ABCMdb

ABCA4 p.Phe2188Ser

ClinVar:	c.6563T>C , p.Phe2188Ser ? , not provided
Predicted by SNAP2:	A: D (71%), C: D (59%), D: D (80%), E: D (66%), G: D (85%), H: D (59%), I: N (57%), K: D (66%), L: N (53%), M: N (61%), N: D (71%), P: D (80%), Q: D (59%), R: D (66%), S: D (71%), T: D (63%), V: D (53%), W: D (53%), Y: N (66%),
Predicted by PROVEAN:	A: D, C: D, D: D, E: D, G: D, H: D, I: D, K: D, L: D, M: D, N: D, P: D, Q: D, R: D, S: D, T: D, V: D, W: D, Y: N,

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[hide] ABCA4 gene mutations in Japanese patients with Sta... Invest Ophthalmol Vis Sci. 2002 Sep;43(9):2819-24. Fukui T, Yamamoto S, Nakano K, Tsujikawa M, Morimura H, Nishida K, Ohguro N, Fujikado T, Irifune M, Kuniyoshi K, Okada AA, Hirakata A, Miyake Y, Tano Y
ABCA4 gene mutations in Japanese patients with Stargardt disease and retinitis pigmentosa.
Invest Ophthalmol Vis Sci. 2002 Sep;43(9):2819-24., [PMID:12202497]

Abstract [show]
PURPOSE: To evaluate photoreceptor cell-specific adenosine triphosphate (ATP)-binding cassette transporter (ABCA4) gene mutations in Japanese patients with Stargardt disease (STGD) and the correlation of these mutations to clinical phenotypes. METHODS: Serum was obtained from 10 unrelated Japanese patients with STGD and 96 unrelated Japanese patients with autosomal recessive retinitis pigmentosa (arRP). All 50 ABCA4 gene exons of the patients with STGD were screened for mutations by a combination of single-strand conformation polymorphism analysis and polymerase chain reaction (PCR) direct-sequencing techniques. By restriction enzyme digestion, primer extension analysis, and PCR direct sequencing techniques, the patients with arRP were screened for three segregated, presumably null ABCA4 gene mutations observed in Japanese patients with STGD. RESULTS: Three novel, presumably null mutations of the ABCA4 gene, IVS7-45_952delinsTCTGACC, IVS12+2T-->G, and 1894delA, were identified. The Arg2149stop mutation that had been found in a white patient with STGD in a prior study was also found in a Japanese patient. Two arRP-affected siblings and two unrelated patients with STGD were found to be homozygous for the same IVS12+2T-->G mutation, and three other arRP-affected siblings were carriers of the IVS12+2T-->G mutation and/or the IVS7-45_952delinsTCTGACC mutation. These three siblings with arRP showed only atrophic degeneration in the macula early after the onset of the disease, and STGD had been diagnosed. CONCLUSIONS: Three novel ABCA4 gene mutations were identified in Japanese patients with STGD and arRP. Mutations in the ABCA4 gene can cause panretinal degeneration that changes its clinical appearance from STGD to arRP over time.

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No. Sentence Comment
39 The IVS7-45_952delinsTCTGACC, IVS12ϩ2T3G, IVS12-50G3A, Ile604Ser, 1894delA, Glu1122Asp, Leu1583Pro, Gly1623Ser, IVS38-36delT, Met1882Val, Arg2149stop, and Phe2188Ser sequence variations were not found in the 192 normal control alleles. Login to comment
46 ABCA4 Gene Sequence Variations Nucleotide change Effect STGD (20†) Control (192†) Reference IVS7-45_952delinsTCTGACC* Splice 0 0 This study IVS12ϩ2T3G* Splice 5 0 This study IVS12-50G3A Unkown 1 0 23 T1811G Ile604Ser 1 0 This study 1894delA Frameshift 1 0 This study G3366C Glu1122Asp 1 0 This study T4748C Leu1583Pro 1 0 This study G4867A Gly1623Ser 1 0 This study IVS38-36delT Unkown 1 0 This study A5644G Met1882Val 2 0 This study G5682C Leu1894Leu 4 32 12,13,14,16,22,23 A5814G Leu1938Leu 4 32 12,14,23 IVS41-11G3A Unkown 4 32 11,14,16,23 A5844G Pro1948Pro 4 32 11,12,14,16,22,23,24,27 T6285C Asp2095Asp 3 27 11,12,14,16,23 C6445T Arg2149Stop 1 0 15 T6563C Phe2188Ser 1 0 This study * Mutations observed in patients with arRP. Login to comment
61 The IVS7-45_952delinsTCTGACC, IVS12ϩ2T3G, Ile604Ser, 1894delA Glu1122Asp, Leu1583Pro, Gly1623Ser, Met1882Val, Arg2149stop, and Phe2188Ser sequence variations were not found in the 192 normal control alleles tested, and hence these FIGURE 2. Login to comment
59 The IVS7-45_952delinsTCTGACC, IVS12af9;2T3G, Ile604Ser, 1894delA Glu1122Asp, Leu1583Pro, Gly1623Ser, Met1882Val, Arg2149stop, and Phe2188Ser sequence variations were not found in the 192 normal control alleles tested, and hence these FIGURE 2. Login to comment

[hide] Identification of Genetic Defects in 33 Probands w... PLoS One. 2015 Jul 10;10(7):e0132635. doi: 10.1371/journal.pone.0132635. eCollection 2015. Xin W, Xiao X, Li S, Jia X, Guo X, Zhang Q
Identification of Genetic Defects in 33 Probands with Stargardt Disease by WES-Based Bioinformatics Gene Panel Analysis.
PLoS One. 2015 Jul 10;10(7):e0132635. doi: 10.1371/journal.pone.0132635. eCollection 2015., [PMID:26161775]

Abstract [show]
Stargardt disease (STGD) is the most common hereditary macular degeneration in juveniles, with loss of central vision occurring in the first or second decade of life. The aim of this study is to identify the genetic defects in 33 probands with Stargardt disease. Clinical data and genomic DNA were collected from 33 probands from unrelated families with STGD. Variants in coding genes were initially screened by whole exome sequencing. Candidate variants were selected from all known genes associated with hereditary retinal dystrophy and then confirmed by Sanger sequencing. Putative pathogenic variants were further validated in available family members and controls. Potential pathogenic mutations were identified in 19 of the 33 probands (57.6%). These mutations were all present in ABCA4, but not in the other four STGD-associated genes or in genes responsible for other retinal dystrophies. Of the 19 probands, ABCA4 mutations were homozygous in one proband and compound heterozygous in 18 probands, involving 28 variants (13 novel and 15 known). Analysis of normal controls and available family members in 12 of the 19 families further support the pathogenicity of these variants. Clinical manifestation of all probands met the diagnostic criteria of STGD. This study provides an overview of a genetic basis for STGD in Chinese patients. Mutations in ABCA4 are the most common cause of STGD in this cohort. Genetic defects in approximately 42.4% of STGD patients await identification in future studies.

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No. Sentence Comment
68 Patient Nucleotide Amino Acid State Computational Prediction Allele Frequency in Reported ID Change Change P/SS Proven SIFT 1000G EVS ExAC NC RC QT058 c.6173T>G p.L2058R Het PrD D D NA NA NA 0/192 0/456 Novel c.4773 +1G>T Splicing defect Het SSA NA NA NA NA NA - 0/456 Pang et al. 2002; Riveiro-Alvarez et al. 2013 QT085 c.6173T>G p.L2058R Het PrD D D NA NA NA 0/192 0/456 Novel c.5932delA p. K1978Qfs*13 Het NA NA NA NA NA NA 0/192 0/456 Novel QT292 c.6389T>A p.M2130K Het PoD D D NA NA NA - 0/456 Yi et al. 2012 c.6118C>T p.R2040* Het NA NA NA NA NA 2/121394 0/192 0/456 Baum et al. 2003 QT302 c.6816 +1G>A Splicing defect Het SSA NA NA NA NA NA - 0/456 Robert et al. 2014 c.4555delA p.T1519Rfs*7 Het NA NA NA NA NA NA 0/192 0/456 Novel QT398 c.4352 +1G>A Splicing defect Het SSA NA NA NA NA 1/121268 - 0/456 Ernest et al. 2009 c.1804C>T p.R602W Het PoD D D NA NA 6/119038 - 2/456 Lewis et al. 1999; Wiszniewski et al. 2005; Heathfield et al. 2013 QT431 c.5646G>A p.M1882I Het PoD D D NA NA 3/121340 - 0/456 Zernant et al. 2011 c.1804C>T p.R602W Het B D D NA NA 6/119038 - 2/456 Lewis et al. 1999; Wiszniewski et al. 2005; Heathfield et al. 2013 QT458 c.4555delA p.T1519Rfs*7 Het NA NA NA NA NA NA 0/192 0/456 Novel c.164A>G p.H55R Het PoD D D NA NA NA - 0/456 Thiadens et al. 2012 QT727 c.161-2A>G Splicing defect Het SSA NA NA NA NA NA 0/192 0/456 Novel c.101_106del p.S34_L35del Het NA NA NA NA NA NA 0/192 0/456 Novel QT833 c.2424C>G p.Y808* Het NA NA NA NA NA NA - 0/456 Zhou et al. 2014 c.1560delG p.V521Sfs*47 Het NA NA NA NA NA NA 0/192 0/456 Novel QT1137 c.6284A>T p.D2095V Het PrD D D NA NA NA 0/192 0/456 Novel c.22C>T p.Q8* Het NA NA NA NA 0.0001 NA 0/192 0/456 Novel QT1160 c.240_241del p.C81Ffs*17 Het NA NA NA NA NA NA 0/192 0/456 Novel c.101_106del p.S34_L35del Het NA NA NA NA NA NA 0/192 0/456 Novel QT1175 c.4195G>T p.E1399* Het NA NA NA NA NA 2/120596 0/192 0/456 Novel c.2894A>G p.N965S Het PrD D D NA 0.0001 21/ 121302 - 0/456 Allikmets et al. 1997; Shanks et al. 2013; Bertelsen et al. 2014 QT1182 c.4773 +1G>T Splicing defect Hom SSA NA NA NA NA NA - 0/456 Pang et al. 2002; Riveiro-Alvarez et al. 2013 QT1198 c.5646G>A p.M1882I Het B D D NA NA 3/121340 - 0/456 Zernant et al. 2011 c.2894A>G p.N965S Het PrD D D NA 0.0001 21/ 121302 - 0/456 Allikmets et al. 1997;Shanks et al. 2013; Bertelsen et al. 2014 QT1200 c.6563T>C p.F2188S Het B D D NA 0.0005 2/121380 - 1/456 Fukui et al. 2002 c.858+2T>A Splicing defect Het SSA NA NA NA NA NA - 0/456 Zhang et al. 2014 QT1230 c.6317G>C p.R2106P Het PrD D D NA NA NA 0/192 0/456 Novel c.101_106del p.S34_L35del Het NA NA NA NA NA NA 0/192 0/456 Novel QT1277 c.6479 +2T>C Splicing defect Het SSA NA NA NA NA NA 0/192 0/456 Novel (Continued) Table 1. Login to comment