ABCA13 p.Leu4464Met
| Predicted by SNAP2: | A: D (63%), C: D (63%), D: D (85%), E: D (71%), F: D (53%), G: D (80%), H: D (63%), I: N (82%), K: D (71%), M: N (66%), N: D (71%), P: D (75%), Q: D (63%), R: D (71%), S: D (71%), T: D (53%), V: N (72%), W: D (80%), Y: D (59%), |
| Predicted by PROVEAN: |
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[hide] A cytogenetic abnormality and rare coding variants... Am J Hum Genet. 2009 Dec;85(6):833-46. Epub . Knight HM, Pickard BS, Maclean A, Malloy MP, Soares DC, McRae AF, Condie A, White A, Hawkins W, McGhee K, van Beck M, MacIntyre DJ, Starr JM, Deary IJ, Visscher PM, Porteous DJ, Cannon RE, St Clair D, Muir WJ, Blackwood DH
A cytogenetic abnormality and rare coding variants identify ABCA13 as a candidate gene in schizophrenia, bipolar disorder, and depression.
Am J Hum Genet. 2009 Dec;85(6):833-46. Epub ., [PMID:19944402]
Abstract [show]
Schizophrenia and bipolar disorder are leading causes of morbidity across all populations, with heritability estimates of approximately 80% indicating a substantial genetic component. Population genetics and genome-wide association studies suggest an overlap of genetic risk factors between these illnesses but it is unclear how this genetic component is divided between common gene polymorphisms, rare genomic copy number variants, and rare gene sequence mutations. We report evidence that the lipid transporter gene ABCA13 is a susceptibility factor for both schizophrenia and bipolar disorder. After the initial discovery of its disruption by a chromosome abnormality in a person with schizophrenia, we resequenced ABCA13 exons in 100 cases with schizophrenia and 100 controls. Multiple rare coding variants were identified including one nonsense and nine missense mutations and compound heterozygosity/homozygosity in six cases. Variants were genotyped in additional schizophrenia, bipolar, depression (n > 1600), and control (n > 950) cohorts and the frequency of all rare variants combined was greater than controls in schizophrenia (OR = 1.93, p = 0.0057) and bipolar disorder (OR = 2.71, p = 0.00007). The population attributable risk of these mutations was 2.2% for schizophrenia and 4.0% for bipolar disorder. In a study of 21 families of mutation carriers, we genotyped affected and unaffected relatives and found significant linkage (LOD = 4.3) of rare variants with a phenotype including schizophrenia, bipolar disorder, and major depression. These data identify a candidate gene, highlight the genetic overlap between schizophrenia, bipolar disorder, and depression, and suggest that rare coding variants may contribute significantly to risk of these disorders.
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No. Sentence Comment
100 All ABCA13 Variants with Provisional dbSNP Identifiers Identified during the Resequencing Discovery Stage of This Study Domain Chr7 Location bp NCBI Build 36.1 Base Change dbSNP Reference AA Change Substitution Type MAF Cases MAF controls Discovery Populationa TMD1 48,382,318 G/A ss136294996 R3604Q missense A: 0.0003 A: 0.0005 case TMD1 48,382,333 A/C ss136295002 H3609P missense C: 0.0085 C: 0.0043 both TMD1 48,382,337 A/C ss136295006 P3610P synonymous C: 0.0096 C: 0.0000 case TMD1 48,382,337 A/T ss136295010 P3610P synonymous T: 0.0048 T: 0.0037 both TMD1 48,382,619 T/G ss136295014 S3704R missense/splice variant G: 0.0003 G: 0.0000 case TMD1 48,384,364 C/T ss136295018 intronic T: 0.0095 T: 0.0160 both TMD1 48,384,474 A/G ss136295022 intronic G: 0.0045 G: 0.0000 case TMD1 48,384,623 T/C ss136295026 intronic C: 0.0048 C: 0.0053 both TMD1 48,398,156 G/A ss136295030 intronic A: 0.0523 nd case TMD1 48,398,232 G/C ss136295034 intronic C: 0.0048 nd case NBD1 48,399,292 C/G ss136295038 L3861L synonymous G: 0.0000 G: 0.0052 control NBD1 48,399,322 T/C ss136295042 T3871T synonymous C: 0.0000 C: 0.0052 control NBD1 48,413,738 C/T ss136295046 intronic T: 0.0092 nd case NBD1 48,420,643 C/T ss136295050 intronic T: 0.1651 T: 0.2067 both NBD1 48,420,683 A/G ss136295054 T4031A missense G: 0.0009 G: 0.0000 case NBD1 48,420,731 C/G ss136295058 L4047V missense (>1% frequency) G: 0.0169 G: 0.0104 both NBD1 48,420,834 C/G ss136295062 intronic G: 0.1651 G: 0.2067 both HDR 48,465,394 T/C ss136295066 P4260P synonymous C: 0.0000 C: 0.0052 control HDR 48,465,399 A/G ss136295070 H4262R missense G: 0.0003 G: 0.0000 case TMD2 48,518,027 C/T ss136295074 R4454C missense (>1% frequency) T: 0.0142 T: 0.0156 both TMD2 48,518,057 C/A ss136295078 L4464M missense (>1% frequency) A: 0.0095 A: 0.0208 both TMD2 48,526,874 A/G ss136295082 T4550A missense A: 0.0056 A: 0.0014 case TMD2 48,526,994 C/T ss136295086 R4590W missense T: 0.0044 T: 0.0019 control TMD2 48,527,112 C/G ss136295090 intronic G: 0.0286 G: 0.0161 both TMD2 48,530,327 C/G ss136295094 P4648A missense G: 0.0000 G: 0.0004 control NBD2 48,534,459 A/G ss136295098 R4707R synonymous G: 0.0500 G: 0.0526 both NBD2 48,534,520 C/T ss136295102 R4728X nonsense T: 0.0025 T: 0.001 case NBD2 48,538,544 C/T ss136295106 intronic T: 0.0000 T: 0.0153 control NBD2 48,538,545 C/T ss136295110 intronic T: 0.0000 T: 0.0052 control NBD2 48,597,311 A/G ss136295114 I4841V missense G: 0.0040 G: 0.0000 case NBD2 48,597,317 C/T ss136295118 R4843C missense T: 0.0050 T: 0.0031 control NBD2 48,604,841 C/A ss136295122 intronic A: 0.0519 A: 0.0789 both The genomic and functional domain location of the variants is displayed together with mutation class and frequency in the discovery set.
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ABCA13 p.Leu4464Met 19944402:100:1740
status: NEW