Full data view for gene VPS53

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

52 entries on 1 page. Showing entries 1 - 52.
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Effect     

Exon     

AscendingDNA change (cDNA)     

RNA change     

Protein     

Allele     

Classification method     

Clinical classification     

DNA change (genomic) (hg19)     

DNA change (hg38)     

Published as     

ISCN     

DB-ID     

Variant remarks     

Reference     

ClinVar ID     

dbSNP ID     

Origin     

Segregation     

Frequency     

Re-site     

VIP     

Methylation     

Template     

Technique     

Tissue     

Remarks     

Disease     

ID_report     

Reference     

Remarks     

Gender     

Consanguinity     

Country     

Population     

Age at death     

VIP     

Data_av     

Treatment     

Panel size     

Owner     
-/. - c.81C>T r.(?) p.(Ile27=) Unknown - benign g.617869G>A g.714629G>A VPS53(NM_001128159.3):c.81C>T (p.I27=) - VPS53_000020 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.219-11T>C r.(=) p.(=) Unknown - benign g.600735A>G g.697495A>G VPS53(NM_001128159.3):c.219-11T>C - VPS53_000014 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. - c.238C>T r.(?) p.(Arg80Ter) Unknown - pathogenic g.600705G>A g.697465G>A VPS53(NM_001128159.3):c.238C>T (p.R80*) - VPS53_000016 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.280C>T r.(?) p.(Arg94Trp) Unknown - VUS g.600663G>A - VPS53(NM_001128159.2):c.280C>T (p.R94W) - VPS53_000025 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.286-1658A>G r.(=) p.(=) Unknown - VUS g.560851T>C g.657611T>C - - VPS53_000005 - - - - Germline - - - - - DNA SEQ-NG-I - - CHTE - PubMed: Sun 2011, Journal: Sun 2011 - M no Netherlands - - - - - 1 Yu Sun
?/. - c.286-1658A>G r.(=) p.(=) Both (homozygous) - VUS g.560851T>C g.657611T>C - - VPS53_000005 - - - - Germline - - - - - DNA SEQ-NG-I - - CHTE - PubMed: Sun 2011, Journal: Sun 2011 - M no Netherlands - - - - - 1 Yu Sun
?/. - c.286-1411A>G r.(=) p.(=) Unknown - VUS g.560604T>C g.657364T>C - - VPS53_000003 - - - - Germline - - - - - DNA SEQ-NG-I - - CHTE - PubMed: Sun 2011, Journal: Sun 2011 - M no Netherlands - - - - - 1 Yu Sun
?/. - c.286-1411A>G r.(=) p.(=) Both (homozygous) - VUS g.560604T>C g.657364T>C - - VPS53_000003 - - - - Germline - - - - - DNA SEQ-NG-I - - CHTE - PubMed: Sun 2011, Journal: Sun 2011 - M no Netherlands - - - - - 1 Yu Sun
?/. - c.286-1028C>T r.(=) p.(=) Unknown - VUS g.560221G>A g.656981G>A - - VPS53_000002 - - - - Germline - - - - - DNA SEQ-NG-I - - CHTE - PubMed: Sun 2011, Journal: Sun 2011 - M no Netherlands - - - - - 1 Yu Sun
?/. - c.286-816A>G r.(=) p.(=) Unknown - VUS g.560009T>C g.656769T>C - - VPS53_000001 - - - - Germline - - - - - DNA SEQ-NG-I - - CHTE - PubMed: Sun 2011, Journal: Sun 2011 - M no Netherlands - - - - - 1 Yu Sun
?/. - c.286-754_286-747del r.(=) p.(=) Unknown - VUS g.559940_559947del g.656700_656707del - - VPS53_000011 - - - - Germline - - - - - DNA SEQ-NG-I - - CHTE - PubMed: Sun 2011, Journal: Sun 2011 - M no Netherlands - - - - - 1 Yu Sun
?/. - c.286-752_286-747del r.(=) p.(=) Both (homozygous) - VUS g.559940_559945del g.656700_656705del - - VPS53_000009 - - - - Germline - - - - - DNA SEQ-NG-I - - CHTE - PubMed: Sun 2011, Journal: Sun 2011 - M no Netherlands - - - - - 1 Yu Sun
?/. - c.286-752_286-747del r.(=) p.(=) Unknown - VUS g.559940_559945del g.656700_656705del - - VPS53_000009 - - - - Germline - - - - - DNA SEQ-NG-I - - CHTE - PubMed: Sun 2011, Journal: Sun 2011 - M no Netherlands - - - - - 1 Yu Sun
?/. - c.286-695T>A r.(=) p.(=) Unknown - VUS g.559888A>T g.656648A>T - - VPS53_000007 - - - - Germline - - - - - DNA SEQ-NG-I - - CHTE - PubMed: Sun 2011, Journal: Sun 2011 - M no Netherlands - - - - - 1 Yu Sun
?/. - c.286-695T>A r.(=) p.(=) Both (homozygous) - VUS g.559888A>T g.656648A>T - - VPS53_000007 - - - - Germline - - - - - DNA SEQ-NG-I - - CHTE - PubMed: Sun 2011, Journal: Sun 2011 - M no Netherlands - - - - - 1 Yu Sun
-?/. - c.522-1122C>T r.(=) p.(=) Unknown - likely benign g.535990G>A - VPS53(NM_001366254.2):c.8C>T (p.(Ser3Leu)) - VPS53_000039 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.863C>T r.(?) p.(Ala288Val) Unknown - VUS g.530438G>A g.627198G>A VPS53(NM_001128159.2):c.950C>T (p.A317V) - VPS53_000021 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.881T>C r.(?) p.(Val294Ala) Unknown - likely benign g.530420A>G - VPS53(NM_001128159.2):c.968T>C (p.V323A) - VPS53_000024 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.988G>C r.(?) p.(Ala330Pro) Unknown - VUS g.526814C>G - VPS53(NM_001128159.2):c.1075G>C (p.A359P) - VPS53_000023 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
./. - c.995G>A r.(?) p.(Arg332His) Unknown - likely pathogenic g.526807C>T g.623567C>T NM_001128159.2(VPS53):c.1082G>A p.(Arg361His) - VPS53_000012 variant could not be associated with disease phenotype PubMed: Vogelaar 2017, Journal: Vogelaar 2017 - - Germline - - - - - DNA SEQ-NG - - cancer, gastric Vogelaar-760A PubMed: Vogelaar 2017, Journal: Vogelaar 2017 54 patients from 53 families with genetically unexplained diffuse-type and intestinal-type gastric cancer - - - - - - - - 1 Marjolijn JL Ligtenberg
-/. - c.1030-3C>T r.spl? p.? Unknown - benign g.505139G>A g.601899G>A VPS53(NM_001128159.3):c.1117-3C>T - VPS53_000019 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.1160C>A r.(?) p.(Pro387Gln) Unknown - VUS g.489576G>T - VPS53(NM_001128159.3):c.1247C>A (p.(Pro416Gln)) - VPS53_000038 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.1227-9dup r.(=) p.(=) Unknown - benign g.466004dup g.562764dup VPS53(NM_001128159.3):c.1314-9dupT - VPS53_000018 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.1367G>T r.(?) p.(Cys456Phe) Unknown - VUS g.465845C>A - VPS53(NM_001128159.3):c.1454G>T (p.(Cys485Phe)) - VPS53_000037 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.1437C>T r.(?) p.(Tyr479=) Unknown - benign g.465775G>A g.562535G>A VPS53(NM_001128159.3):c.1524C>T (p.Y508=) - VPS53_000015 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. - c.1469+5G>A r.spl p.? Parent #1 - pathogenic (recessive) g.465738C>T g.562498C>T - - VPS53_000030 - PubMed: Hady-Cohen 2018 - - Germline - - - - - DNA SEQ, SEQ-NG - WES NDD Fam1 PubMed: Hady-Cohen 2018 2-generation family, 1 affected, unaffected heterozygous carrier parents F - Israel Jewish;Morocco - - - - 1 Johan den Dunnen
+/. - c.1469+5G>A r.spl p.? Paternal (confirmed) - pathogenic (recessive) g.465738C>T g.562498C>T - - VPS53_000030 - PubMed: Feinstein 2014 - - Germline yes - - - - DNA, RNA RT-PCR, SEQ, SEQ-NG - WES NDD Fam2 PubMed: Feinstein 2014 2-generation family, 2 affected sisters, unaffected heterozygous carrier parents F - Israel Jewish;Morocco - - - - 2 Johan den Dunnen
+/. - c.1469+5G>A r.spl p.? Maternal (inferred) - pathogenic (recessive) g.465738C>T g.562498C>T - - VPS53_000030 - PubMed: Feinstein 2014 - - Germline yes - - - - DNA, RNA RT-PCR, SEQ, SEQ-NG - WES NDD Fam3 PubMed: Feinstein 2014 2-generation family, 2 affected brothers, unaffected heterozygous carrier mother M - Israel Jewish;Morocco - - - - 2 Johan den Dunnen
+/. - c.1469+5G>A r.spl p.? Parent #1 - pathogenic (recessive) g.465738C>T g.562498C>T - - VPS53_000030 - PubMed: Feinstein 2014 - - Germline yes - - - - DNA, RNA RT-PCR, SEQ, SEQ-NG - WES NDD Fam4 PubMed: Feinstein 2014 4-generation family, 5 affected (2F, 3M), unaffected heterozygous carrier parents F;M no Israel Jewish;Morocco - - - - 5 Johan den Dunnen
+/. - c.1469+5G>A r.spl p.? Parent #1 - pathogenic (recessive) g.465738C>T g.562498C>T - - VPS53_000030 - PubMed: Feinstein 2014 - - Germline - 2/156 control individuals - - - DNA, RNA RT-PCR, SEQ, SEQ-NG - WES Healthy/Control controls PubMed: Feinstein 2014 analysis 156 controls F - Israel Jewish;Morocco - - - - 2 Johan den Dunnen
+/. - c.1469+5G>A r.spl p.? Parent #1 - pathogenic (recessive) g.465738C>T g.562498C>T - - VPS53_000030 - PubMed: Hady-Cohen 2018 - - Germline - - - - - DNA SEQ, SEQ-NG - WES NDD Fam2 PubMed: Hady-Cohen 2018 2-generation family, 1 affected, unaffected heterozygous carrier parents M - Israel Jewish;Morocco - - - - 1 Johan den Dunnen
-?/. - c.1587G>A r.(?) p.(Thr529=) Unknown - likely benign g.463696C>T - VPS53(NM_001128159.2):c.1674G>A (p.T558=) - VPS53_000029 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.1647T>C r.(?) p.(Asp549=) Unknown - likely benign g.456673A>G - VPS53(NM_001128159.2):c.1734T>C (p.D578=) - VPS53_000035 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.1691C>T r.(?) p.(Thr564Met) Unknown - VUS g.456629G>A - VPS53(NM_001128159.3):c.1778C>T (p.(Thr593Met), p.T593M) - VPS53_000027 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.1691C>T r.(?) p.(Thr564Met) Unknown - VUS g.456629G>A - VPS53(NM_001128159.3):c.1778C>T (p.(Thr593Met), p.T593M) - VPS53_000027 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.1707C>T r.(?) p.(Ile569=) Unknown - likely benign g.455184G>A g.551944G>A VPS53(NM_001128159.2):c.1794C>T (p.I598=) - VPS53_000022 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.1744G>A r.(?) p.(Ala582Thr) Unknown - likely benign g.455147C>T - VPS53(NM_001128159.2):c.1831G>A (p.A611T) - VPS53_000028 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.1858G>T r.(?) p.(Val620Phe) Unknown - VUS g.440338C>A - - - VPS53_000041 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.1959C>T r.(?) p.(Leu653=) Unknown - likely benign g.436121G>A - VPS53(NM_001128159.2):c.2046C>T (p.L682=), VPS53(NM_001128159.3):c.2046C>T (p.(Leu682=)) - VPS53_000034 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.1959C>T r.(?) p.(Leu653=) Unknown - likely benign g.436121G>A - VPS53(NM_001128159.2):c.2046C>T (p.L682=), VPS53(NM_001128159.3):c.2046C>T (p.(Leu682=)) - VPS53_000034 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
+/. - c.1997A>G r.(?) p.(Gln666Arg) Parent #2 - pathogenic (recessive) g.436083T>C g.532843T>C - - VPS53_000031 - PubMed: Hady-Cohen 2018 - - Germline - - - - - DNA SEQ, SEQ-NG - WES NDD Fam1 PubMed: Hady-Cohen 2018 2-generation family, 1 affected, unaffected heterozygous carrier parents F - Israel Jewish;Morocco - - - - 1 Johan den Dunnen
+/. - c.1997A>G r.(?) p.(Gln666Arg) Maternal (confirmed) - pathogenic (recessive) g.436083T>C g.532843T>C - - VPS53_000031 - PubMed: Feinstein 2014 - - Germline yes - - - - DNA, RNA RT-PCR, SEQ, SEQ-NG - WES NDD Fam2 PubMed: Feinstein 2014 2-generation family, 2 affected sisters, unaffected heterozygous carrier parents F - Israel Jewish;Morocco - - - - 2 Johan den Dunnen
+/. - c.1997A>G r.(?) p.(Gln666Arg) Maternal (confirmed) - pathogenic (recessive) g.436083T>C g.532843T>C - - VPS53_000031 - PubMed: Feinstein 2014 - - Germline yes - - - - DNA, RNA RT-PCR, SEQ, SEQ-NG - WES NDD Fam3 PubMed: Feinstein 2014 2-generation family, 2 affected brothers, unaffected heterozygous carrier mother M - Israel Jewish;Morocco - - - - 2 Johan den Dunnen
+/. - c.1997A>G r.(?) p.(Gln666Arg) Parent #2 - pathogenic (recessive) g.436083T>C g.532843T>C - - VPS53_000031 - PubMed: Feinstein 2014 - - Germline yes - - - - DNA, RNA RT-PCR, SEQ, SEQ-NG - WES NDD Fam4 PubMed: Feinstein 2014 4-generation family, 5 affected (2F, 3M), unaffected heterozygous carrier parents F;M no Israel Jewish;Morocco - - - - 5 Johan den Dunnen
+/. - c.1997A>G r.(?) p.(Gln666Arg) Unknown - pathogenic (recessive) g.436083T>C g.532843T>C - - VPS53_000031 - PubMed: Feinstein 2014 - - Germline - 2/143 control individuals - - - DNA, RNA RT-PCR, SEQ, SEQ-NG - WES Healthy/Control controls PubMed: Feinstein 2014 analysis 143 controls F - Israel Jewish;Morocco - - - - 2 Johan den Dunnen
+/. - c.1997A>G r.(?) p.(Gln666Arg) Parent #2 - pathogenic (recessive) g.436083T>C g.532843T>C - - VPS53_000031 - PubMed: Hady-Cohen 2018 - - Germline - - - - - DNA SEQ, SEQ-NG - WES NDD Fam2 PubMed: Hady-Cohen 2018 2-generation family, 1 affected, unaffected heterozygous carrier parents M - Israel Jewish;Morocco - - - - 1 Johan den Dunnen
+/. - c.1997A>G r.(?) p.(Gln666Arg) Both (homozygous) - pathogenic (recessive) g.436083T>C g.532843T>C - - VPS53_000031 - PubMed: Hausman-Kedem 2019 - - Germline yes - - - - DNA SEQ - WES NDD family PubMed: Hausman-Kedem 2019 3-generation family, 2 affected sisters, unaffected heterozygous carrier parents F no Israel Jewish;Morocco - - - - 2 Johan den Dunnen
?/. - c.*11162A>C r.(=) p.(=) Unknown - VUS g.424905T>G - VPS53(NM_001128159.3):c.2159A>C (p.K720T) - VPS53_000026 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.*12912C>G r.(=) p.(=) Unknown - VUS g.423155G>C - VPS53(NM_001128159.3):c.2239C>G (p.(His747Asp)) - VPS53_000040 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-?/. - c.*12926G>A r.(=) p.(=) Unknown - likely benign g.423141C>T - VPS53(NM_001128159.2):c.2253G>A (p.V751=) - VPS53_000033 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
-/. - c.*13016A>G r.(=) p.(=) Unknown - benign g.423051T>C g.519811T>C VPS53(NM_001128159.3):c.2328+15A>G - VPS53_000017 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
?/. - c.*13658C>T r.(=) p.(=) Unknown - VUS g.422409G>A - VPS53(NM_001128159.2):c.2458C>T (p.R820C) - VPS53_000032 VKGL data sharing initiative Nederland - - - CLASSIFICATION record - - - - - - - - - - - - - - - - - - - - - - -
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