Full data view for gene PGAP1

Information The variants shown are described using the NM_024989.3 transcript reference sequence.

37 entries on 1 page. Showing entries 1 - 37.
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Effect     

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AscendingDNA change (cDNA)     

RNA change     

Protein     

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Clinical classification     

DNA change (genomic) (hg19)     

DNA change (hg38)     

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ISCN     

DB-ID     

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ClinVar ID     

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Origin     

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VIP     

Methylation     

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Technique     

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Disease     

ID_report     

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?/. - c.148A>G r.(?) p.(Lys50Glu) Unknown - VUS g.197784874T>C - PGAP1(NM_024989.3):c.148A>G (p.K50E) - PGAP1_000030 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. 2 c.274_276del r.(?) p.(Pro92del) Paternal (confirmed) - pathogenic g.197784747_197784749del g.196920023_196920025del - - PGAP1_000001 variant heterozygous in sister PubMed: Bosch 2015, Journal: Bosch 2015, dear8LOV - - Germline - - - 0 - DNA PCR, SEQ, SEQ-NG - - CVI, ID 26350515-Pat12 PubMed: Bosch 2015, Journal: Bosch 2015, PubMed: Bosch 2016, Journal: Bosch 2016 - M ? Netherlands white - 0 - - 1 Danielle Bosch
?/. - c.331A>G r.(?) p.(Lys111Glu) Unknown - VUS g.197781288T>C g.196916564T>C - - PGAP1_000025 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+?/. - c.334_335insA r.(?) p.(Ala112Aspfs*5) Maternal (confirmed) - likely pathogenic g.197781284_197781285insT g.196916560_196916561insT - - PGAP1_000010 - PubMed: Kettwig et al. 2016 - - Germline - - - 0 - DNA SEQ-NG - WES ? II-1 PubMed: Kettwig 2016 - M no - white - 0 - - 2 Philippe Campeau
+?/. - c.334_335insA r.(?) p.(Ala112Aspfs*5) Maternal (confirmed) - likely pathogenic g.197781284_197781285insT g.196916560_196916561insT - - PGAP1_000010 - PubMed: Kettwig et al. 2016 - - Germline - - - 0 - DNA SEQ-NG - WES - II-2 PubMed: Kettwig 2016 dizygotic twins with ID00155047 M no - white - 0 - - 1 Philippe Campeau
+/. - c.427C>T r.(?) p.(Gln143Ter) Unknown - pathogenic g.197781192G>A g.196916468G>A - - PGAP1_000024 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.492T>G r.(?) p.(Ala164=) Unknown - likely benign g.197777763A>C - PGAP1(NM_024989.3):c.492T>G (p.A164=) - PGAP1_000029 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/+ - c.589_591del r.(?) p.(Leu197del) Both (homozygous) - pathogenic g.197777668_197777670del g.196912944_196912946del - - PGAP1_000005 The mutation was not found in in 372 healthy Syrian adults using Sanger sequencing. Molecular modeling showed that this mutation disrupts the packing of the hydrophobic core and consequently of the entire β-sheet topology, thus leading to a loss of tertiary structure and enzymatic activity. Surface expression of GPI-APs on B-lymphoblastoid cell lines derived from an affected person, parents and controls showed no significant difference. Structural abnormality of GPI-anchors was tested. All GPI-APs on the affected LCLs had abnormal GPI anchors resistant to PI-PLC. This is an indication that the p.Leu197del mutation causes null or almost null activity of the PGAP1 enzyme. GPI-APs on LCLs from heterozygous parents were only partially sensitive to PI-PLC indicating haploinsufficiency. These defective sensitivities were restored by wt-PGAP1 cDNA transfection. PubMed: Murakami et al. 2014 - rs587777378 Germline yes - - 0 - DNA SEQ-NG - - MRT42;GPIBD9 - PubMed: Murakami 2014 Two siblings,4 and 2-year-old, with mental retardation. - yes Syria African - 0 - - 1 Philippe Campeau
-?/. - c.861-14_861-11del r.(=) p.(=) Unknown - likely benign g.197761936_197761939del g.196897212_196897215del PGAP1(NM_001321099.2):c.339-14_339-11delACTT - PGAP1_000028 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+?/. - c.861-2A>G r.spl p.? Both (homozygous) ACMG likely pathogenic g.197761923T>C g.196897199T>C - - PGAP1_000032 ACMG PVS1, PM2 PubMed: Anazi 2017 - - Germline - - - 0 - DNA SEQ-NG - WES ID 13DG1641 PubMed: Anazi 2017 simplex case F yes Saudi Arabia - - 0 - - 1 Johan den Dunnen
-?/. - c.906T>C r.(?) p.(Leu302=) Unknown - likely benign g.197761876A>G g.196897152A>G PGAP1(NM_001321099.2):c.384T>C (p.L128=) - PGAP1_000023 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. 7 c.914C>T r.(?) p.(Ala305Val) Maternal (confirmed) - likely benign g.197761868G>A g.196897144G>A - - PGAP1_000002 - PubMed: Bosch 2015, Journal: Bosch 2015 - - Germline - - - 0 - DNA PCR, SEQ, SEQ-NG - - CVI, ID 26350515-Pat12 PubMed: Bosch 2015, Journal: Bosch 2015, PubMed: Bosch 2016, Journal: Bosch 2016 - M ? Netherlands white - 0 - - 1 Danielle Bosch
-?/. - c.914C>T r.(?) p.(Ala305Val) Unknown - likely benign g.197761868G>A g.196897144G>A PGAP1(NM_024989.4):c.914C>T (p.A305V) - PGAP1_000002 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
+/. 7 c.921_925del r.(?) p.(Lys308Asnfs*25) Maternal (confirmed) - pathogenic g.197761859_197761863del g.196897135_196897139del - - PGAP1_000003 variant not present in sister PubMed: Bosch 2015, Journal: Bosch 2015, PubMed: Bosch 2016, Journal: Bosch 2016 - - Germline - - - 0 - DNA PCR, SEQ, SEQ-NG - - CVI, ID 26350515-Pat12 PubMed: Bosch 2015, Journal: Bosch 2015, PubMed: Bosch 2016, Journal: Bosch 2016 - M ? Netherlands white - 0 - - 1 Danielle Bosch
?/. - c.1089+1G>A r.(?) p.() Unknown - VUS g.197757069C>T g.196892345C>T - - PGAP1_000016 - - - - Unknown - - - 0 - DNA SEQ - - ? - - - F - - - - 0 - - 1 IMGAG
?/. - c.1089+5del r.(?) p.() Unknown - VUS g.197757065del g.196892341del 1089+5delG - PGAP1_000015 - - - - Unknown - - - 0 - DNA SEQ - - ? - - - F - - - - 0 - - 1 IMGAG
+?/. - c.1090-2A>G r.spl? p.? Both (homozygous) - likely pathogenic g.197755637T>C g.196890913T>C - - PGAP1_000012 - PubMed: Granzow et al. 2015 - - Germline - - - 0 - DNA SEQ-NG peripheral blood WES - Patient_1 PubMed: Granzow 2015 - F yes Turkey - - 0 - - 2 Philippe Campeau
+?/. - c.1090-2A>G r.spl? p.? Both (homozygous) - likely pathogenic g.197755637T>C g.196890913T>C - - PGAP1_000012 - PubMed: Granzow et al. 2015 - - Germline - - - 0 - DNA SEQ-NG peripheral blood WES - Patient_2 PubMed: Granzow 2015 - M yes Turkey - - 0 - - 1 Philippe Campeau
+?/. - c.1173G>C r.(=) p.(=) Paternal (confirmed) - likely pathogenic g.197755552C>G g.196890828C>G - - PGAP1_000011 - PubMed: Kettwig et al. 2016 - - Germline - - - 0 - DNA SEQ-NG - WES ? II-1 PubMed: Kettwig 2016 - M no - white - 0 - - 2 Philippe Campeau
+?/. - c.1173G>C r.(=) p.(=) Paternal (confirmed) - likely pathogenic g.197755552C>G g.196890828C>G - - PGAP1_000011 - PubMed: Kettwig et al. 2016 - - Germline - - - 0 - DNA SEQ-NG - WES - II-2 PubMed: Kettwig 2016 dizygotic twins with ID00155047 M no - white - 0 - - 1 Philippe Campeau
+/. - c.1271A>G r.(?) p.(Lys424Arg) Unknown - pathogenic g.197750149T>C g.196885425T>C - - PGAP1_000009 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
+?/. 14 c.1370T>G r.(?) p.(Phe457Cys) Both (homozygous) - likely pathogenic g.197740526A>C g.196875802A>C - - PGAP1_000026 - - - - Germline yes - - 0 - DNA SEQ-NG lymphocytes confimed by Sanger MRT - - - M yes Turkey Kurdish - 0 - - 2 Isabel Filges
+?/. 14 c.1370T>G r.(1370u>g) p.(Phe457Cys) Both (homozygous) - likely pathogenic g.197740526A>C g.196875802A>C - - PGAP1_000026 - - - - Germline yes - - 0 - DNA SEQ-NG lymphocytes confimed by Sanger MRT - - - F yes Turkey Kurdish - 0 - - 1 Isabel Filges
+?/. - c.1396C>T r.(?) p.(Gln466*) Maternal (confirmed) - likely pathogenic g.197740500G>A g.196875776G>A - - PGAP1_000014 - PubMed: Williams et al. 2015 - - Germline - - - 0 - DNA SEQ-NG - WES - - PubMed: Williams 2015 - M no - - - 0 - - 1 Philippe Campeau
+?/. - c.1572T>A r.(?) p.(Tyr524*) Paternal (confirmed) - likely pathogenic g.197737731A>T g.196873007A>T - - PGAP1_000013 - PubMed: Williams et al. 2015 - - Germline - - - 0 - DNA SEQ-NG - WES - - PubMed: Williams 2015 - M no - - - 0 - - 1 Philippe Campeau
?/. - c.1729-4C>T r.spl? p.? Unknown - VUS g.197735707G>A g.196870983G>A - - PGAP1_000022 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.1753C>G r.(?) p.(Gln585Glu) Unknown - likely benign g.197735679G>C g.196870955G>C PGAP1(NM_024989.3):c.1753C>G (p.(Gln585Glu)) - PGAP1_000021 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.1787G>T r.(?) p.(Gly596Val) Unknown - likely benign g.197729785C>A g.196865061C>A PGAP1(NM_024989.3):c.1787G>T (p.(Gly596Val)) - PGAP1_000020 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. - c.1952+1G>T r.spl? p.? Both (homozygous) - pathogenic g.197712670C>A g.196847946C>A - - PGAP1_000004 Functional validation in a knockdown model in zebrafish was performed. Morphants were phenotyped for touch-induced and spontaneous locomotion behavior. Average touch-response distance was blunted in 72-hpf larvae. Immediate touch-response trajectory was reduced. Representative kymographs recording fish position over 30-min recording showed reduced movements per recording. PubMed: Novarino et al. - rs587777202 Germline yes - - 0 - DNA SEQ-NG - - MRT42;GPIBD9 - PubMed: Novarino 2014 4-generation family, 2 affected siblings (9m, 6y) with spastic paraplegia, unaffected heterozygous carrier parents M yes ? (unknown) Middle East - 0 - - 2 Philippe Campeau
-?/. - c.2058C>T r.(?) p.(Leu686=) Unknown - likely benign g.197711819G>A g.196847095G>A PGAP1(NM_001321099.1):c.1536C>T (p.L512=) - PGAP1_000027 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.2189C>T r.(?) p.(Pro730Leu) Unknown - VUS g.197710703G>A g.196845979G>A PGAP1(NM_024989.3):c.2189C>T (p.(Pro730Leu)) - PGAP1_000008 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
?/. - c.2276A>G r.(?) p.(Tyr759Cys) Both (homozygous) - VUS g.197710616T>C g.196845892T>C - - PGAP1_000031 - PubMed: Riazuddin 2017 - - Germline - - - 0 - DNA SEQ, SEQ-NG - WES ID PKMR119 PubMed: Riazuddin 2017 - - yes Pakistan - - 0 - - 1 Johan den Dunnen
-?/. - c.2306G>A r.(?) p.(Ser769Asn) Unknown - likely benign g.197709279C>T g.196844555C>T PGAP1(NM_001321099.1):c.1784G>A (p.S595N) - PGAP1_000019 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.2335G>A r.(?) p.(Val779Met) Unknown - VUS g.197709250C>T g.196844526C>T PGAP1(NM_024989.3):c.2335G>A (p.(Val779Met)) - PGAP1_000007 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
+?/. - c.2349delinsATAATCCCAAACAA r.(?) p.(His783Glnfs*2) Both (homozygous) ACMG likely pathogenic g.197708788delinsTTGTTTGGGATTAT g.196844064delinsTTGTTTGGGATTAT - - PGAP1_000006 - PubMed: Trujillano 2017 - - Germline - - - 0 - DNA SEQ, SEQ-NG - - MRT42;GPIBD9 - PubMed: Trujillano 2017 unaffected parents - - - - - 0 - - 1 Daniel Trujillano
-?/. - c.2408G>A r.(?) p.(Arg803His) Unknown - likely benign g.197708729C>T g.196844005C>T PGAP1(NM_024989.3):c.2408G>A (p.(Arg803His)) - PGAP1_000018 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.2661A>G r.(?) p.(Pro887=) Unknown - likely benign g.197706066T>C - PGAP1(NM_001321099.1):c.2139A>G (p.P713=) - PGAP1_000033 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
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