574Lys Missense 52/81 -
5-7878243-C-G MTRR c.588C>G p.Phe196Leu Missense 5/15 -
1-94578600-A-G ABCA4 c.89T>C p.Val30Ala Missense 2/50 -
3-42774382-G-A CCDC13 c.1592C>T p.Pro531Leu Missense 12/16 -
9-136310925-G-A ADAMTS13 c.2716G>A p.Val906Ile Missense 21/29 -
12-124220103-C-T ATP6V0A2 c.757C>T p.Pro253Ser Missense 8/20 -
7-34118693-C-A BMPER c.1303C>A p.His435Asn Missense 13/16 -
3-39228099-C-T XIRP1 c.2838G>A p.Trp946* Nonsense 2/2 -
6-152823788-T-C SYNE1 c.868A>G p.Thr290Ala Missense 10/146 -
1-200818774-T-A CAMSAP2 c.2877T>A p.Ser959Ser Synonymous 11/17 -
7-12401142-A-G VWDE c.2904T>C p.Asn968Asn Synonymous 14/29 -
1-200818774-T-C CAMSAP2 c.2877T>C p.Ser959Ser Synonymous 11/17 -
1-200818774-T-G CAMSAP2 c.2877T>G p.Ser959Ser Synonymous 11/17 -
X-142718846-A-G SLITRK4 c.79T>C p.Cys27Arg Missense 2/2 -
13-25483933-G-A CENPJ c.860C>T p.Pro287Leu Missense 4/17 -
12-25272144-G-C CASC1 c.1331C>G p.Thr444Arg Missense 12/16 -
3-196199634-T-G RNF168 c.772A>C p.Ser258Arg Missense 6/6 -
8-68007747-G-A CSPP1 c.730G>A p.Ala244Thr Missense 6/29 -
1-216465642-C-T USH2A c.1715G>A p.Cys572Tyr Missense 10/21 -
1-197071207-G-A ASPM c.7174C>T p.Gln2392* Nonsense 18/28 -
21-40800211-T-C LCA5L c.209A>G p.Asp70Gly Missense 4/10 -
14-94041530-C-G UNC79 c.1666C>G p.Leu556Val Missense 17/50 -
12-109495771-C-G USP30 c.234C>G p.Phe78Leu Missense 3/13 -
12-109495771-C-A USP30 c.234C>A p.Phe78Leu Missense 3/13 -
1-228473926-A-T OBSCN c.9152A>T p.Asn3051Ile Missense 34/81 -
11-88242461-C-T GRM5 c.2842G>A p.Ala948Thr Missense 9/9 -
6-149771910-A-G ZC3H12D c.1493T>C p.Met498Thr Missense 6/6 -
8-48839827-TCT-TGG PRKDC c.2344_2346delAGAinsTGG p.Arg782Trp Missense 21/86 -
2-103335510-T-C MFSD9 c.794A>G p.Gln265Arg Missense 6/6 -
12-123687234-G-C MPHOSPH9 c.1718C>G p.Thr573Arg Missense 10/24 -
9-139371224-C-T SEC16A c.844G>A p.Glu282Lys Missense 3/32 -
13-79191102-T-C RNF219 c.794A>G p.Glu265Gly Missense 6/6 -
12-122359453-C-G WDR66 c.242C>G p.Ala81Gly Missense 2/22 -
12-132626674-A-T DDX51 c.878T>A p.Leu293Gln Missense 5/15 -
12-104044332-A-C STAB2 c.1233A>C p.Thr411Thr Synonymous 11/69 -