Legend
Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column's header and hold it still. Below, a more detailed description is shown per column.
Effect: The variant's effect on the function of the gene/protein, displayed in the format 'R/C'. R is the value reported by the source (publication, submitter) and this classification may vary between records. C is the value concluded by the curator. Note that in some database the curator uses Summary records to give details on the classification of the variant.Values used: '+' indicating the variant affects function, '+?' probably affects function, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect was not classified.
Exon: number of exon/intron containing variant; 2 = exon 2, 12i = intron 12, 2i_7i = from intron 2 to intron 7, 8i_9 = intron 8/exon 9 boundary, _1 = 5' to exon 1, 18_ = 3' of exon 18, _1_18_ = encompassing the entire 18-exon gene
DNA change (cDNA): description of variant at DNA level, based on a coding DNA reference sequence (following HGVS recommendations); e.g. c.123C>T, c.123_145del, c.123_126dup. For deletions/duplications extending beyond the reference transcript resp. {0}/{2} is used to replace del/dup. Extent of the deletion/duplication should be specified using the genomic description (g.). "-" indicates the variant described on genomic level does not affect the coding DNA reference sequence.
RNA change: description of variant at RNA level (following HGVS recommendations).
- r.123c>u
- r.? = unknown
- r.(?) = RNA not analysed but probably transcribed copy of DNA variant
- r.spl? = RNA not analysed but variant probably affects splicing
- r.(spl?) = RNA not analysed but variant may affect splicing
- r.0? = change expected to abolish transcription
Protein: description of variant at protein level (following HGVS recommendations).
- p.(Arg345Pro) = change predicted from DNA (RNA not analysed)
- p.Arg345Pro = change derived from RNA analysis
- p.? = unknown effect
- p.0? = probably no protein produced
Allele: On which allele is the variant located? Does not necessarily imply inheritance! 'Paternal' (confirmed or inferred), 'Maternal' (confirmed or inferred), 'Parent #1' or #2 for compound heterozygosity without having screened the parents, 'Unknown' for heterozygosity without having screened the parents, 'Both' for homozygozity.
Classification method: The method used for the clinical classification of this variant.
All options:
- ACMG
- ACGS
- EAHAD-CFDB
- ENIGMA
- IARC
- InSiGHT
- kConFab
- other
Clinical classification: Clinical classification of variant, preferably based on standardised criteria (e.g. ACMG), directed on the clinical consequences as published/submitted, indicated using an enriched system including inheritance: e.g. pathogenic, pathogenic (dominant), pathogenic (recessive), pathogenic (!), pathogenic (maternal), pathogenic (paternal). Standard inheritance is covered by dominant/recessive, imprinting by maternal/paternal. A '!' warns for exceptional circumstances to be explained in the 'Remarks' field (low penetrance, variants pathogenic in heterozygous state only, hypomorphic/hypermorphic variants, protective variants, etc.). Non-disease consequences (e.g. drug metabolism (pharmacogenetics), risk factor, blood group, tasting bitter) are indicated using additions to the benign classification; benign (dominant), benign (recessive), benign (!), etc. The value 'association' is used for variants associated with a phenotype and 'NA' for variants from in vitro/in silico records. NOTE: classification may differ from the opinion of the curator as given in a variant SUMMARY-record or the 'Functional effect concluded'). NOTE: pathogenic/likely pathogenic should go together with "variant (probably) affects function" In ClassFunctional.
All options:
- pathogenic
- pathogenic (dominant)
- pathogenic (recessive)
- pathogenic (!)
- pathogenic (maternal)
- pathogenic (paternal)
- likely pathogenic
- likely pathogenic (dominant)
- likely pathogenic (recessive)
- likely pathogenic (!)
- likely pathogenic (maternal)
- likely pathogenic (paternal)
- VUS
- VUS (!)
- likely benign
- likely benign (dominant)
- likely benign (recessive)
- likely benign (!)
- likely benign (maternal)
- likely benign (paternal)
- benign
- benign (dominant)
- benign (recessive)
- benign (!)
- benign (maternal)
- benign (paternal)
- association
- unclassified
- NA
DNA change (genomic) (hg19): HGVS description of variant at DNA level, based on the genomic (chromosomal) DNA reference sequence; e.g. g.12345678C>T, g.12345679del, g.12345678_12345890dup
DNA change (hg38): HGVS description of variant at DNA level, based on the hg38 genomic (chromosomal) eference sequence; e.g. g.12345678C>T, g.12345679del, g.12345678_12345890dup
Published as: listed only when different from "DNA change"; variant as reported originally (e.g. 521delT). Variants seen in animal models, tested in vitro, predicted from RNA analysis, etc. are described between brackets like c.(456C>G)
ISCN: description of the variant according to ISCN nomenclature
DB-ID: database ID of variant, grouping multiple observations of the same variant together, starting with the HGNC gene symbol, followed by an underscore (_) and a six digit number (e.g. DMD_012345). _000000 is used for variants where DNA was not analysed (change predicted from RNA analysis), variants seen in animal models or variants not seen in humans but functionally tested in vitro
Variant remarks: remarks regarding variant described, e.g. germline mosaicism in mother, 345 kb deletion, muscle RNA analysed, not in 200 control chromosomes tested, on founder haplotype, etc.
Reference: publication describing the variant submitted, incl. links to OMIM, PubMed or other source, e.g. "den Dunnen ASHG2003 P2346"
ClinVar ID: ID of variant in ClinVar database
dbSNP ID: the dbSNP ID
Origin: Origin of variant/record: Germline = in all cells, De novo = in all cells, but not in either parent, Germline/De novo (untested) = in all cells, parents not tested (use only when De novo is likely, e.g. isolated/sporadic cases with dominant disease), Somatic = present in a subset of cells, but not in either parent, Uniparental disomy = from parental disomy (maternal or paternal), CLASSIFICATION record = submitter only sharing variant classification (note another report may share Individual data), SUMMARY record = master summary record from curator (may link to another database), In vitro (cloned) = data resulting from in vitro functional assays, animal model = data from animal model, Artefact = false positive variant call, DUPLICATE record = variant already described on another chromosome (e.g. unbalanced translocation, duplicating transposition, 2nd fusion transcript, etc.)
All options:
- Germline
- De novo
- Germline/De novo (untested)
- Somatic
- Uniparental disomy
- Uniparental disomy, maternal allele
- Uniparental disomy, paternal allele
- CLASSIFICATION record
- SUMMARY record
- In vitro (cloned)
- In silico
- animal model
- Artefact
- DUPLICATE record
- Unknown
- Not applicable
Segregation: Indicates whether the variant segregates with the phenotype (yes), does not segregate with the phenotype (no) or segregation is unknown (?)
All options:
- ? = unknown
- yes = segregates with phenotype
- no = does not segregate with phenotype
- - = not applicable
Frequency: frequency in which the variant was found; e.g 5/760 chromosomes (in 5 of 760 chromosomes tested), 1/33 patients (in 1 of 33 patients analysed in study), 0.05 controls (in 5% of control cases tested)
Re-site: restriction enzyme recognition site created (+) or destroyed (-); e.g. BglII+;BamHI-
VIP: variant VIP-status was requested for matchmaking - need collaboration(s) to crack the case - please contact the submitter/curator.
NOTE: to get VIP status ask the curator.
Methylation: result of methylation test; GOM (gain of methylation), LOM (loss of methylation), 30% (30% methylated). NOTE: when several tests were done mention the method as well (e.g. MS-PCR 75%)

 Effect
|

 Exon
|

 DNA change (cDNA)
|

 RNA change
|

 Protein
|

 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
|

 Owner
|
?/. |
- |
c.-39951del |
r.(?) |
p.(=) |
- |
VUS |
g.37884223del |
g.39727970del |
ERBB2(NM_001289936.1):c.3649delG (p.A1217Lfs*70) |
- |
ERBB2_000012 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Rotterdam |
-/. |
- |
c.-39770G>C |
r.(?) |
p.(=) |
- |
benign |
g.37884037C>G |
g.39727784C>G |
ERBB2(NM_001005862.2):c.3418C>G (p.P1140A) |
- |
ERBB2_000004 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
0 |
- |
VKGL-NL_Groningen |
-?/. |
- |
c.-39429G>A |
r.(?) |
p.(=) |
- |
likely benign |
g.37883696C>T |
- |
ERBB2(NM_001289936.1):c.3263C>T (p.T1088I) |
- |
ERBB2_000017 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Rotterdam |
-?/. |
- |
c.-38874C>T |
r.(?) |
p.(=) |
- |
likely benign |
g.37883141G>A |
g.39726888G>A |
ERBB2(NM_001289936.1):c.2999G>A (p.G1000E) |
- |
ERBB2_000015 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Rotterdam |
-?/. |
- |
c.-37694A>C |
r.(?) |
p.(=) |
- |
likely benign |
g.37881961T>G |
g.39725708T>G |
ERBB2(NM_001289936.1):c.2682T>G (p.G894=) |
- |
ERBB2_000003 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
0 |
- |
VKGL-NL_Rotterdam |
?/. |
- |
c.-27878G>A |
r.(?) |
p.(=) |
- |
VUS |
g.37872145C>T |
g.39715892C>T |
ERBB2(NM_001289936.1):c.1421C>T (p.P474L) |
- |
ERBB2_000010 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Rotterdam |
?/. |
- |
c.-27447G>A |
r.(?) |
p.(=) |
- |
VUS |
g.37871714C>T |
g.39715461C>T |
ERBB2(NM_001289936.1):c.1193C>T (p.S398L) |
- |
ERBB2_000009 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Rotterdam |
-?/. |
- |
c.-27280G>T |
r.(?) |
p.(=) |
- |
likely benign |
g.37871547C>A |
g.39715294C>A |
ERBB2(NM_001289936.1):c.1112C>A (p.A371D) |
- |
ERBB2_000008 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Rotterdam |
-/. |
- |
c.-24448G>A |
r.(?) |
p.(=) |
- |
benign |
g.37868715C>T |
g.39712462C>T |
ERBB2(NM_001005862.2):c.1058+14C>T |
- |
ERBB2_000001 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
0 |
- |
VKGL-NL_Groningen |
-?/. |
- |
c.-21866G>C |
r.(?) |
p.(=) |
- |
likely benign |
g.37866133C>G |
g.39709880C>G |
ERBB2(NM_001289936.1):c.597C>G (p.S199R) |
- |
ERBB2_000007 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Rotterdam |
-?/. |
- |
c.100C>T |
r.(?) |
p.(Leu34=) |
- |
likely benign |
g.37844168G>A |
g.39687915G>A |
PGAP3(NM_033419.4):c.100C>T (p.L34=) |
- |
ERBB2_000014 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Rotterdam |
-?/. |
- |
c.124T>G |
r.(?) |
p.(Ser42Ala) |
- |
likely benign |
g.37844144A>C |
- |
PGAP3(NM_033419.3):c.124T>G (p.(Ser42Ala)) |
- |
ERBB2_000016 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Leiden |
?/. |
- |
c.200A>G |
r.(?) |
p.(Asp67Gly) |
- |
VUS |
g.37842254T>C |
g.39686001T>C |
PGAP3(NM_033419.4):c.200A>G (p.D67G) |
- |
ERBB2_000013 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Rotterdam |
+/. |
- |
c.275G>A |
r.(?) |
p.(Gly92Asp) |
- |
pathogenic |
g.37842179C>T |
g.39685926C>T |
- |
- |
PGAP3_000001 |
This mutation causes a substitution at a highly conserved residue in a juxtamembrane position on the luminal side. This mutation was absent in the Exome Variant Server, dbSNP (build 137), or 1000 Genomes Project databases, or in 108 ethnically matched controls. CHO cells showed that the mutant G92D protein had almost no or absent enzyme activity. Mutant PGAP3 cDNA bearing G92D did not reduce or reduced only slightly the surface levels of CD59, CD55 and uPAR indicating that the substitution caused a null or nearly null phenotype. |
PubMed: Howard et al. 2014 |
- |
rs587777251 |
Germline |
yes |
- |
- |
0 |
- |
Philippe Campeau |
+/. |
3 |
c.314C>A |
r.(?) |
p.(Pro105Gln) |
- |
pathogenic |
g.37840968G>T |
g.39684715G>T |
- |
- |
PGAP3_000022 |
Missense variant. This mutation was predicted as pathogenic by the in silico software: SIFT=0, PolyPhen2=1, and MutationTaster=disease causing. This new mutation was inherited from both unaffected carrier parents. |
- |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+/. |
- |
c.314C>G |
r.(?) |
p.(Pro105Arg) |
- |
pathogenic |
g.37840968G>C |
g.39684715G>C |
- |
- |
PGAP3_000004 |
Substitution at a highly conserved residue in the first transmembrane domain. The mutation was absent in 52 Arabic controls or in the Exome Variant Server database. CHO cells showed that the mutant P105R protein had low residual enzyme activity. Electrophoresis and immunoblotting studies showed that the P105R protein had only immature ER-form N-glycan and did not localize properly to the Golgi, but was retained in the ER. |
PubMed: Howard et al. 2014 |
- |
rs371549948 |
Germline |
yes |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.320C>T |
r.(?) |
p.(Ser107Leu) |
- |
likely pathogenic |
g.37840962G>A |
g.39684709G>A |
- |
- |
PGAP3_000011 |
- |
PubMed: Knaus et al. 2016 |
- |
- |
Unknown |
- |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.320C>T |
r.(?) |
p.(Ser107Leu) |
- |
likely pathogenic |
g.37840962G>A |
g.39684709G>A |
- |
- |
PGAP3_000011 |
- |
PubMed: Knaus et al. 2016 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.320C>T |
r.(?) |
p.(Ser107Leu) |
- |
likely pathogenic |
g.37840962G>A |
g.39684709G>A |
- |
- |
PGAP3_000011 |
- |
PubMed: Pagnamenta et al. 2017 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.320C>T |
r.(?) |
p.(Ser107Leu) |
- |
likely pathogenic |
g.37840962G>A |
g.39684709G>A |
- |
- |
PGAP3_000011 |
- |
PubMed: Pagnamenta et al. 2017 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+/. |
2 |
c.320C>T |
r.(?) |
p.(Ser107Leu) |
- |
pathogenic |
g.37840962G>A |
g.39684709G>A |
- |
- |
PGAP3_000011 |
Missense mutation. The wild type S107 residue is more hydrophobic and smaller than the mutant residue. This mutation will affect the hydrophobic interactions with the lipid membrane and protein function. |
- |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+/. |
2 |
c.320C>T |
r.(?) |
p.(Ser107Leu) |
- |
pathogenic |
g.37840962G>A |
g.39684709G>A |
- |
- |
PGAP3_000011 |
Missense mutation. The wild type S107 residue is more hydrophobic and smaller than the mutant residue. This mutation will affect the hydrophobic interactions with the lipid membrane and protein function. |
- |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.402dup |
r.(?) |
p.(Met135Hisfs*28) |
- |
likely pathogenic |
g.37840884dup |
g.39684631dup |
- |
- |
PGAP3_000013 |
- |
PubMed: Knaus et al. 2016 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.402dup |
r.(?) |
p.(Met135Hisfs*28) |
- |
likely pathogenic |
g.37840884dup |
g.39684631dup |
- |
- |
PGAP3_000013 |
- |
PubMed: Abdel-Hamid et al. 2017 |
- |
- |
Germline |
yes |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.402dup |
r.(?) |
p.(Met135Hisfs*28) |
- |
likely pathogenic |
g.37840884dup |
g.39684631dup |
- |
- |
PGAP3_000013 |
- |
PubMed: Abdel-Hamid et al. 2017 |
- |
- |
Germline |
yes |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.402dup |
r.(?) |
p.(Met135Hisfs*28) |
- |
likely pathogenic |
g.37840884dup |
g.39684631dup |
- |
- |
PGAP3_000013 |
- |
PubMed: Abdel-Hamid et al. 2017 |
- |
- |
Germline |
yes |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.402dup |
r.(?) |
p.(Met135Hisfs*28) |
- |
likely pathogenic |
g.37840884dup |
g.39684631dup |
- |
- |
PGAP3_000013 |
- |
PubMed: Abdel-Hamid et al. 2017 |
- |
- |
Germline |
yes |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.402dup |
r.(?) |
p.(Met135Hisfs*28) |
- |
likely pathogenic |
g.37840884dup |
g.39684631dup |
- |
- |
PGAP3_000013 |
- |
PubMed: Abdel-Hamid et al. 2017 |
- |
- |
Germline |
yes |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.402dup |
r.(?) |
p.(Met135Hisfs*28) |
- |
likely pathogenic |
g.37840884dup |
g.39684631dup |
- |
- |
PGAP3_000013 |
- |
PubMed: Abdel-Hamid et al. 2017 |
- |
- |
Germline |
yes |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.402dup |
r.(?) |
p.(Met135Hisfs*28) |
- |
likely pathogenic |
g.37840884dup |
g.39684631dup |
- |
- |
PGAP3_000013 |
- |
PubMed: Abdel-Hamid et al. 2017 |
- |
- |
Germline |
yes |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.402dup |
r.(?) |
p.(Met135Hisfs*28) |
- |
likely pathogenic |
g.37840884dup |
g.39684631dup |
- |
- |
PGAP3_000013 |
- |
PubMed: Abdel-Hamid et al. 2017 |
- |
- |
Germline |
yes |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.402dup |
r.(?) |
p.(Met135Hisfs*28) |
- |
likely pathogenic |
g.37840884dup |
g.39684631dup |
- |
- |
PGAP3_000013 |
- |
PubMed: Abdel-Hamid et al. 2017 |
- |
- |
Germline |
yes |
- |
- |
0 |
- |
Philippe Campeau |
-?/. |
- |
c.404T>C |
r.(?) |
p.(Met135Thr) |
- |
likely benign |
g.37840878A>G |
g.39684625A>G |
PGAP3(NM_033419.3):c.404T>C (p.(Met135Thr)) |
- |
PGAP3_000007 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
0 |
- |
VKGL-NL_Leiden |
+/. |
- |
c.432+1G>A |
r.spl |
p.? |
ACMG |
pathogenic (recessive) |
g.37840849C>T |
g.39684596C>T |
- |
- |
PGAP3_000030 |
- |
PubMed: Hu 2019 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Johan den Dunnen |
+/. |
- |
c.439dup |
r.(?) |
p.(Leu147Profs*16) |
- |
pathogenic |
g.37830928dup |
g.39674675dup |
- |
- |
PGAP3_000003 |
In vitro functional expression studies in CHO cells showed that the mutant c.439dupC mutant had no residual enzyme activity, and was likely degraded by nonsense-mediated mRNA decay. Flow cytometric analysis of patient cells showed a reduction in the cell surface levels of GPI-anchored proteins. |
PubMed: Howard et al. 2014 |
- |
- |
Germline |
yes |
- |
- |
0 |
- |
Philippe Campeau |
-?/. |
- |
c.495+10C>T |
r.(=) |
p.(=) |
- |
likely benign |
g.37830860G>A |
- |
PGAP3(NM_033419.4):c.495+10C>T |
- |
PGAP3_000029 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Rotterdam |
?/. |
- |
c.496-9_496-8insCAGAGTA |
r.(=) |
p.(=) |
- |
VUS |
g.37830315_37830316insTACTCTG |
g.39674062_39674063insTACTCTG |
- |
- |
PGAP3_000027 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Nijmegen |
+/. |
5 |
c.507C>A |
r.(?) |
p.(Tyr169*) |
- |
pathogenic |
g.37830296G>T |
g.39674043G>T |
- |
- |
PGAP3_000021 |
Parents were heterozygous carriers for p.Tyr169Ter. This nonsense alteration was predicted to cause a truncated protein with lacking functionally structural 5 transmembrane domains (TMD) |
- |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+/. |
5 |
c.507C>A |
r.(?) |
p.(Tyr169*) |
- |
pathogenic |
g.37830296G>T |
g.39674043G>T |
- |
- |
PGAP3_000021 |
Parents were heterozygous carriers for p.Tyr169Ter. This nonsense alteration was predicted to cause a truncated protein with lacking functionally structural 5 transmembrane domains (TMD) |
- |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.511T>C |
r.(?) |
p.(Cys171Arg) |
- |
likely pathogenic |
g.37830292A>G |
g.39674039A>G |
- |
- |
PGAP3_000017 |
- |
PubMed: Knaus et al. 2016 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.558-10G>A |
r.(=) |
p.(=) |
- |
likely pathogenic |
g.37829913C>T |
g.39673660C>T |
- |
- |
PGAP3_000012 |
- |
PubMed: Knaus et al. 2016 |
- |
- |
Unknown |
- |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.558-10G>A |
r.(=) |
p.(=) |
- |
likely pathogenic |
g.37829913C>T |
g.39673660C>T |
- |
- |
PGAP3_000012 |
- |
PubMed: Knaus et al. 2016 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+/. |
- |
c.663T>G |
r.(?) |
p.(Tyr221Ter) |
- |
pathogenic |
g.37829798A>C |
g.39673545A>C |
PGAP3(NM_033419.5):c.663T>G (p.Y221*) |
- |
PGAP3_000028 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Groningen |
?/. |
- |
c.715_717del |
r.(?) |
p.(Trp239del) |
- |
VUS |
g.37829490_37829492del |
g.39673237_39673239del |
- |
- |
PGAP3_000009 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
0 |
- |
VKGL-NL_Nijmegen |
-?/. |
- |
c.811C>A |
r.(?) |
p.(Leu271Met) |
- |
likely benign |
g.37829392G>T |
- |
PGAP3(NM_033419.4):c.811C>A (p.L271M) |
- |
PGAP3_000031 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Rotterdam |
+?/. |
- |
c.817_820del |
r.(?) |
p.(Asp273Serfs*37) |
- |
likely pathogenic |
g.37829384_37829387del |
g.39673131_39673134del |
- |
- |
PGAP3_000019 |
- |
PubMed: Abdel-Hamid et al. 2017 |
- |
- |
Germline |
yes |
- |
- |
0 |
- |
Philippe Campeau |
?/. |
- |
c.827C>T |
r.(?) |
p.(Pro276Leu) |
- |
VUS |
g.37829376G>A |
g.39673123G>A |
PGAP3(NM_033419.5):c.827C>T (p.P276L) |
- |
PGAP3_000006 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
0 |
- |
VKGL-NL_Groningen |
+?/+? |
- |
c.827C>T |
r.(?) |
p.(Pro276Leu) |
- |
likely pathogenic |
g.37829376G>A |
g.39673123G>A |
- |
- |
PGAP3_000006 |
- |
PubMed: Knaus et al. 2018 |
- |
- |
Germline/De novo (untested) |
- |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.842T>C |
r.(?) |
p.(Leu281Pro) |
- |
likely pathogenic |
g.37829361A>G |
g.39673108A>G |
- |
- |
PGAP3_000018 |
- |
PubMed: Knaus et al. 2016 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.845A>G |
r.(?) |
p.(Asp282Gly) |
- |
likely pathogenic |
g.37829358T>C |
g.39673105T>C |
- |
- |
PGAP3_000016 |
- |
PubMed: Knaus et al. 2016 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.845A>G |
r.(?) |
p.(Asp282Gly) |
- |
likely pathogenic |
g.37829358T>C |
g.39673105T>C |
- |
- |
PGAP3_000016 |
- |
PubMed: Knaus et al. 2016 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
?/. |
- |
c.850C>T |
r.(?) |
p.(His284Tyr) |
- |
VUS |
g.37829353G>A |
g.39673100G>A |
- |
- |
PGAP3_000008 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
0 |
- |
VKGL-NL_Nijmegen |
+/. |
- |
c.850C>T |
r.(?) |
p.(His284Tyr) |
- |
pathogenic |
g.37829353G>A |
g.39673100G>A |
- |
- |
PGAP3_000008 |
Mutation is heterozygous in the available parents. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane. |
- |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+/. |
7 |
c.850C>T |
r.(?) |
p.(His284Tyr) |
- |
pathogenic |
g.37829353G>A |
g.39673100G>A |
- |
- |
PGAP3_000008 |
Missense mutation. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane. |
- |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+/. |
7 |
c.850C>T |
r.(?) |
p.(His284Tyr) |
- |
pathogenic |
g.37829353G>A |
g.39673100G>A |
- |
- |
PGAP3_000008 |
Missense mutation. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane. |
- |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+/. |
7 |
c.850C>T |
r.(?) |
p.(His284Tyr) |
- |
pathogenic |
g.37829353G>A |
g.39673100G>A |
- |
- |
PGAP3_000008 |
Missense mutation. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane. |
- |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+/. |
- |
c.850C>T |
r.(?) |
p.(His284Tyr) |
- |
pathogenic (recessive) |
g.37829353G>A |
g.39673100G>A |
NM_033419.3:c.850C>T:p.(His284Tyr) |
- |
PGAP3_000008 |
- |
PubMed: Maddirevula 2018 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
LOVD |
+/. |
- |
c.850C>T |
r.(?) |
p.(His284Tyr) |
- |
pathogenic (recessive) |
g.37829353G>A |
g.39673100G>A |
NM_033419.3:c.850C>T:p.(His284Tyr) |
- |
PGAP3_000008 |
- |
PubMed: Maddirevula 2018 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
LOVD |
+/. |
- |
c.850C>T |
r.(?) |
p.(His284Tyr) |
- |
pathogenic (recessive) |
g.37829353G>A |
g.39673100G>A |
NM_033419.3:c.850C>T:p.(His284Tyr) |
- |
PGAP3_000008 |
- |
PubMed: Maddirevula 2018 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
LOVD |
+/. |
- |
c.850C>T |
r.(?) |
p.(His284Tyr) |
- |
pathogenic (recessive) |
g.37829353G>A |
g.39673100G>A |
NM_033419.3:c.850C>T:p.(His284Tyr) |
- |
PGAP3_000008 |
- |
PubMed: Maddirevula 2018 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
LOVD |
+/. |
- |
c.850C>T |
r.(?) |
p.(His284Tyr) |
- |
pathogenic (recessive) |
g.37829353G>A |
g.39673100G>A |
NM_033419.3:c.850C>T:p.(His284Tyr) |
- |
PGAP3_000008 |
- |
PubMed: Maddirevula 2018 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
LOVD |
+?/. |
7 |
c.851A>G |
r.(?) |
p.(His284Arg) |
- |
likely pathogenic |
g.37829352T>C |
g.39673099T>C |
- |
- |
PGAP3_000020 |
- |
PubMed: Nampoothiri et al. 2017 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
7 |
c.851A>G |
r.(?) |
p.(His284Arg) |
- |
likely pathogenic |
g.37829352T>C |
g.39673099T>C |
- |
- |
PGAP3_000020 |
- |
PubMed: Nampoothiri et al. 2017 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+/. |
- |
c.851A>G |
r.(?) |
p.(His284Arg) |
- |
pathogenic |
g.37829352T>C |
g.39673099T>C |
- |
- |
PGAP3_000020 |
The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane. |
- |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+/. |
- |
c.851A>G |
r.(?) |
p.(His284Arg) |
- |
pathogenic |
g.37829352T>C |
g.39673099T>C |
- |
- |
PGAP3_000020 |
Missense mutation. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane. |
- |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+/. |
- |
c.851A>G |
r.(?) |
p.(His284Arg) |
- |
pathogenic |
g.37829352T>C |
g.39673099T>C |
- |
- |
PGAP3_000020 |
Missense mutation. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane. |
- |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+/. |
- |
c.851A>G |
r.(?) |
p.(His284Arg) |
- |
pathogenic |
g.37829352T>C |
g.39673099T>C |
- |
- |
PGAP3_000020 |
Missense mutation. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane. |
- |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+/. |
- |
c.851A>G |
r.(?) |
p.(His284Arg) |
- |
pathogenic |
g.37829352T>C |
g.39673099T>C |
- |
- |
PGAP3_000020 |
Missense mutation. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane. |
- |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+/. |
7 |
c.851A>G |
r.(?) |
p.(His284Arg) |
- |
pathogenic |
g.37829352T>C |
g.39673099T>C |
- |
- |
PGAP3_000020 |
Missense mutation. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane. |
- |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+/. |
7 |
c.851A>G |
r.(?) |
p.(His284Arg) |
- |
pathogenic |
g.37829352T>C |
g.39673099T>C |
- |
- |
PGAP3_000020 |
Missense mutation. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane. |
- |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+/. |
7 |
c.851A>G |
r.(?) |
p.(His284Arg) |
- |
pathogenic |
g.37829352T>C |
g.39673099T>C |
- |
- |
PGAP3_000020 |
Missense mutation. The wild-type histidine residue (H284) is located in the transmembrane domain. The mutation is expected to lead bumps in the protein thus affecting the contacts with the lipid-membrane. |
- |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+/. |
- |
c.851A>G |
r.(?) |
p.(His284Arg) |
- |
pathogenic |
g.37829352T>C |
g.39673099T>C |
- |
- |
PGAP3_000020 |
- |
- |
- |
- |
De novo |
- |
- |
- |
0 |
- |
Philippe Campeau |
+/. |
- |
c.851A>G |
r.(?) |
p.(His284Arg) |
- |
pathogenic |
g.37829352T>C |
g.39673099T>C |
- |
- |
PGAP3_000020 |
- |
- |
- |
- |
De novo |
- |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.861G>T |
r.(?) |
p.(Trp287Cys) |
- |
likely pathogenic |
g.37829342C>A |
g.39673089C>A |
- |
- |
PGAP3_000014 |
- |
PubMed: Knaus et al. 2016 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.861G>T |
r.(?) |
p.(Trp287Cys) |
- |
likely pathogenic |
g.37829342C>A |
g.39673089C>A |
- |
- |
PGAP3_000014 |
- |
PubMed: Knaus et al. 2016 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+/. |
8 |
c.914A>G |
r.(?) |
p.(Asp305Gly) |
- |
pathogenic |
g.37829105T>C |
g.39672852T>C |
- |
- |
PGAP3_000002 |
CHO cell line defective in both PGAP3 have GPI-APs at mildly reduced levels because of a lack of GPI fatty acid remodelling. When wild-type PGAP3 cDNA was transfected, the first step in the fatty acid remodelling was restored, whereas the second step remained defective, leading to the release of lyso-GPI intermediates and resulting in a severe reduction in the surface levels of GPI-APs. Mutant PGAP3 cDNA bearing the mutation p.Asp305Gly significantly reduced levels of all three GPI-APs, indicating some residual activity. The p.Asp305Gly protein was readily detectable but had immature N-glycan and was mislocalized in the ER by immunoblot. |
PubMed: Howard et al. 2014 |
- |
rs587777252 |
Germline |
yes |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.914A>G |
r.(?) |
p.(Asp305Gly) |
- |
likely pathogenic |
g.37829105T>C |
g.39672852T>C |
- |
- |
PGAP3_000002 |
- |
PubMed: Knaus et al. 2016 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.914A>G |
r.(?) |
p.(Asp305Gly) |
- |
likely pathogenic |
g.37829105T>C |
g.39672852T>C |
- |
- |
PGAP3_000002 |
- |
PubMed: Pagnamenta et al. 2017 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.914A>G |
r.(?) |
p.(Asp305Gly) |
- |
likely pathogenic |
g.37829105T>C |
g.39672852T>C |
- |
- |
PGAP3_000002 |
- |
PubMed: Pagnamenta et al. 2017 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.924C>A |
r.(?) |
p.(Tyr308*) |
ACMG |
likely pathogenic |
g.37829095G>T |
g.39672842G>T |
- |
- |
PGAP3_000005 |
- |
PubMed: Trujillano 2017 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Daniel Trujillano |
+?/. |
- |
c.*559C>T |
r.(=) |
p.(=) |
- |
likely pathogenic |
g.37828497G>A |
g.39672244G>A |
- |
- |
PGAP3_000015 |
- |
PubMed: Knaus et al. 2016 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
+?/. |
- |
c.*559C>T |
r.(=) |
p.(=) |
- |
likely pathogenic |
g.37828497G>A |
g.39672244G>A |
- |
- |
PGAP3_000015 |
- |
PubMed: Knaus et al. 2016 |
- |
- |
Germline |
- |
- |
- |
0 |
- |
Philippe Campeau |
-/. |
- |
c.*6299G>T |
r.(=) |
p.(=) |
- |
benign |
g.37822757C>A |
g.39666504C>A |
- |
- |
PGAP3_000024 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Nijmegen |
-?/. |
- |
c.*6317C>G |
r.(=) |
p.(=) |
- |
likely benign |
g.37822739G>C |
g.39666486G>C |
- |
- |
TCAP_000021 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Nijmegen |
-?/. |
- |
c.*6495C>A |
r.(=) |
p.(=) |
- |
likely benign |
g.37822561G>T |
g.39666308G>T |
- |
- |
TCAP_000015 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Nijmegen |
-/. |
- |
c.*6616A>C |
r.(=) |
p.(=) |
- |
benign |
g.37822440T>G |
g.39666187T>G |
- |
- |
PGAP3_000023 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Nijmegen |
-?/. |
- |
c.*6618C>A |
r.(=) |
p.(=) |
- |
likely benign |
g.37822438G>T |
g.39666185G>T |
TCAP(NM_003673.3):c.*76G>T |
- |
TCAP_000027 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
0 |
- |
VKGL-NL_Utrecht |
-?/. |
- |
c.*6618C>A |
r.(=) |
p.(=) |
- |
likely benign |
g.37822438G>T |
g.39666185G>T |
TCAP(NM_003673.3):c.*76G>T |
- |
TCAP_000027 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Nijmegen |