Full data view for gene PGAP2

Information The variants shown are described using the NM_001256240.1 transcript reference sequence.

24 entries on 1 page. Showing entries 1 - 24.
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Effect     

Exon     

AscendingDNA change (cDNA)     

RNA change     

Protein     

Allele     

Classification method     

Clinical classification     

DNA change (genomic) (hg19)     

DNA change (hg38)     

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ISCN     

DB-ID     

Variant remarks     

Reference     

ClinVar ID     

dbSNP ID     

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Frequency     

Re-site     

VIP     

Methylation     

Template     

Technique     

Tissue     

Remarks     

Disease     

ID_report     

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Gender     

Consanguinity     

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VIP     

Data_av     

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Panel size     

Owner     
+?/. 2 c.2T>G r.(?) p.(Met1?) Maternal (confirmed) - - g.3832491T>G g.3811261T>G - - PGAP2_000010 - PubMed: Jezela-Stanek et al. 2016 - - Germline - - - 0 - DNA SEQ-NG peripheral blood WES ? - PubMed: Jezela-Stanek 2016 - F no ? (unknown) - - 0 - - 1 Philippe Campeau
+/. - c.2T>G r.(?) p.(Met1?) Maternal (confirmed) - - g.3832491T>G g.3811261T>G - - PGAP2_000010 - PubMed: Pronicka 2016 - - Germline - 1/113 cases - 0 - DNA SEQ, SEQ-NG - WES ? Pat73 PubMed: Pronicka 2016 - F - Poland - - 0 - - 1 Johan den Dunnen
+/. - c.46C>T r.(?) p.(Arg16Trp) Paternal (inferred) - - g.3832535C>T g.3811305C>T - - PGAP2_000003 Substitution in a highly conserved residue. Transfection with protein construct showed partial restoration of GPI-anchored marker proteins. Higer residual activity with this mutation. PubMed: Krawitz et al 2013 - - Germline yes - - 0 - DNA SEQ-NG - - HPMRS-3;GPIBD-8 - PubMed: Krawitz 2013 Index case F no Finland Caucasian - 0 - - 1 Philippe Campeau
?/. - c.53G>A r.(?) p.(Arg18His) Unknown - VUS g.3832542G>A g.3811312G>A PGAP2(NM_001256236.1):c.224G>A (p.R75H) - NUP98_000005 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.165+5945T>C r.(=) p.(=) Unknown - VUS g.3838599T>C g.3817369T>C PGAP2(NM_001256236.1):c.353T>C (p.M118T) - PGAP2_000006 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
?/. - c.165+6112G>A r.(=) p.(=) Unknown - VUS g.3838766G>A g.3817536G>A PGAP2(NM_001256236.1):c.519+1G>A - PGAP2_000007 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
+?/. - c.191C>T r.? p.(Ala64Val) Both (homozygous) - - g.3845138C>T - c.191C>T - PGAP2_000012 Variant Error [EREF/EREF]: This genomic variant does not match the reference sequence; the transcript variant does not match the reference sequence either. Please fix this entry and then remove this message. PubMed: Naseer et al. 2016 - - Germline - - - 0 - DNA SEQ-NG Blood WES HPMRS-3;GPIBD-8 patient_1 PubMed: Naseer 2016 - M yes Saudi Arabia - - 0 - - 2 Philippe Campeau
+?/. - c.191C>T r.? p.(Ala64Val) Unknown - - g.3845138C>T - c.191C>T - PGAP2_000012 Variant Error [EREF/EREF]: This genomic variant does not match the reference sequence; the transcript variant does not match the reference sequence either. Please fix this entry and then remove this message. PubMed: Naseer et al. 2016 - - Germline - - - 0 - DNA SEQ-NG Blood WES HPMRS-3;GPIBD-8 patient_2 PubMed: Naseer 2016 - F yes Saudi Arabia - - 0 - - 1 Philippe Campeau
+?/. - c.220C>T r.(?) p.(Arg74Cys) Both (homozygous) - likely pathogenic g.3845167C>T g.3823937C>T - - PGAP2_000015 - - - - Unknown - - - 0 - DNA SEQ - - ? - - - ? - - - - 0 - - 1 IMGAG
+?/. 3 c.221G>A r.(?) p.(Arg74His) Paternal (confirmed) - - g.3845168G>A g.3823938G>A - - PGAP2_000011 - PubMed: Jezela-Stanek et al. 2016 - - Germline - - - 0 - DNA SEQ-NG peripheral blood WES ? - PubMed: Jezela-Stanek 2016 - F no ? (unknown) - - 0 - - 1 Philippe Campeau
+/. - c.221G>A r.(?) p.(Arg74His) Paternal (confirmed) - - g.3845168G>A g.3823938G>A - - PGAP2_000011 - PubMed: Pronicka 2016 - - Germline - 1/113 cases - 0 - DNA SEQ, SEQ-NG - WES ? Pat73 PubMed: Pronicka 2016 - F - Poland - - 0 - - 1 Johan den Dunnen
./. - c.296A>G r.(?) p.(Tyr99Cys) Both (homozygous) - - g.3845243A>G g.3824013A>G - - PGAP2_000001 Rescue experiments with the altered proteins in PGAP2-deficient Chinese hamster ovary cell lines showed less expression of cell-surface GPI-anchored proteins DAF and CD59 than of the wild-type protein. atient lymphoblastoid cells showed essentially normal expression of the GPI-anchored proteins supporting a hypomorphic effect of this mutation. PubMed: Hansen et al. 2013 - - Germline yes - - 0 - DNA SEQ-NG - - HPMRS-3;GPIBD-8 - PubMed: Hansen 2013 Family with three girls with autosomal recessive hyperphosphatasia with mental retardation-3. F yes Syria African - 0 - - 1 Philippe Campeau
+/. - c.380T>C r.(?) p.(Leu127Ser) Both (homozygous) - - g.3845327T>C g.3824097T>C - - PGAP2_000005 Substitution at highly conserved residue. Transfection of the altered protein constructsinto PGAP2-null cells showed only partial restoration of GPI-anchored marker proteins, CD55 and CD59, on the cell surface. PubMed: Krawitz et al 2013 - - Germline yes - - 0 - DNA SEQ-NG - - HPMRS-3;GPIBD-8 - PubMed: Krawitz et al 2013 Index case M yes Turkey - - 0 - - 1 Philippe Campeau
+/. - c.479C>T r.(?) p.(Thr160Ile) Maternal (confirmed) - - g.3845560C>T g.3824330C>T - - PGAP2_000004 Sustitution at highly conserved residue. Transfection of altered protein construct showed partial restoration of GPI-anchored marker proteins. PubMed: Krawitz et al 2013 - - Germline yes - - 0 - DNA SEQ-NG - - HPMRS-3;GPIBD-8 - PubMed: Krawitz 2013 Index case F no Finland Caucasian - 0 - - 1 Philippe Campeau
?/. - c.525+71C>T r.(=) p.(=) Unknown - VUS g.3845677C>T g.3824447C>T PGAP2(NM_001256237.1):c.767C>T (p.S256L) - PGAP2_000008 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
+/. - c.530G>C r.(?) p.(Arg177Pro) Both (homozygous) - - g.3846254G>C g.3825024G>C - - PGAP2_000002 Substitution between transmembrane segments 3 and 4 in the Golgi lumen. Predicted to be pathogenic. In vitro CHO cells study showed that the mutant protein was expressed but had significantly decreased activity compared to wildtype. Lymphoblastoid cells of patient showed normal levels of DAF and CD59, which suggest a hypomorphic effect. PubMed: Hansen et al 2013 - - Germline yes - - 0 - DNA SEQ-NG - - HPMRS-3;GPIBD-8 - PubMed: Hansen et al 2013 PubMed: Rehman et al 2011 Family with 4 affected siblings. (2 males and 2 females) - yes Pakistan - - 0 - - 1 Philippe Campeau
+/. - c.554G>A r.(?) p.(Arg185Gln) Both (homozygous) - - g.3846278G>A g.3825048G>A NM_001256240.1:c.554G>A, p.(Arg185Gln) - PGAP2_000013 The mutation replaces a highly conserved arginine residue with glutamine within the Frag1 (FGF receptor activating) domain of PGAP2. The mutation was also found to be possibly damaging by Polyphen-2 predictions with a score of 0.942. - - rs745521288 Germline - 0.00000824 in dbSNP. In ExAC database: allele frequency of 0.000008122 - 0 - DNA PCRq, SEQ, SEQ-NG - WES, Homozygosity mapping HPMRS-3;GPIBD-8 IV-3 PubMed: Perez et al., 2017 Consanguineous Bedouin kindred presenting with an autosomal recessive syndrome of intellectual disability and elevated serum alkaline phosphatase.  M yes Saudi Arabia Bedouin >25y 0 - - 1 Philippe Campeau
+/. - c.554G>A r.(?) p.(Arg185Gln) Both (homozygous) - - g.3846278G>A g.3825048G>A NM_001256240.1:c.554G>A, p.(Arg185Gln) - PGAP2_000013 The mutation replaces a highly conserved arginine residue with glutamine within the Frag1 (FGF receptor activating) domain of PGAP2. The mutation was also found to be possibly damaging by Polyphen-2 predictions with a score of 0.942. - - rs745521288 Germline - 0.00000824 in dbSNP. In ExAC database: allele frequency of 0.000008122 - 0 - DNA PCRq, SEQ, SEQ-NG - WES, Homozygosity mapping HPMRS-3;GPIBD-8 IV-5 PubMed: Perez et al., 2017 consanguineous Bedouin kindred presenting with an autosomal recessive syndrome of intellectual disability and elevated serum alkaline phosphatase.  M yes Saudi Arabia Bedouin >18y 0 - - 1 Philippe Campeau
+/. - c.554G>A r.(?) p.(Arg185Gln) Both (homozygous) - - g.3846278G>A g.3825048G>A NM_001256240.1:c.554G>A, p.(Arg185Gln) - PGAP2_000013 The mutation replaces a highly conserved arginine residue with glutamine within the Frag1 (FGF receptor activating) domain of PGAP2. The mutation was also found to be possibly damaging by Polyphen-2 predictions with a score of 0.942. - - rs745521288 Germline - 0.00000824 in dbSNP. In ExAC database: allele frequency of 0.000008122 - 0 - DNA PCRq, SEQ, SEQ-NG - - HPMRS-3;GPIBD-8 IV-6 PubMed: Perez et al., 2017 consanguineous Bedouin kindred presenting with an autosomal recessive syndrome of intellectual disability and elevated serum alkaline phosphatase.  F yes Saudi Arabia Bedouin >15y 0 - - 1 Philippe Campeau
+/. - c.554G>A r.(?) p.(Arg185Gln) Both (homozygous) - - g.3846278G>A g.3825048G>A NM_001256240.1:c.554G>A, p.(Arg185Gln) - PGAP2_000013 The mutation replaces a highly conserved arginine residue with glutamine within the Frag1 (FGF receptor activating) domain of PGAP2. The mutation was also found to be possibly damaging by Polyphen-2 predictions with a score of 0.942. - - rs745521288 Germline - 0.00000824 in dbSNP. In ExAC database: allele frequency of 0.000008122 - 0 - DNA PCRq, SEQ, SEQ-NG - WES, Homozygosity mapping HPMRS-3;GPIBD-8 IV-7 PubMed: Perez et al., 2017 consanguineous Bedouin kindred presenting with an autosomal recessive syndrome of intellectual disability and elevated serum alkaline phosphatase.  F yes Saudi Arabia Bedouin >11y 0 - - 1 Philippe Campeau
+/. - c.560C>T r.(?) p.Ala187Val Both (homozygous) - - g.3846284C>T - - - PGAP2_000014 SIFT=deleterious, Polyphen-2=Probably damaging , CADD score=23.3 Variant Error [EREF/EREF]: This genomic variant does not match the reference sequence; the transcript variant does not match the reference sequence either. Please fix this entry and then remove this message. - - - Germline - - - 0 - DNA SEQ - Gene panel, Sanger seq HPMRS-3;GPIBD-8 U6 PubMed: Reid et al., 2016 Found in a gene panel targeting (614) genes causing inborn errors of metabolism M - - - >02y03m 0 - - 1 Philippe Campeau
?/. - c.567C>T r.(?) p.(Ile189=) Unknown - VUS g.3846291C>T g.3825061C>T PGAP2(NM_001256237.1):c.817C>T (p.Q273*) - NUP98_000006 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.631G>C r.(?) p.(Gly211Arg) Unknown - VUS g.3846355G>C g.3825125G>C - - NUP98_000007 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.635T>C r.(?) p.(Val212Ala) Unknown - VUS g.3846558T>C g.3825328T>C PGAP2(NM_001256236.1):c.989T>C (p.V330A) - PGAP2_000009 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - 0 - - - - - - - - - - - - - - - - - - -
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