| Literature DB >> 31915033 |
Hang Yang1, Yanyun Ma1, Mingyao Luo2, Guoyan Zhu1, Yinhui Zhang1, Binbin Li1, Chang Shu3, Zhou Zhou4.
Abstract
BACKGROUND: Loeys-Dietz syndrome (LDS) is a rare connective tissue disorder for which 6 genes in the TGF-β pathway have been identified as causative. With the widespread use of genetic testing, the range of known clinical and genetic profiles has broadened, but these features have not been fully elucidated thus far. METHODS ANDEntities:
Keywords: Genetic testing; Loeys-Dietz syndrome; Phenotypic spectrum
Mesh:
Substances:
Year: 2020 PMID: 31915033 PMCID: PMC6950884 DOI: 10.1186/s13023-019-1282-3
Source DB: PubMed Journal: Orphanet J Rare Dis ISSN: 1750-1172 Impact factor: 4.123
Definite pathogenic and highly suspected variants in LDS genes detected in our cohort
| Patient ID | Gene | Transcript | Nucleotide change | Amino acid change | MAF | MAF in gnomAD | Domain | Source | Pathogenicity | Evidence | Note |
|---|---|---|---|---|---|---|---|---|---|---|---|
| AD1413 | NM_004612 | c.614 T > C | p.Ile205Thr | . | . | Pkinase_Tyr | Maternal | LP | PM2, PP3, PS2$ | ||
| AD623–1 | NM_004612 | c.644G > C | p.Arg215Pro | . | . | De novo | LP | PS2, PM2, PP3 | |||
| AD808 | NM_004612 | c.664G > A | p.Gly222Arg | . | 0.0000289 | Pkinase_Tyr | LP | PM2, PP1_Strong, PP3 | |||
| AD264 | NM_004612 | c.683_685del | p.228del | . | . | De novo | LP | PS2, PM2, PS4_Supporting, PM4 | a | ||
| AD692–1 | NM_004612 | c.702_704del | p.235del | . | . | De novo | LP | PS2, PM2, PM4 | |||
| AD453 | NM_004612 | c.722C > T | p.Ser241Leu | . | . | NA | LP | PM2, PS4_Supporting, PS2 | |||
| AD371 | NM_004612 | c.934G > A | p.Gly312Ser | 0.00000942 | 0.00000398 | NA | LP | PP3, PM2, PS4_Supporting, PP1_Strong | a | ||
| AD641–1 | NM_004612 | c.997G > A | p.Asp333Asn | . | . | De novo | LP | PS2, PM2, PP3 | |||
| AD78 | NM_004612 | c.1459C > T | p.Arg487Trp | . | . | NA | P | PS4, PM2, PM5, PP1_Strong, PP3 | a | ||
| AD703–1 | NM_004612 | c.1459C > T | p.Arg487Trp | . | . | Maternal | P | PS4, PM2, PM5, PP1_Strong, PP3 | |||
| AD1346 | NM_004612 | c.1459C > T | p.Arg487Trp | . | . | NA | P | PS4, PM2, PM5, PP1_Strong, PP3 | |||
| AD1362 | NM_004612 | c.1460G > A | p.Arg487Gln | . | . | Paternal | P | PS2, PS3_Supporting, PS4_Moderate, PM2, PP3 | |||
| AD1804 | NM_003242 | c.95-2A > G | 0.0000293 | 0.0006 | Paternal | LP | PVS1, PM2 | ||||
| AD257 | NM_003242 | c.1067G > C | p.Arg356Pro | . | . | Pkinase_Tyr | Paternal (Mosaic) | P | PS2_Very Strong, PS4_Moderate, PM2, PP3 | ab | |
| AD22 | NM_003242 | c.1139 T > G | p.Leu380Arg | . | . | De novo | LP | PS2, PM2, PP3 | a | ||
| AD888 | NM_003242 | c.1275G > C | p.Met425Ile | . | . | Pkinase_Tyr | De novo | LP | PS2, PM2, PP3 | ||
| AD1181 | NM_003242 | c.1363 T > C | p.Trp455Arg | . | . | Pkinase_Tyr | VUSLP | PM2, PP3 | Assumed de novo in AD1181’s mother | ||
| AD536 | NM_003242 | c.1449dupT | p.Cys483fs | . | . | Pkinase_Tyr | NA | LP | PVS1, PM2 | ||
| AD617–1 | NM_003242 | 1517delA | p.Asn506fs | . | . | Pkinase_Tyr | NA | P | PVS1, PM2, PP1 | ||
| AD1784 | NM_003242 | c.1525-1G > C | . | . | NA | LP | PVS1, PM2 | ||||
| AD153 | NM_003242 | c.1538 T > C | p.Val513Ala | . | . | Pkinase_Tyr | De novo | LP | PS2, PM2 | a | |
| AD682–1 | NM_003242 | c.1582C > T | p.Arg528Cys | . | . | De novo | P | PS2, PP3, PM2, PS4_Moderate, PS3_Supporting, PM5 | |||
| AD497 | NM_003242 | c.1609C > T | p.Arg537Cys | . | . | NA | P | PS2, PS3_Moderate, PS4_Moderate, PM2,PP3, PP1_Strong | a | ||
| AD1550 | NM_005902 | c.233_234insGG | p.Ser78fs | . | . | NA | LP | PVS1, PM2 | |||
| AD1736 | NM_005902 | c.365_366insGAATCCCTACCAC | p.Val122fs | . | . | Paternal | LP | PVS1, PM2 | |||
| AD1061 | NM_005902 | c.1041delG | p.Glu347fs | . | . | NA | LP | PVS1, PM2 | |||
| AD792 | NM_005902 | c.1118G > A | p.Arg373His | . | . | VUSLP | PM2, PP3, PS3_Supporting, PS4_Supporting | ||||
| AD1297 | NM_005902 | c.1247C > T | p.Ser416Phe | . | . | De novo | LP | PS2, PM2, PP3 | |||
| AD535 | NM_005901 | c.593dupA | p.His198fs | . | . | De novo | LP | PS2, PM2 | |||
| AD802 | NM_003238 | c.905G > A | p.Arg302His | . | . | TGF_beta | Paternal | VUSLP | PM2, PM5, PP3 | ||
| AD1065 | NM_003239 | c.605_623del | p.Phe202fs | . | . | Maternal | LP | PVS1, PM2 | |||
| AD631–1 | NM_003239 | c.646 + 2 T > G | . | . | Paternal | LP | PVS1, PM2 |
Note: NA not available; MAF in ExAC was the maximal allele frequency from the public version (20160423), and MAF in gnomAD was the maximal allele frequency from gnomAD v2.1.1; P, pathogenic; LP, likely pathogenic; VUS, variant of uncertain significance; a, reported in our previous article [11]; bThis variant was previously classified as VUS, and then upgraded into pathogenic after the father was confirmed to carry a mosaic mutation in the same site; $ This variant was confirmed to be de novo in patient AD1413’s mother
Variants of unknown significance in LDS genes detected in our cohort
| Patient ID | Gene | Transcript | Nucleotide change | Amino acid change | MAF in ExAC | MAF in gnomAD | Domain | Source | Pathogenicity | Evidence | Note |
|---|---|---|---|---|---|---|---|---|---|---|---|
| AD1039 | NM_004612 | c.341C > G | p.Thr114Ser | . | . | VUS | PM2, BP4 | ||||
| AD1248 | NM_004612 | c.439A > G | p.Ile147Val | 0.0000221 | 0.000098 | Pkinase_Tyr | VUS | BP4 | |||
| AD589 | NM_004612 | c.605C > T | p.Ala202Val | . | . | VUS | PM2, PP3 | ||||
| AD823 | NM_004612 | c.767A > G | p.His256Arg | . | . | VUS | PM2, PP3 | ||||
| AD1802 | NM_004612 | c.782G > C | p.Gly261Ala | . | . | VUS | PM2, PP3 | ||||
| AD183 | NM_004612 | c.929C > T | p.Ala310Val | 0.0000221 | 0.0006 | VUS | PP3 | ||||
| AD436 | NM_004612 | c.935G > T | p.Gly312Val | . | . | VUS | PM2, PP3 | ||||
| AD1158 | NM_004612 | c.1054 T > G | p.Leu352Val | . | . | VUS | PM2, PP3 | ||||
| AD1753 | NM_003242 | c.81C > A | p.His27Gln | . | . | NA | VUS | PM2, BP4 | |||
| AD1432 | NM_003242 | c.467G > T | p.Ser156Ile | . | . | VUS | PM2, BP4 | ||||
| AD1348 | NM_003242 | c.578G > A | p.Arg193Gln | 0.000011 | 0.0000544 | TGF_beta | Paternal | VUS | PM2 | ||
| AD1156 | NM_003242 | c.617C > T | p.Thr206Met | 0.0000377 | 0.0006 | VUS | BP4 | ||||
| AD259 | NM_003242 | c.830A > G | p.Lys277Arg | . | . | Pkinase_Tyr | VUS | PM2, PP3 | a | ||
| AD667 | NM_003242 | c.1188 T > G | p.Cys396Trp | . | . | Pkinase_Tyr | VUS | PM2, PP3 | |||
| AD1162 | NM_003242 | c.1254G > T | p.Gln418His | . | . | Pkinase_Tyr | Maternal | VUS | PM2, PP3 | ||
| AD324 | NM_005902 | c.5C > T | p.Ser2Leu | . | . | Paternal | VUS | PM2 | ab | ||
| AD1250 | NM_001145103 | c.53G > A | p.Arg18Gln | . | . | VUS | NA | ||||
| AD76 | NM_005902 | c.140_148del | p.47_50del | . | . | VUS | PM2, PM4, BS2 | a | |||
| AD997 | NM_005902 | c.364G > A | p.Val122Met | . | . | VUS | PM2, PP3 | ||||
| AD850 | NM_005902 | c.773A > T | p.Asp258Val | . | . | VUS | PM2, PP3 | ||||
| AD1288 | NM_005902 | c.1027 T > C | p.Phe343Leu | . | . | VUS | PM2, PP3 | ||||
| AD148 | NM_005902 | c.1027 T > C | p.Phe343Leu | . | . | VUS | PM2, PP3 | ||||
| AD1759 | NM_003238 | c.893G > A | p.Arg298Gln | 0.0000221 | 0.0002 | NA | VUS | NA | |||
| AD1599 | NM_003238 | c.1239C > G | p.Cys413Trp | . | . | VUS | PM2, PP3 | ||||
| AD985 | NM_003239 | c.352 + 5G > A | . | . | VUS | PM2, PP3 |
Note: NA not available; MAF in ExAC was the maximal allele frequency from the public version (20160423), and MAF in gnomAD was the maximal allele frequency from gnomAD v2.1.1; P, pathogenic; LP, likely pathogenic; VUS, variant of uncertain significance; a, reported in our previous article [11]; bThis variant was previously misclassified as likely pathogenic [11], and now corrected into VUS
Fig. 1The pedigree of patient AD1181. Black indicated affected while white indicated unaffected.? represented that the person was suspected to have a sudden death due to an aortopathy
Fig. 2Mosaicism in patient AD257’s family. a, Sanger sequencing indicated an unequal peak height at the mutation site in patient AD257’s father; b, Deep sequencing at the specific location revealed a mosaic mutation in patient AD257’s father
Fig. 3The pedigree of patient AD1162. Black on the top left corner indicated a vascular event, and black on the bottom right corner indicated an ocular event (lens subluxation or retinal detachment).? represented that the person was suspected to have a sudden death due to an aortopathy
Main cardiovascular phenotypic information in two subgroups of LDS
| LP/P | VUSLP | VUS | LP/P | VUSLP | VUS | |
|---|---|---|---|---|---|---|
| Numbers | 26 | 2 | 20 | 3 | 1 | 3 |
| Age, years | 29.5 ± 13.3 | 34.0 ± 4.2 | 38.0 ± 11.5 | 20.3 ± 10.4 | 20 | 43.0 ± 8.5 |
| Normal or mild dilation | 3 | 0 | 4 | 3 | 0 | 0 |
| Surgery due to an aortic aneurysm/valve disease | 8 | 0 | 8 | 0 | 1 | 0 |
| Aortic dissection and related death | 15 | 2 | 8 | 0 | 0 | 3 |
Fig. 4Kaplan–Meier analysis of event-free survival. Event-free survival was compared in probands with P/LP/VUSLP variants (green curve) versus those with VUS (blue curve). a, Events were defined as aortic dissections and related deaths; b, Events were defined as aortic dissections and related death or aortic surgeries