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
|
?/. |
_1 |
c.-669C>T |
r.(=) |
p.(=) |
- |
VUS |
g.48367540C>T |
g.48509152C>T |
- |
- |
PORCN_000120 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
?/. |
_1 |
c.-669C>T |
r.(=) |
p.(=) |
- |
VUS |
g.48367540C>T |
g.48509152C>T |
- |
- |
PORCN_000120 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
?/. |
_1 |
c.-474T>C |
r.(=) |
p.(=) |
- |
VUS |
g.48367735T>C |
g.48509347T>C |
- |
- |
PORCN_000125 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
?/. |
_1 |
c.-474T>C |
r.(=) |
p.(=) |
- |
VUS |
g.48367735T>C |
g.48509347T>C |
- |
- |
PORCN_000125 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
?/. |
_1 |
c.-468C>T |
r.(=) |
p.(=) |
- |
VUS |
g.48367741C>T |
g.48509353C>T |
- |
- |
PORCN_000126 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
?/. |
_1 |
c.-468C>T |
r.(=) |
p.(=) |
- |
VUS |
g.48367741C>T |
g.48509353C>T |
- |
- |
PORCN_000126 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
+/+ |
_1_8i |
c.-37_(845+1_846-1)del |
r.0? |
p.0? |
- |
pathogenic (dominant) |
g.(?_48367100)_(48372899_?)del |
- |
del ex1-8 |
- |
PORCN_000119 |
mosaic |
PubMed: Sellars 2013 |
- |
- |
Somatic |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+/+ |
_1_8i |
c.-37_(845+1_846-1)del |
r.0? |
p.0? |
- |
pathogenic (dominant) |
g.(?_48367100)_(48372899_?)del |
- |
del ex1-8 |
- |
PORCN_000119 |
fetus of case 1, prenatal diagnosis by ultrasound analysis and array CGH, |
PubMed: Sellars 2013 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+/+ |
_1_14_ |
c.0 |
r.0 |
p.0 |
- |
pathogenic (dominant) |
g.(?_48368172)_(48379202_?)del |
- |
del PORCN |
- |
PORCN_000065 |
microdeletion 1 |
PubMed: Bornholdt 2009 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 98/2 |
Maria Paola Lombardi |
+/+ |
_1_14_ |
c.0 |
r.0 |
p.0 |
- |
pathogenic (dominant) |
g.(?_48368172)_(48379202_?)del |
- |
del PORCN |
- |
PORCN_000065 |
microdeletion 2 |
PubMed: Bornholdt 2009 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 100/0 |
Maria Paola Lombardi |
+/+ |
_1_14_ |
c.0 |
r.0 |
p.0 |
- |
pathogenic (dominant) |
g.(?_48368172)_(48379202_?)del |
- |
del PORCN |
- |
PORCN_000065 |
microdeletion 3 |
PubMed: Bornholdt 2009 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 100/0 |
Maria Paola Lombardi |
+/+ |
_1_14_ |
c.0 |
r.0 |
p.0 |
- |
pathogenic (dominant) |
g.48306152_48443561delinsCACGTGTGTTCTGGA |
g.48447780_48585173delinsCACGTGTGTTCTGGA |
hg18 48191096_48328505delinsCACGTGTGTTCTGGA |
- |
PORCN_000068 |
137,411 bp deletion incl. SLC38A5, FTSJ1, PORCN,EBP and OATL1
Variant Error [EBUILDMISMATCH]: This variant seems to mismatch; the genomic variants on hg19 and hg38 seem to not belong together. Please fix this entry and then remove this message. |
PubMed: Grzeschik 2007, PubMed: Bornholdt 2009 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 95/5 |
Maria Paola Lombardi |
+/+ |
_1_14_ |
c.0 |
r.0 |
p.0 |
- |
pathogenic (dominant) |
g.48036369_48401246del |
g.48176941_48542858del |
hg18 47921313_48286190del |
- |
PORCN_000069 |
364,864 bp deletion incl. SLC38A5, FTSJ1, PORCN, EBP
Variant Error [EBUILDMISMATCH]: This variant seems to mismatch; the genomic variants on hg19 and hg38 seem to not belong together. Please fix this entry and then remove this message. |
PubMed: Grzeschik 2007, PubMed: Bornholdt 2009 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 99/1 |
Maria Paola Lombardi |
+/+ |
_1_14_ |
c.0 |
r.0 |
p.0 |
- |
pathogenic (dominant) |
g.48063411_48467943del |
g.48203975_48609555del |
hg18 47948355_48352887del |
- |
PORCN_000070 |
377,520 bp deletion PORCN
Variant Error [EBUILDMISMATCH]: This variant seems to mismatch; the genomic variants on hg19 and hg38 seem to not belong together. Please fix this entry and then remove this message. |
PubMed: Grzeschik 2007, PubMed: Bornholdt 2009 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 97/3 |
Maria Paola Lombardi |
+/+ |
_1_14_ |
c.0 |
r.0 |
p.0 |
- |
pathogenic (dominant) |
g.(?_48175056)_(48365056_?)del |
- |
hg18 48060000_48250000del |
- |
PORCN_000071 |
~219 kb deletion incl. FTSJ1, SLC38A5, PORCN, EBP, OATL1, RBM3, WDR13 |
PubMed: Wang 2007 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 100/0 |
Maria Paola Lombardi |
+/+ |
_1_14_ |
c.0 |
r.0 |
p.0 |
- |
pathogenic (dominant) |
g.(?_48368172)_(48379202_?)del |
- |
del PORCN |
- |
PORCN_000065 |
219 kb deletion |
PubMed: Wang 2007 |
- |
- |
De novo |
- |
- |
- |
- |
X-inactivation 100/0 |
Maria Paola Lombardi |
+/+ |
_1_14_ |
c.0 |
r.0 |
p.0 |
- |
pathogenic (dominant) |
g.(48210000_48170000)_(48330000_48460000)del |
- |
del PORCN |
- |
PORCN_000073 |
150 kb del |
PubMed: Froyen 2009 |
- |
- |
De novo |
- |
- |
- |
- |
X-inactivation non informative |
Maria Paola Lombardi |
+/+ |
_1_14_ |
c.0 |
r.0 |
p.0 |
- |
pathogenic (dominant) |
g.(?_48313056)_(48425056_?)del |
- |
hg18 48198000_48310000del |
- |
PORCN_000075 |
112 kb del PORCN |
PubMed: Houge, 2008 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 100/0 |
Maria Paola Lombardi |
+?/+? |
_1_14_ |
c.0 |
r.0 |
p.0 |
- |
likely pathogenic (dominant) |
g.(?_48368172)_(48379202_?)del |
- |
del PORCN +? |
- |
PORCN_000065 |
502 kb deletion |
PubMed: Lombardi 2011 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 99/1 |
Maria Paola Lombardi |
+/+ |
_1_14_ |
c.0 |
r.0 |
p.0 |
- |
pathogenic (dominant) |
g.(?_48368172)_(48387104_?)del |
- |
deletion PORCN and EBP +? |
- |
PORCN_000115 |
- |
PubMed: Patrizi 2012 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+/+ |
_1_14_ |
c.0 |
r.? |
p.? |
- |
pathogenic |
g.(?_48368172)_(48379202_?)del |
- |
- |
- |
PORCN_000065 |
- |
- |
- |
- |
Germline |
yes |
9/157 patients |
- |
- |
- |
Maria Paola Lombardi |
+/+ |
_1_14_ |
c.0 |
r.0 |
p.0 |
- |
pathogenic |
g.(?_48368172)_(48379202_?)del |
- |
~0.459 Mb del in Xp11.23 including PORCN |
- |
PORCN_000065 |
- |
PubMed: Bostwick et al, 2016 |
- |
- |
Germline/De novo (untested) |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+/+ |
2 |
c.1A>G |
r.(?) |
p.0? |
- |
pathogenic (dominant) |
g.48368209A>G |
g.48509821A>G |
p.Met1? |
- |
PORCN_000001 |
- |
PubMed: Lombardi 2011 |
- |
- |
De novo |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+/+ |
2 |
c.3G>A |
r.(?) |
p.0? |
- |
pathogenic (dominant) |
g.48368211G>A |
g.48509823G>A |
p.Met1Ile |
- |
PORCN_000002 |
- |
PubMed: Bornholdt 2009 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 79/21 |
Maria Paola Lombardi |
+/+ |
_1_3i |
c.26_373+155del |
r.0? |
p.0? |
- |
pathogenic (dominant) |
g.48361709_48370478del |
g.48503321_48512090del |
del ex1-4 hg1848246653_48255422del |
- |
PORCN_000064 |
- |
PubMed: Bornholdt 2009 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 83/17 |
Maria Paola Lombardi |
+/+ |
2 |
c.49dup |
r.(?) |
p.(Cys17Leufs*11) |
- |
pathogenic (dominant) |
g.48368257dup |
g.48509869dup |
49dupT |
- |
PORCN_000003 |
- |
PubMed: Harmsen 2009 |
- |
- |
De novo |
- |
- |
- |
- |
X-inactivation 54/46 |
Maria Paola Lombardi |
+/+ |
2 |
c.53dup |
r.(?) |
p.(Leu19Profs*9) |
- |
pathogenic (dominant) |
g.48368261dup |
g.48509873dup |
49dupT (Leu18LeufsX10) |
- |
PORCN_000004 |
- |
PubMed: Wang 2007 |
- |
- |
De novo |
- |
- |
- |
- |
X-inactivation 50/50 |
Maria Paola Lombardi |
+/+ |
2 |
c.67C>T |
r.(?) |
p.Gln23* |
- |
pathogenic |
g.48368275C>T |
g.48509887C>T |
- |
- |
PORCN_000143 |
- |
PubMed: Ramirez-Botero et al., 2016 |
- |
- |
Germline/De novo (untested) |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+/+ |
2 |
c.74del |
r.(?) |
p.(Gly25Alafs*27) |
- |
pathogenic (dominant) |
g.48368282del |
g.48509894del |
74delG |
- |
PORCN_000005 |
- |
PubMed: Clements 2009 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 66.6/33.4 |
Maria Paola Lombardi |
+/+ |
2 |
c.107G>A |
r.(?) |
pCys36Tyr |
- |
pathogenic |
g.48368315G>A |
g.48509927G>A |
- |
- |
PORCN_000145 |
- |
PubMed: Bostwick et al, 2016 |
- |
- |
Germline/De novo (untested) |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+/+ |
2 |
c.108C>A |
r.(?) |
p.(Cys36*) |
- |
pathogenic (dominant) |
g.48368316C>A |
g.48509928C>A |
- |
- |
PORCN_000082 |
- |
PubMed: Fernandes 2010 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Raoul Hennekam |
+?/. |
- |
c.115T>C |
r.(?) |
p.(Cys39Arg) |
- |
likely pathogenic |
g.48368323T>C |
g.48509935T>C |
- |
- |
PORCN_000171 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Nijmegen |
+/+ |
2 |
c.129G>A |
r.(?) |
p.(Trp43*) |
- |
pathogenic (dominant) |
g.48368337G>A |
g.48509949G>A |
truncation, detected in blood |
- |
PORCN_000099 |
de novo, somatic mosaicism |
PubMed: Yoshihashi 2010 |
- |
- |
Somatic |
- |
- |
- |
- |
- |
Raoul Hennekam |
+?/+? |
2 |
c.129G>A |
r.(?) |
p.(Trp43*) |
- |
likely pathogenic (dominant) |
g.48368337G>A |
g.48509949G>A |
- |
- |
PORCN_000099 |
truncation, detected in blood |
PubMed: Nakanishi 2013 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+/+ |
2i |
c.136+1G>A |
r.spl |
p.? |
- |
pathogenic (dominant) |
g.48368345G>A |
g.48509957G>A |
IVS2+1G>A |
- |
PORCN_000098 |
splicing defect |
PubMed: Kapoor 2012 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Raoul Hennekam |
+/+ |
2i |
c.136+2del |
r.spl |
p.? |
- |
pathogenic (dominant) |
g.48368346del |
g.48509958del |
136+2delT |
- |
PORCN_000083 |
splicing defect |
PubMed: Fernandes 2010 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Raoul Hennekam |
+/+ |
2 |
c.136+2del |
r.spl |
p.(?) |
- |
pathogenic |
g.48368346del |
g.48509958del |
- |
- |
PORCN_000083 |
- |
PubMed: Bostwick et al, 2016 |
- |
- |
Germline/De novo (untested) |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+/+ |
intron 2 |
c.136+2T>C |
r.spl |
p.? |
- |
pathogenic |
g.48368346T>C |
g.48509958T>C |
- |
- |
PORCN_000166 |
- |
- |
- |
- |
Germline/De novo (untested) |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
-/- |
i2 |
c.137-4A>T |
r.(?) |
p.? |
- |
likely benign |
g.48369679A>T |
g.48511291A>T |
- |
- |
PORCN_000151 |
variant found in unaffected father (hemizygote) and mother |
- |
- |
- |
Germline |
no |
0.000009798 in gnomAD (2x hemizygotes) |
- |
- |
- |
Maria Paola Lombardi |
-?/. |
- |
c.137-4A>T |
r.spl? |
p.? |
- |
likely benign |
g.48369679A>T |
- |
PORCN(NM_203475.3):c.137-4A>T |
- |
PORCN_000151 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Groningen |
+?/+? |
2i |
c.137-3A>G |
r.spl? |
p.? |
- |
likely pathogenic (dominant) |
g.48369680A>G |
g.48511292A>G |
- |
- |
PORCN_000105 |
splicing defect predicted with in silico analysis |
unpublished |
- |
- |
Germline |
- |
- |
- |
- |
- |
Robert Smigiel |
+/+ |
Intron 2 |
c.137-3A>G |
r.(?) |
p.? |
- |
pathogenic |
g.48369680A>G |
g.48511292A>G |
- |
- |
PORCN_000105 |
- |
PubMed: Mary 2016 |
- |
- |
Germline/De novo (untested) |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+/+ |
3 |
c.166_167dup |
r.(?) |
p.(Val57Profs*60) |
- |
pathogenic (dominant) |
g.48369712_48369713dup |
g.48511324_48511325dup |
- |
- |
PORCN_000006 |
- |
PubMed: Harmsen 2009 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 83/17 |
Maria Paola Lombardi |
+/+ |
3 |
c.166_167dup |
r.(?) |
p.(Val57Profs*60) |
- |
pathogenic (dominant) |
g.48369712_48369713dup |
g.48511324_48511325dup |
- |
- |
PORCN_000006 |
mother to daughter transmission |
PubMed: Harmsen 2009 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 80/20 |
Maria Paola Lombardi |
+/+ |
- |
c.173_178delinsACT |
r.(?) |
p.Ala58_Gly60delins |
- |
pathogenic |
g.48369719_48369724delinsACT |
g.48511331_48511336delinsACT |
- |
- |
PORCN_000139 |
mosaic in buccal swab DNA, variant not detected in DNA extracted from blood |
PubMed: Severino-Freire 2017 |
- |
- |
Somatic |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+/+ |
3 |
c.178G>A |
r.(?) |
p.(Gly60Arg) |
- |
pathogenic (dominant) |
g.48369724G>A |
g.48511336G>A |
- |
- |
PORCN_000007 |
mother low level mosaicism |
PubMed: Wang 2007 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 63/37 |
Maria Paola Lombardi |
+/+ |
3 |
c.178G>A |
r.(?) |
p.(Gly60Arg) |
- |
pathogenic (dominant) |
g.48369724G>A |
g.48511336G>A |
- |
- |
PORCN_000007 |
- |
PubMed: Wang 2007 |
- |
- |
De novo |
- |
- |
- |
- |
X-inactivation 50/50 |
Maria Paola Lombardi |
+/+ |
3 |
c.178G>A |
r.(?) |
p.(Gly60Arg) |
- |
pathogenic (dominant) |
g.48369724G>A |
g.48511336G>A |
- |
- |
PORCN_000007 |
- |
PubMed: Fernandes 2010 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+/+ |
3 |
c.178G>A |
r.(?) |
p.(Gly60Arg) |
- |
pathogenic (dominant) |
g.48369724G>A |
g.48511336G>A |
- |
- |
PORCN_000007 |
- |
PubMed: Fernandes 2010 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+/+ |
3 |
c.178G>A |
r.(?) |
p.(Gly60Arg) |
- |
pathogenic (dominant) |
g.48369724G>A |
g.48511336G>A |
- |
- |
PORCN_000007 |
- |
PubMed: Fernandes 2010 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+/+ |
3 |
c.178G>A |
r.(?) |
p.(Gly60Arg) |
- |
pathogenic (dominant) |
g.48369724G>A |
g.48511336G>A |
- |
- |
PORCN_000007 |
de novo, in patient |
unpublished |
- |
- |
De novo |
- |
- |
- |
- |
- |
Raoul Hennekam |
+/+ |
3 |
c.178G>A |
r.(?) |
p.(Gly60Arg) |
- |
pathogenic (dominant) |
g.48369724G>A |
g.48511336G>A |
- |
- |
PORCN_000007 |
detected in blood |
unpublished |
- |
- |
Germline |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+/+ |
3 |
c.178G>A |
r.(?) |
p.Gly60Arg |
- |
pathogenic |
g.48369724G>A |
g.48511336G>A |
- |
- |
PORCN_000007 |
- |
PubMed: Bostwick et al, 2016 |
ClinVar-RCV000011447.6 |
- |
Germline/De novo (untested) |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+?/. |
- |
c.178G>A |
r.(?) |
p.(Gly60Arg) |
- |
likely pathogenic |
g.48369724G>A |
g.48511336G>A |
c.178G-->A; p.Gly60Arg |
- |
PORCN_000007 |
confirmed with Sanger sequencing; heterozygous |
PubMed: Patel 2019 |
- |
- |
De novo |
? |
- |
- |
- |
- |
LOVD |
+?/. |
- |
c.178G>A |
r.(?) |
p.(Gly60Arg) |
- |
likely pathogenic |
g.48369724G>A |
g.48511336G>A |
PORCN c.178G>A |
- |
PORCN_000007 |
no protein change given, probably hemizygous (gender unknown) |
PubMed: Zanolli 2020 |
- |
- |
Unknown |
? |
- |
- |
- |
- |
LOVD |
+/. |
3 |
c.205C>T |
r.(?) |
p.(Gln69*) |
- |
pathogenic |
g.48369751C>T |
g.48511363C>T |
- |
- |
PORCN_000135 |
- |
- |
- |
- |
Germline/De novo (untested) |
- |
- |
- |
- |
- |
Gemeinschaftspraxis für Humangenetik Dresden |
-?/. |
- |
c.209T>G |
r.(?) |
p.(Leu70Arg) |
- |
likely benign |
g.48369755T>G |
g.48511367T>G |
PORCN(NM_203475.2):c.209T>G (p.L70R) |
- |
PORCN_000154 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Rotterdam |
+/+ |
3 |
c.221G>A |
r.(?) |
p.(Trp74*) |
- |
pathogenic (dominant) |
g.48369767G>A |
g.48511379G>A |
- |
- |
PORCN_000008 |
- |
PubMed: Harmsen 2009 |
- |
- |
De novo |
- |
- |
- |
- |
X-inactivation 76/24 |
Maria Paola Lombardi |
+/+ |
3 |
c.222G>A |
r.(?) |
p.(Trp74*) |
- |
pathogenic (dominant) |
g.48369768G>A |
g.48511380G>A |
- |
- |
PORCN_000009 |
- |
PubMed: Grzeschik 2007 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 65/35 |
Maria Paola Lombardi |
+/+ |
3 |
c.268C>T |
r.(?) |
p.(Arg90*) |
- |
pathogenic (dominant) |
g.48369814C>T |
g.48511426C>T |
- |
- |
PORCN_000010 |
- |
PubMed: Wang 2007 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 81/19 |
Maria Paola Lombardi |
+/+ |
3 |
c.268C>T |
r.(?) |
p.(Arg90*) |
- |
pathogenic (dominant) |
g.48369814C>T |
g.48511426C>T |
- |
- |
PORCN_000010 |
postzygotic mosaic |
PubMed: Bornholdt 2009 |
- |
- |
Somatic |
- |
- |
- |
- |
X-inactivation 60/40 |
Maria Paola Lombardi |
+/+ |
3 |
c.268C>T |
r.(?) |
p.(Arg90*) |
- |
pathogenic (dominant) |
g.48369814C>T |
g.48511426C>T |
- |
- |
PORCN_000010 |
mosaic |
PubMed: Harmsen 2009 |
- |
- |
Somatic |
- |
- |
- |
- |
X-inactivation 37/63 |
Maria Paola Lombardi |
+?/+? |
3 |
c.268C>T |
r.(?) |
p.(Arg90*) |
- |
likely pathogenic (dominant) |
g.48369814C>T |
g.48511426C>T |
- |
- |
PORCN_000010 |
- |
not published |
- |
- |
Germline |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+/+ |
3 |
c.283C>T |
r.(?) |
p.(Arg95*) |
- |
pathogenic (dominant) |
g.48369829C>T |
g.48511441C>T |
- |
- |
PORCN_000011 |
- |
PubMed: Bornholdt 2009 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 55/45 |
Maria Paola Lombardi |
+/+ |
3 |
c.283C>T |
r.(?) |
p.(Arg95*) |
- |
pathogenic (dominant) |
g.48369829C>T |
g.48511441C>T |
- |
- |
PORCN_000011 |
- |
PubMed: Maas 2009 |
- |
- |
De novo |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+/+ |
3 |
c.283C>T |
r.(?) |
p.(Arg95*) |
- |
pathogenic (dominant) |
g.48369829C>T |
g.48511441C>T |
- |
- |
PORCN_000011 |
mosaic |
PubMed: Fernandes 2010 |
- |
- |
Somatic |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
-?/. |
- |
c.289G>A |
r.(?) |
p.(Val97Ile) |
- |
likely benign |
g.48369835G>A |
g.48511447G>A |
PORCN(NM_001282167.2):c.76G>A (p.V26I) |
- |
PORCN_000155 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Groningen |
-?/. |
- |
c.329+9A>G |
r.(=) |
p.(=) |
- |
likely benign |
g.48369884A>G |
- |
PORCN(NM_001282167.1):c.116+9A>G |
- |
PORCN_000176 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Rotterdam |
-?/-? |
3i |
c.330-27del |
r.(?) |
p.(=) |
- |
likely benign |
g.48370253del |
g.48511865del |
330-27delG |
- |
PORCN_000101 |
predicted to be benign with in silico analysis |
PubMed: Fernandes 2010 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Raoul Hennekam |
-?/-? |
3i |
c.330-11T>A |
r.(?) |
p.(=) |
- |
likely benign |
g.48370269T>A |
g.48511881T>A |
- |
- |
PORCN_000100 |
possible begnin |
PubMed: Fernandes 2010 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
?/. |
- |
c.340A>G |
r.(?) |
p.(Met114Val) |
- |
VUS |
g.48370290A>G |
g.48511902A>G |
- |
- |
PORCN_000134 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Nijmegen |
?/. |
- |
c.343G>A |
r.(?) |
p.(Val115Ile) |
- |
VUS |
g.48370293G>A |
- |
PORCN(NM_203475.3):c.343G>A (p.V115I) |
- |
PORCN_000179 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Groningen |
+/+ |
4 |
c.360G>A |
r.(?) |
p.(Trp120*) |
- |
pathogenic (dominant) |
g.48370310G>A |
g.48511922G>A |
- |
- |
PORCN_000084 |
mosaic |
PubMed: Fernandes 2010 |
- |
- |
Somatic |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
?/+? |
- |
c.368T>G |
r.(?) |
p.(Met123Arg) |
- |
VUS |
g.48370318T>G |
g.48511930T>G |
- |
- |
PORCN_000136 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Kaori Yamoto |
+/+ |
4 |
c.370C>T |
r.(?) |
p.(Arg124*) |
- |
pathogenic (dominant) |
g.48370320C>T |
g.48511932C>T |
- |
- |
PORCN_000012 |
mosaic |
PubMed: Wang 2007 |
- |
- |
Somatic |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+/+ |
4 |
c.370C>T |
r.(?) |
p.(Arg124*) |
- |
pathogenic (dominant) |
g.48370320C>T |
g.48511932C>T |
- |
- |
PORCN_000012 |
- |
PubMed: Grzeschik 2007 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 50/50 |
Maria Paola Lombardi |
+/+ |
4 |
c.370C>T |
r.(?) |
p.(Arg124*) |
- |
pathogenic (dominant) |
g.48370320C>T |
g.48511932C>T |
- |
- |
PORCN_000012 |
postzygotic mosaic |
PubMed: Grzeschik 2007 |
- |
- |
Somatic |
- |
- |
- |
- |
X-inactivation 50/50 |
Maria Paola Lombardi |
+/+ |
4 |
c.370C>T |
r.(?) |
p.(Arg124*) |
- |
pathogenic (dominant) |
g.48370320C>T |
g.48511932C>T |
- |
- |
PORCN_000012 |
- |
PubMed: Bornholdt 2009 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 52/48 |
Maria Paola Lombardi |
+/+ |
4 |
c.370C>T |
r.(?) |
p.(Arg124*) |
- |
pathogenic (dominant) |
g.48370320C>T |
g.48511932C>T |
- |
- |
PORCN_000012 |
- |
MP Lombardi (unpublished) |
- |
- |
De novo |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+/+? |
4 |
c.373G>A |
r.spl? |
p.(Gly125Arg) |
- |
pathogenic (dominant) |
g.48370323G>A |
g.48511935G>A |
- |
- |
PORCN_000081 |
- |
unpublished |
- |
- |
Germline |
- |
- |
- |
- |
- |
John Dean |
+/+ |
4i |
c.373+1G>A |
r.spl |
p.? |
- |
pathogenic (dominant) |
g.48370324G>A |
g.48511936G>A |
- |
- |
PORCN_000013 |
- |
PubMed: Leoyklang 2009 |
- |
- |
De novo |
- |
- |
- |
- |
X-inactivation 61/39 |
Maria Paola Lombardi |
?/. |
3i |
c.373+150G>A |
r.(=) |
p.(=) |
- |
VUS |
g.48370473G>A |
g.48512085G>A |
- |
- |
PORCN_000121 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
?/. |
3i |
c.373+150G>A |
r.(=) |
p.(=) |
- |
VUS |
g.48370473G>A |
g.48512085G>A |
- |
- |
PORCN_000121 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Yu Sun |
+/+ |
4i |
c.374-46T>A |
r.spl |
p.(=) |
- |
pathogenic (dominant) |
g.48370668T>A |
g.48512280T>A |
- |
- |
PORCN_000016 |
- |
PubMed: Harmsen 2009 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 86/14 |
Maria Paola Lombardi |
+/? |
4i |
c.374-15T>A |
r.spl |
p.? |
- |
pathogenic (dominant) |
g.48370699T>A |
- |
- |
- |
PORCN_000015 |
de novo (inferred)
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: Schaffer 2009 |
- |
- |
De novo |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+?/+? |
4i |
c.374-15T>A |
r.spl |
p.? |
- |
likely pathogenic (dominant) |
g.48370699T>A |
- |
- |
- |
PORCN_000015 |
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: Fernandes 2010 |
- |
- |
Germline |
- |
- |
- |
- |
- |
Maria Paola Lombardi |
+/+ |
4i |
c.374-1G>A |
r.spl |
p.? |
- |
pathogenic (dominant) |
g.48370713G>A |
g.48512325G>A |
- |
- |
PORCN_000014 |
- |
PubMed: Bornholdt 2009 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 84/16 |
Maria Paola Lombardi |
+/+ |
5 |
c.387del |
r.[373_374ins374-13_374-1,387del] |
p.Ala126_Ile129delinsTTHRGTDD |
- |
pathogenic (dominant) |
g.48370727del |
g.48512339del |
- |
- |
PORCN_000118 |
mRNA analysis shows a 13bp insertion created by an alternative splicing site |
PubMed: Nakanishi 2013 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation slightly skewed pattern in lesional skin |
Maria Paola Lombardi |
+/+ |
5 |
c.407C>T |
r.(?) |
p.(Ser136Phe) |
- |
pathogenic (dominant) |
g.48370747C>T |
g.48512359C>T |
- |
- |
PORCN_000017 |
- |
PubMed: Bornholdt 2009 |
- |
- |
Germline |
- |
- |
- |
- |
X-inactivation 57/43 |
Maria Paola Lombardi |
-?/. |
- |
c.443C>T |
r.(?) |
p.(Thr148Met) |
- |
likely benign |
g.48370783C>T |
g.48512395C>T |
PORCN(NM_022825.2):c.443C>T (p.(Thr148Met)) |
- |
PORCN_000156 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Leiden |
?/. |
- |
c.446T>A |
r.(?) |
p.(Val149Glu) |
- |
VUS |
g.48370786T>A |
g.48512398T>A |
PORCN(NM_001282167.1):c.233T>A (p.V78E) |
- |
PORCN_000157 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Rotterdam |
-?/. |
- |
c.453G>A |
r.(?) |
p.(Ser151=) |
- |
likely benign |
g.48370793G>A |
- |
PORCN(NM_001282167.1):c.240G>A (p.S80=) |
- |
PORCN_000177 |
VKGL data sharing initiative Nederland |
- |
- |
- |
CLASSIFICATION record |
- |
- |
- |
- |
- |
VKGL-NL_Rotterdam |
+?/? |
4 |
c.470G>A |
r.(?) |
p.(Gly157Asp) |
- |
likely pathogenic |
g.48370810G>A |
g.48512422G>A |
- |
- |
PORCN_000127 |
- |
- |
- |
- |
Germline |
yes |
- |
- |
- |
- |
Paul Brady |
+?/? |
4 |
c.470G>A |
r.(?) |
p.(Gly157Asp) |
- |
likely pathogenic |
g.48370810G>A |
g.48512422G>A |
- |
- |
PORCN_000127 |
- |
- |
- |
- |
Germline |
yes |
- |
- |
- |
- |
Paul Brady |
+?/? |
4 |
c.470G>A |
r.(?) |
p.(Gly157Asp) |
- |
likely pathogenic |
g.48370810G>A |
g.48512422G>A |
- |
- |
PORCN_000127 |
- |
- |
- |
- |
Germline |
yes |
- |
- |
- |
- |
Paul Brady |
+?/? |
4 |
c.470G>A |
r.(?) |
p.(Gly157Asp) |
- |
likely pathogenic |
g.48370810G>A |
g.48512422G>A |
- |
- |
PORCN_000127 |
- |
- |
- |
- |
Germline |
yes |
- |
- |
- |
- |
Paul Brady |
+?/? |
4 |
c.470G>A |
r.(?) |
p.(Gly157Asp) |
- |
likely pathogenic |
g.48370810G>A |
g.48512422G>A |
- |
- |
PORCN_000127 |
- |
- |
- |
- |
Unknown |
yes |
- |
- |
- |
- |
Paul Brady |
+/+ |
5 |
c.479dup |
r.(?) |
p.(Tyr160*) |
- |
pathogenic (dominant) |
g.48370819dup |
g.48512431dup |
479dupA |
- |
PORCN_000018 |
- |
PubMed: Wang 2007 |
- |
- |
De novo |
- |
- |
- |
- |
X-inactivation 52/48 |
Maria Paola Lombardi |
+?/. |
- |
c.484dup |
r.(?) |
p.(Val162GlyfsTer63) |
- |
likely pathogenic (recessive) |
g.48370824dup |
g.48512436dup |
- |
- |
PORCN_000178 |
ACMG PVS1, PM2, PP3, PP4 |
PubMed: Schuermans 2022 |
- |
- |
Germline/De novo (untested) |
- |
- |
- |
- |
- |
Johan den Dunnen |
+?/. |
5 |
c.487G>A |
r.(?) |
p.(Gly163Ser) |
- |
VUS |
g.48370827G>A |
g.48512439G>A |
- |
- |
PORCN_000128 |
- |
- |
- |
- |
Germline |
- |
- |
- |
- |
- |
Emma Wakeling |