Full data view for gene PLOD1

Ehlers Danlos Syndrome Variant Database


Information The variants shown are described using the NM_000302.3 transcript reference sequence.

262 entries on 3 pages. Showing entries 1 - 100.
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Effect     

Exon     

AscendingDNA change (cDNA)     

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DNA change (genomic) (hg19)     

DNA change (hg38)     

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DB-ID     

Variant remarks     

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ClinVar ID     

dbSNP ID     

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Methylation     

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ID_report     

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Owner     
+/. - c.-2794836_*665135del r.0? p.0? - - Unknown - likely pathogenic g.9200001_12700000del g.9100001_12500000del CGH array deletion in Cr1p36.22 involving NMNAT1 gene, - MTHFR_000084 am apparent homozygous NMNAT1 mutation was found, probably on the other allele PubMed: Ruberto 2020 - - Unknown ? - - 0 - DNA arrayCGH - targeted sequencing with 1 of 4 panels of OFTALMOgenics probes retinal disease 16 PubMed: Ruberto 2020 - ? - Italy - - 0 - - 1 LOVD
+?/+? 10i c.(1097+1_1098-1)_(1328+1_1329-1)del r.(?) p.(Asp367_Val443del) deletion deletion Unknown - likely pathogenic g.? - - - PLOD1_000045 - - - - Unknown - - - 0 - DNA SEQ-NG - - EDS, EDSKSCL1 - - The patient had a positive family history: her younger sister died at 9 years because of spontaneous abdominal aortic rupture. Urinary pyridinoline analysis showed a significantly increased lysyl-pyridinoline to hydroxylysyl-pyridinoline (LH/HP).The technique used was the custom NGS Gene panel. - - - white - 0 - - 1 Anne Legrand
+?/+? 13i c.(1470+1_1471-1)_(1650+1_1651-1)del r.(?) p.(Asp491_Thr550del) deletion deletion Unknown - likely pathogenic g.? - - - PLOD1_000046 - - - - Unknown - - - 0 - DNA SEQ-NG - - EDS, EDSKSCL1 - - The patient had a positive family history: her younger sister died at 9 years because of spontaneous abdominal aortic rupture. Urinary pyridinoline analysis showed a significantly increased lysyl-pyridinoline to hydroxylysyl-pyridinoline (LH/HP).The technique used was the custom NGS Gene panel. - - - white - 0 - - 1 Anne Legrand
+/+ 17 c.[1760_1761delinsGA; 1775_1788del; 1790C>G] r.(?) p.[(Asn587Arg);Gly592Alafs*4;(Pro597Arg)] frameshift other/complex Parent #2 - pathogenic g.[12030731_12030732delinsGA;12030746_12030759del;12030761C>G] - - - PLOD1_000023 - PubMed: Heikkinen et al., 1997 - - Unknown - - +Hgal, -Bsll 0 - DNA, RNA PCR, RT-PCR, SEQ - - EDS, EDSKSCL1 - PubMed: Heikkinen et al., 1997 - - - Germany German - 0 - - 1 Raymond Dalgleish
+?/. - c.2T>C r.(?) p.0? - - Unknown - likely pathogenic (recessive) g.11994838T>C g.11934781T>C - - PLOD1_000100 - - - - Germline - - - 0 - DNA SEQ-NG - CES(Clinical Exome Sequencing) EDS5 - - - F no China - - 0 - - 1 Li Ma
?/. - c.2T>C r.? p.? - - Parent #2 - likely pathogenic g.11994838T>C - - - PLOD1_000100 - - - - Germline - - - - - DNA SEQ-NG - - EDSCV 88 - - F - - - - - - - 1 Sha Hong
-/. - c.76+17C>T r.(=) p.(=) - - Unknown - benign g.11994929C>T g.11934872C>T PLOD1(NM_000302.3):c.76+17C>T - PLOD1_000111 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-?/. - c.76+264A>G r.(=) p.(=) - - Unknown - likely benign g.11995176A>G g.11935119A>G PLOD1(NM_000302.3):c.76+264A>G - PLOD1_000112 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-?/. - c.77-3473C>T r.(=) p.(=) - - Unknown - likely benign g.12004560C>T g.11944503C>T PLOD1(NM_001316320.2):c.77-19C>T - PLOD1_000164 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.77-3383C>T r.(=) p.(=) - - Unknown - likely benign g.12004650C>T - PLOD1(NM_001316320.1):c.148C>T (p.L50=) - PLOD1_000171 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.77-3370G>A r.(=) p.(=) - - Unknown - likely benign g.12004663G>A g.11944606G>A PLOD1(NM_000302.3):c.77-3370G>A - PLOD1_000086 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.77-3358C>T r.(=) p.(=) - - Unknown - likely benign g.12004675C>T g.11944618C>T PLOD1(NM_000302.3):c.77-3358C>T, PLOD1(NM_001316320.2):c.173C>T (p.S58F) - PLOD1_000165 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.77-3358C>T r.(=) p.(=) - - Unknown - likely benign g.12004675C>T - PLOD1(NM_000302.3):c.77-3358C>T, PLOD1(NM_001316320.2):c.173C>T (p.S58F) - PLOD1_000165 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.77-7T>C r.(=) p.(=) - - Unknown - likely benign g.12008026T>C g.11947969T>C PLOD1(NM_000302.3):c.77-7T>C, PLOD1(NM_001316320.2):c.218-7T>C - PLOD1_000113 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-?/. - c.77-7T>C r.(=) p.(=) - - Unknown - likely benign g.12008026T>C g.11947969T>C PLOD1(NM_000302.3):c.77-7T>C, PLOD1(NM_001316320.2):c.218-7T>C - PLOD1_000113 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.77-7T>C r.(=) p.(=) - - Unknown - likely benign g.12008026T>C g.11947969T>C PLOD1(NM_000302.3):c.77-7T>C, PLOD1(NM_001316320.2):c.218-7T>C - PLOD1_000113 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.109G>A r.(?) p.(Glu37Lys) - - Unknown - VUS g.12008065G>A g.11948008G>A PLOD1(NM_000302.3):c.109G>A (p.E37K) - PLOD1_000114 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
?/. - c.128G>A r.(?) p.(Arg43His) - - Unknown - VUS g.12008084G>A g.11948027G>A PLOD1(NM_001316320.1):c.269G>A (p.R90H) - PLOD1_000115 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-?/. - c.135G>A r.(?) p.(Lys45=) - - Unknown - likely benign g.12008091G>A g.11948034G>A PLOD1(NM_000302.3):c.135G>A (p.K45=) - PLOD1_000116 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
?/. - c.136C>T r.(?) p.(Arg46Cys) - - Unknown - VUS g.12008092C>T g.11948035C>T PLOD1(NM_000302.3):c.136C>T (p.R46C) - PLOD1_000117 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
?/. - c.137G>A r.(?) p.(Arg46His) - - Unknown - VUS g.12008093G>A g.11948036G>A PLOD1(NM_000302.3):c.137G>A (p.R46H), PLOD1(NM_000302.4):c.137G>A (p.R46H) - PLOD1_000096 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.137G>A r.(?) p.(Arg46His) - - Unknown - likely benign g.12008093G>A - PLOD1(NM_000302.3):c.137G>A (p.R46H), PLOD1(NM_000302.4):c.137G>A (p.R46H) - PLOD1_000096 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/+ 2 c.145C>T r.(?) p.(Gln49*) nonsense substitution Paternal (confirmed) - pathogenic g.12008101C>T - - - PLOD1_000020 - PubMed: Yeowell et al., 2000 - - Unknown - - -BspCNI 0 - DNA, RNA PCR, RT-PCR, SEQ - - EDS, EDSKSCL1 - PubMed: Yeowell et al., 2000 The PLOD1 variants, c.169C>T and the 15-bp deletion at position c.1123_1137, are both incorrectly described in {PMID10686424:Yeowell et al., 2000}. This is due to incorrect use of an alternative PLOD1 mRNA sequence: GenBank accession M98252. The patient died at the age of 14 due to an arterial rupture.This patient is also described as Cell Line 716 by {PMID10874315:Yeowell et al., 2000}. - - - - - 0 - - 1 Raymond Dalgleish
+/+ 2 c.153_154insC r.(?) p.(Asn52Glnfs*52) frameshift insertion Maternal (confirmed) - pathogenic g.12008109_12008110insC - - - PLOD1_000011 - PubMed: Heikkinen et al., 1999 - - Unknown - - +Mmel 0 - DNA, RNA PCR, RT-PCR, SEQ - - EDS, EDSKSCL1 - PubMed: Heikkinen et al., 1999 - - - United Kingdom (Great Britain) British - 0 - - 1 Raymond Dalgleish
-?/. - c.168+6G>C r.(=) p.(=) - - Unknown - likely benign g.12008130G>C - PLOD1(NM_000302.3):c.168+6G>C - PLOD1_000175 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.169-310A>G r.(=) p.(=) - - Unknown - likely benign g.12009520A>G g.11949463A>G PLOD1(NM_000302.3):c.169-310A>G - PLOD1_000097 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.177C>T r.(?) p.(Gly59=) - - Unknown - benign g.12009838C>T g.11949781C>T PLOD1(NM_000302.3):c.177C>T (p.G59=) - PLOD1_000118 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-?/. - c.243G>A r.(?) p.(Leu81=) - - Unknown - likely benign g.12009904G>A g.11949847G>A PLOD1(NM_000302.3):c.243G>A (p.L81=) - PLOD1_000119 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-?/. - c.243G>A r.(?) p.(Leu81=) - - Unknown - likely benign g.12009904G>A g.11949847G>A PLOD1(NM_000302.3):c.243G>A (p.L81=) - PLOD1_000119 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
+?/. - c.244A>T r.(?) p.(Lys82Ter) - - Unknown - likely pathogenic g.12009905A>T g.11949848A>T PLOD1(NM_000302.3):c.244A>T (p.K82*) - PLOD1_000052 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
+/+ 3 c.244A>T r.(?) p.(Lys82*) nonsense substitution Both (homozygous) - pathogenic g.12009905A>T - - - PLOD1_000052 - PubMed: Micha et al., 2019 - - Unknown - - - 0 - DNA PCR, SEQ - - EDS, EDSKSCL1 P9 PubMed: Micha et al., 2019 - - - - - - 0 - - 1 Raymond Dalgleish
+/+ 3 c.244A>T r.(?) p.(Lys82*) nonsense substitution Both (homozygous) - pathogenic g.12009905A>T - - - PLOD1_000052 - PubMed: van Dijk et al., 2017 - - Unknown - - - 0 - DNA SEQ - - EDS, EDSKSCL1 P1 PubMed: van Dijk et al., 2017 - - - - - - 0 - - 1 Raymond Dalgleish
-/. - c.250G>A r.(?) p.(Ala84Thr) - - Unknown - benign g.12009911G>A g.11949854G>A PLOD1(NM_000302.3):c.250G>A (p.(Ala84Thr), p.A84T) - PLOD1_000121 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-?/. - c.250G>A r.(?) p.(Ala84Thr) - - Unknown - likely benign g.12009911G>A g.11949854G>A PLOD1(NM_000302.3):c.250G>A (p.(Ala84Thr), p.A84T) - PLOD1_000121 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.250G>A r.(?) p.(Ala84Thr) - - Parent #1 - likely benign g.12009911G>A g.11949854G>A - - PLOD1_000121 90 heterozygous; Clinindb (India) PubMed: Narang 2020, Journal: Narang 2020 - rs34878020 Germline - 90/2794 individuals - 0 - DNA arraySNP - Infinium Global Screening Array v1.0 ? - PubMed: Narang 2020, Journal: Narang 2020 analysis 2794 individuals (India) - - India - - 0 - - 90 Mohammed Faruq
-?/. - c.250G>A r.(?) p.(Ala84Thr) - - Both (homozygous) - likely benign g.12009911G>A g.11949854G>A - - PLOD1_000121 1 homozygous; Clinindb (India) PubMed: Narang 2020, Journal: Narang 2020 - rs34878020 Germline - 1/2794 individuals - 0 - DNA arraySNP - Infinium Global Screening Array v1.0 ? - PubMed: Narang 2020, Journal: Narang 2020 analysis 2794 individuals (India) - - India - - 0 - - 1 Mohammed Faruq
+/+ 3 c.254T>C r.(?) p.(Leu85Pro) missense substitution Both (homozygous) - pathogenic g.12009915T>C - - - PLOD1_000035 - PubMed: Rohrbach et al., 2011 - - Unknown - - +MspI, -BpmI 0 - DNA PCR, SEQ - - EDS, EDSKSCL1 P2 PubMed: Rohrbach et al., 2011 - - - Serbia Serbian - 0 - - 1 Raymond Dalgleish
-?/. - c.276G>A r.(?) p.(Glu92=) - - Unknown - likely benign g.12009937G>A g.11949880G>A PLOD1(NM_000302.3):c.276G>A (p.E92=) - PLOD1_000166 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.294C>T r.(?) p.(Phe98=) - - Unknown - benign g.12009955C>T g.11949898C>T PLOD1(NM_000302.3):c.294C>T (p.F98=) - PLOD1_000028 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-/. - c.294C>T r.(?) p.(Phe98=) - - Unknown - benign g.12009955C>T g.11949898C>T PLOD1(NM_000302.3):c.294C>T (p.F98=) - PLOD1_000028 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-/- 3 c.294C>T r.(?) p.(=) silent substitution Unknown - likely benign g.12009955C>T - - - PLOD1_000028 - PubMed: Huang et al., 2009 - rs7529452 Unknown - - +HpyCH4V 0 - DNA SEQ - - ? - PubMed: Huang et al., 2009 A study by {PMID19442614:Huang et al., 2009} reported a significant genotypic/allelic association between the polymorphism and bone mineral density within the chinese population. {PMID16758144:Tasker et al., 2006} also observed a weak association between this SNP and spinal bone mineral density. - - - - - 0 - - 1 Raymond Dalgleish
-/. - c.295G>A r.(?) p.(Ala99Thr) - - Unknown - benign g.12009956G>A g.11949899G>A PLOD1(NM_000302.3):c.295G>A (p.A99T) - PLOD1_000022 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-/. - c.295G>A r.(?) p.(Ala99Thr) - - Unknown - benign g.12009956G>A g.11949899G>A PLOD1(NM_000302.3):c.295G>A (p.A99T) - PLOD1_000022 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-/- 3 c.295G>A r.(?) p.(Ala99Thr) missense substitution Unknown - likely benign g.12009956G>A - - - PLOD1_000022 - PubMed: Tasker et al., 2006 - rs7551175 Unknown - - - 0 - DNA PCR, SEQ - - ? - PubMed: Tasker et al., 2006 A study by {PMID16758144:Tasker et al., 2006} found an association between this PLOD1 variant and bone mineral density for the lumbar spine in a cohort of 678 Scottish women. A similar association is also reported in {PMID17390085:Yamada et al., 2007} found within the Japanese population. Both studies have incorrectly described the variant as 386G>A. - - - - - 0 - - 1 Raymond Dalgleish
+?/- 3 c.295G>A r.(?) p.(Ala99Thr) missense substitution Unknown - VUS g.12009956G>A - - - PLOD1_000022 - PubMed: Tasker et al., 2005 - - Unknown - - - 0 - DNA PCR, SEQ - - ? - PubMed: Tasker et al., 2005 The variant is shown to be associated with decreased lumbar spine bone mineral density measurements, but this only occurs when the variant is heterozygous, not homozygous, in the patient. The authors incorrectly described this variant as G386A, and incorrectly described it as causing a change in codon 99. - - Scotland Scottish - 0 - - 1 Raymond Dalgleish
-?/. - c.302+15G>A r.(=) p.(=) - - Unknown - likely benign g.12009978G>A g.11949921G>A PLOD1(NM_000302.3):c.302+15G>A - PLOD1_000124 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-?/. - c.302+79C>T r.(=) p.(=) - - Unknown - likely benign g.12010042C>T - PLOD1(NM_000302.3):c.302+79C>T - PLOD1_000105 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.303C>T r.(?) p.(Ser101=) - - Unknown - likely benign g.12010414C>T g.11950357C>T PLOD1(NM_000302.3):c.303C>T (p.S101=), PLOD1(NM_000302.4):c.303C>T (p.S101=), PLOD1(NM_001316320.2):c.444C>T (p.S148=) - PLOD1_000167 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.303C>T r.(?) p.(Ser101=) - - Unknown - likely benign g.12010414C>T g.11950357C>T PLOD1(NM_000302.3):c.303C>T (p.S101=), PLOD1(NM_000302.4):c.303C>T (p.S101=), PLOD1(NM_001316320.2):c.444C>T (p.S148=) - PLOD1_000167 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.303C>T r.(?) p.(Ser101=) - - Unknown - likely benign g.12010414C>T g.11950357C>T PLOD1(NM_000302.3):c.303C>T (p.S101=), PLOD1(NM_000302.4):c.303C>T (p.S101=), PLOD1(NM_001316320.2):c.444C>T (p.S148=) - PLOD1_000167 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.303C>T r.(?) p.(Ser101=) - - Unknown - likely benign g.12010414C>T g.11950357C>T PLOD1(NM_000302.3):c.303C>T (p.S101=), PLOD1(NM_000302.4):c.303C>T (p.S101=), PLOD1(NM_001316320.2):c.444C>T (p.S148=) - PLOD1_000167 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.358G>T r.(?) p.(Ala120Ser) - - Unknown - benign g.12010469G>T g.11950412G>T PLOD1(NM_000302.3):c.358G>T (p.A120S), PLOD1(NM_000302.3):c.358_359delGCinsTC (p.A120S) - PLOD1_000030 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.358G>T r.(?) p.(Ala120Ser) - - Unknown - benign g.12010469G>T g.11950412G>T PLOD1(NM_000302.3):c.358G>T (p.A120S), PLOD1(NM_000302.3):c.358_359delGCinsTC (p.A120S) - PLOD1_000030 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/- 4 c.358G>T r.(?) p.(Ala120Ser) missense substitution Unknown - likely benign g.12010469G>T - - - PLOD1_000030 - - - rs2273285 Unknown - - +Hpy188I 0 - DNA SEQ - - ? - - - - - - - - 0 - - 1 Raymond Dalgleish
-/. - c.358G>T r.(?) p.(Ala120Ser) - - Unknown - benign g.12010469G>T - PLOD1(NM_000302.3):c.358G>T (p.A120S), PLOD1(NM_000302.3):c.358_359delGCinsTC (p.A120S) - PLOD1_000030 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.376T>G r.(?) p.(Phe126Val) - - Parent #1 - VUS g.12010487T>G g.11950430T>G - - PLOD1_000092 1 heterozygous, no homozygous; Clinindb (India) PubMed: Narang 2020, Journal: Narang 2020 - rs144702307 Germline - 1/2794 individuals - 0 - DNA arraySNP - Infinium Global Screening Array v1.0 ? - PubMed: Narang 2020, Journal: Narang 2020 analysis 2794 individuals (India) - - India - - 0 - - 1 Mohammed Faruq
-?/. - c.411G>A r.(?) p.(Arg137=) - - Unknown - likely benign g.12010522G>A g.11950465G>A PLOD1(NM_000302.3):c.411G>A (p.R137=), PLOD1(NM_001316320.1):c.552G>A (p.R184=) - PLOD1_000125 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-?/. - c.411G>A r.(?) p.(Arg137=) - - Unknown - likely benign g.12010522G>A g.11950465G>A PLOD1(NM_000302.3):c.411G>A (p.R137=), PLOD1(NM_001316320.1):c.552G>A (p.R184=) - PLOD1_000125 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.412C>G r.(?) p.(Leu138Val) - - Unknown - VUS g.12010523C>G - PLOD1(NM_000302.4):c.412C>G (p.L138V) - PLOD1_000176 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/+ 4 c.426T>A r.(?) p.(Tyr142*) nonsense substitution Parent #1 - pathogenic g.12010537T>A - - - PLOD1_000017 - PubMed: Yeowell et al., 2000 - - Unknown - - +AgeI, -BciVI 0 - DNA, RNA PCR, RT-PCR, SEQ - - EDS, EDSKSCL1 - PubMed: Yeowell et al., 2000 The PLOD1 variants are incorrectly described as 450T>A and 1003C>T in {PMID10874315:Yeowell et al., 2000}. This is due to incorrect use of an alternative PLOD1 mRNA sequence: GenBank accession no. M98252. - - United States North American - 0 - - 1 Raymond Dalgleish
+/+ 4i c.466+1G>A r.? - splicing affected? substitution Both (homozygous) - pathogenic g.12010578G>A - - - PLOD1_000036 - PubMed: Rohrbach et al., 2011 - - Unknown - - -MnlI, -HphI 0 - DNA PCR, SEQ - - EDS, EDSKSCL1 P10 PubMed: Rohrbach et al., 2011 The splice-site variant in this patient is predicted to result in skipping of exon 4. - - Spain Spanish - 0 - - 1 Raymond Dalgleish
?/. - c.467-2A>G r.spl? p.? - - Unknown - VUS g.12012678A>G g.11952621A>G PLOD1(NM_000302.3):c.467-2A>G - PLOD1_000050 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
+?/+? 4i c.467-2A>G r.? - splicing affected? substitution Unknown - likely pathogenic g.12012678A>G - - - PLOD1_000050 - PubMed: Micha et al., 2019 - - Unknown - - - 0 - DNA PCR, SEQ - - EDS, EDSKSCL1 P8 PubMed: Micha et al., 2019 - - - - - - 0 - - 1 Raymond Dalgleish
+/+ 4i c.467-2del r.? - splicing affected? deletion Paternal (confirmed) - pathogenic g.12012678del - - - PLOD1_000010 - PubMed: Heikkinen et al., 1999 - - Unknown - - +BslI, -Acul 0 - DNA, RNA PCR, RT-PCR, SEQ - - EDS, EDSKSCL1 - PubMed: Heikkinen et al., 1999 - - - United Kingdom (Great Britain) British - 0 - - 1 Raymond Dalgleish
-?/. - c.508G>A r.(?) p.(Glu170Lys) - - Unknown - likely benign g.12012721G>A g.11952664G>A PLOD1(NM_001316320.1):c.649G>A (p.E217K) - PLOD1_000127 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-?/. - c.508G>A r.(?) p.(Glu170Lys) - - Unknown - likely benign g.12012721G>A g.11952664G>A PLOD1(NM_001316320.1):c.649G>A (p.E217K) - PLOD1_000127 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.509A>T r.(?) p.(Glu170Val) - - Unknown - likely benign g.12012722A>T g.11952665A>T PLOD1(NM_000302.3):c.509A>T (p.(Glu170Val), p.E170V) - PLOD1_000128 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-?/. - c.509A>T r.(?) p.(Glu170Val) - - Unknown - likely benign g.12012722A>T g.11952665A>T PLOD1(NM_000302.3):c.509A>T (p.(Glu170Val), p.E170V) - PLOD1_000128 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.535G>T r.(?) p.(Asp179Tyr) - - Parent #1 - VUS g.12012748G>T g.11952691G>T - - PLOD1_000093 conflicting interpretations of pathogenicity; 2 heterozygous, no homozygous; Clinindb (India) PubMed: Narang 2020, Journal: Narang 2020 - rs188165334 Germline - 2/2795 individuals - 0 - DNA arraySNP - Infinium Global Screening Array v1.0 ? - PubMed: Narang 2020, Journal: Narang 2020 analysis 2794 individuals (India) - - India - - 0 - - 2 Mohammed Faruq
-?/. - c.535G>T r.(?) p.(Asp179Tyr) - - Unknown - likely benign g.12012748G>T - PLOD1(NM_000302.3):c.535G>T (p.(Asp179Tyr)) - PLOD1_000093 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.540G>A r.(?) p.(Gln180=) - - Unknown - benign g.12012753G>A g.11952696G>A PLOD1(NM_000302.3):c.540G>A (p.Q180=) - PLOD1_000129 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-?/. - c.555G>T r.(?) p.(Lys185Asn) - - Unknown - likely benign g.12012768G>T g.11952711G>T PLOD1(NM_001316320.1):c.696G>T (p.K232N) - PLOD1_000169 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.557T>C r.(?) p.(Ile186Thr) - - Unknown - VUS g.12012770T>C g.11952713T>C PLOD1(NM_001316320.1):c.698T>C (p.I233T) - PLOD1_000170 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.567_572del r.(?) p.(Asp189_Pro190del) - - Unknown - VUS g.12012780_12012785del g.11952723_11952728del PLOD1(NM_000302.3):c.567_572delCCCGGA (p.D189_P190del) - PLOD1_000130 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
+/+ 5i c.579+1G>A r.? - splicing affected? substitution Maternal (confirmed) - pathogenic g.12012793G>A - - - PLOD1_000024 - PubMed: Yeowell and Walker, 1997 - - Unknown - - - 0 - DNA PCR, SEQ, Southern - - EDS, EDSKSCL1 - PubMed: Yeowell and Walker, 1997 The paternally inherited variant is incorrectly described as c.1557C>G in {PMID9220536:Yeowell and Walker, 1997}. This is due to incorrect use of an alternative PLOD1 mRNA sequence: GenBank accession no. M98252.The patient's unaffected younger sibling was one of the first individuals to have a prenatal assessment of EDS VI by mutational anaylsis. This is reported in {PMID9893157:Yeowell and Walker, 1999}; the outcome of the assessment revealed the foetus had inherited the maternal allele containing the splice-site mutation and a normal non-mutated allele from the father. Although a carrier of this disease, the individual was born healthy.The patient is also described as cell line 996 by {PMID10874315:Yeowell et al., 2000}. - - - - - 0 - - 1 Raymond Dalgleish
-?/. - c.579+17G>A r.(=) p.(=) - - Unknown - likely benign g.12012809G>A g.11952752G>A PLOD1(NM_000302.3):c.579+17G>A - PLOD1_000131 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
+/+ 6 c.622C>T r.(?) p.(Gln208*) nonsense substitution Both (homozygous) - pathogenic g.12014929C>T - - - PLOD1_000043 - PubMed: Abdalla et al., 2015 - - Unknown - - - 0 - DNA PCR, SEQ - - EDS, EDSKSCL1 Family 1 PubMed: Abdalla et al., 2015 The parents are first cousins. - - Egypt Egyptian - 0 - - 1 Raymond Dalgleish
-/. - c.644-17T>G r.(=) p.(=) - - Unknown - benign g.12016957T>G g.11956900T>G PLOD1(NM_000302.3):c.644-17T>G - PLOD1_000025 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-/. - c.644-17T>G r.(=) p.(=) - - Unknown - benign g.12016957T>G g.11956900T>G PLOD1(NM_000302.3):c.644-17T>G - PLOD1_000025 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-/- 6i c.644-17T>G r.(?) p.(=) silent substitution Unknown - likely benign g.12016957T>G - - - PLOD1_000025 - PubMed: Spotila et al., 2003 - rs41307745 Unknown - - -HpyCH4III 0 - DNA PCR, SEQ - - ? - PubMed: Spotila et al., 2003 A study by {PMID14565595:Spotila et al., 2003} found an association between this SNP in the PLOD1 gene and bone mineral density in the lumbar spine and femoral neck among a population of European descent. - - - - - 0 - - 1 Raymond Dalgleish
?/. - c.652G>A r.(?) p.(Val218Met) - - Unknown - VUS g.12016982G>A - PLOD1(NM_001316320.1):c.793G>A (p.V265M) - PLOD1_000102 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.680G>A r.(?) p.(Arg227Lys) - - Unknown - VUS g.12017010G>A g.11956953G>A PLOD1(NM_000302.3):c.680G>A (p.R227K) - PLOD1_000062 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+?/. - c.741G>A r.(?) p.(Lys247=) - - Unknown - likely pathogenic g.12017071G>A g.11957014G>A PLOD1(NM_000302.3):c.741G>A (p.K247=) - PLOD1_000053 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/- 7 c.741G>A r.? - silent substitution Unknown - likely benign g.12017071G>A - - - PLOD1_000053 - PubMed: van Dijk et al., 2017 - - Unknown - - - 0 - DNA SEQ-NG, SEQ - - EDS, EDSKSCL1 P2 PubMed: van Dijk et al., 2017 The technique used was the custom NGS Gene panel. - - - - - 0 - - 1 Raymond Dalgleish
-?/. - c.741+261C>T r.(=) p.(=) - - Unknown - likely benign g.12017332C>T - PLOD1(NM_000302.3):c.741+261C>T - PLOD1_000103 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.742-9C>G r.(=) p.(=) - - Unknown - likely benign g.12017890C>G g.11957833C>G PLOD1(NM_000302.3):c.742-9C>G - PLOD1_000133 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-?/. - c.802A>G r.(?) p.(Thr268Ala) - - Unknown - likely benign g.12017959A>G g.11957902A>G PLOD1(NM_000302.3):c.802A>G (p.(Thr268Ala), p.T268A) - PLOD1_000064 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.802A>G r.(?) p.(Thr268Ala) - - Unknown - likely benign g.12017959A>G - PLOD1(NM_000302.3):c.802A>G (p.(Thr268Ala), p.T268A) - PLOD1_000064 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.804C>T r.(?) p.(Thr268=) - - Unknown - likely benign g.12017961C>T g.11957904C>T PLOD1(NM_000302.3):c.804C>T (p.T268=) - PLOD1_000134 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-?/. - c.804C>T r.(?) p.(Thr268=) - - Unknown - likely benign g.12017961C>T g.11957904C>T PLOD1(NM_000302.3):c.804C>T (p.T268=) - PLOD1_000134 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
?/. - c.805G>A r.(?) p.(Val269Met) - - Unknown - VUS g.12017962G>A g.11957905G>A PLOD1(NM_000302.3):c.805G>A (p.V269M) - PLOD1_000135 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-?/. - c.843+17G>C r.(=) p.(=) - - Unknown - likely benign g.12018017G>C g.11957960G>C PLOD1(NM_000302.3):c.843+17G>C - PLOD1_000136 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-?/. - c.844-16G>A r.(=) p.(=) - - Unknown - likely benign g.12018557G>A g.11958500G>A PLOD1(NM_000302.3):c.844-16G>A - PLOD1_000137 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
?/. - c.856C>T r.(?) p.(Pro286Ser) - - Unknown - VUS g.12018585C>T g.11958528C>T PLOD1(NM_000302.3):c.856C>T (p.P286S) - PLOD1_000138 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
-?/. - c.870C>T r.(?) p.(Val290=) - - Unknown - likely benign g.12018599C>T g.11958542C>T PLOD1(NM_000302.3):c.870C>T (p.V290=) - PLOD1_000139 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
+/+ 9 c.926_934del r.(?) p.(Leu309_Leu311del) deletion deletion Paternal (confirmed) - pathogenic g.12018655_12018663del - - - PLOD1_000048 - PubMed: Shin et al., 2020 - - Unknown - - - 0 - DNA SEQ-NG, PCR, SEQ - - EDS, EDSKSCL1 - PubMed: Shin et al., 2020 Compound heterozygous variants resulting in a kyphoscoliotic EDS phenotype were found in two korean siblings. The technique used was the custom NGS Gene panel. - - Korea Korean - 0 - - 1 Raymond Dalgleish
?/. - c.952A>G r.(?) p.(Met318Val) - - Unknown - VUS g.12018681A>G g.11958624A>G - - PLOD1_000087 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/+ 9 c.955C>T r.(?) p.(Arg319*) nonsense substitution Both (homozygous) - pathogenic g.12018684C>T - - - PLOD1_000001 - PubMed: Hyland et al., 1992 - - Unknown - - +AflIII 0 - RNA RT-PCR, SEQ - - EDS, EDSKSCL1 - PubMed: Hyland et al., 1992 According to the pedigree in figure 3, the probands are actually the second (H.A.) and fourth (N.A.) children in the family, rather than the third and fifth, as reported. The parents are first cousins. - - - Turkish(?) - 0 - - 1 Raymond Dalgleish
+/+ 9 c.955C>T r.(?) p.(Arg319*) nonsense substitution Both (homozygous) - pathogenic g.12018684C>T - - - PLOD1_000001 - PubMed: Giunta et al., 2005b - - Unknown - - +AflIII 0 - DNA PCR, SEQ - - EDS, EDSKSCL1 P6 PubMed: Giunta et al., 2005b Patient has consanguineous parents. The PLOD1 variant is incorrectly described as c.845C>T in {PMID15979919:Giunta et al., 2005b}. The correct variant description has been confirmed with the authors. - - - Arab - 0 - - 1 Raymond Dalgleish
+/+ 9 c.955C>T r.(?) p.(Arg319*) nonsense substitution Both (homozygous) - pathogenic g.12018684C>T - - - PLOD1_000001 - PubMed: Giunta et al., 2005a - - Unknown - - +AflIII 0 - DNA PCR, SEQ - - EDS, EDSKSCL1 P1 PubMed: Giunta et al., 2005a The parents of P1 are first cousins. The PLOD1 variant is incorrectly described as c.954CGA>TGA in {PMID15666309:Giunta et al., 2005a}. - - - Arab - 0 - - 1 Raymond Dalgleish
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