Individual #00020882

Reference	-
Gender	M
Geographic origin	Tripoli
Geographic origin	Megalopoli, Arcadia
Population	Greek
Consanguinity	no
Remarks	-
Panel size	1
Diseases	NDL, PNCA2
Owner name	Despoina Kalfakakou

Phenotypes

Pancreatic cancer 2 (PNCA2)

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35y = 35 years
04y08m = 4 years and 8 months
18y? = around 18 years
>54y = older than 54
? = unknown

Phenotype details: Additional information on the phenotype of the individual.

Inheritance: Indicates the inheritance of the phenotype in the family; unknown, familial (autosomal/X-linked, dominant/ recessive), paternal (Y-linked), maternal (mitochondrial), isolated (sporadic) or complex
All options:

Unknown
Familial
Familial, autosomal dominant
Familial, autosomal recessive
Familial, X-linked dominant
Familial, X-linked dominant, male sparing
Familial, X-linked recessive
Paternal, Y-linked
Maternal, mitochondrial
Isolated (sporadic)
Complex

Subtype: Subtype

Phenotype ID	Age of onset	Phenotype details	Inheritance	Subtype	Owner
0000012737	39y	-	-	-	Despoina Kalfakakou

Nodules (NDL)

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35y = 35 years
04y08m = 4 years and 8 months
18y? = around 18 years
>54y = older than 54
? = unknown

Unknown
Familial
Familial, autosomal dominant
Familial, autosomal recessive
Familial, X-linked dominant
Familial, X-linked dominant, male sparing
Familial, X-linked recessive
Paternal, Y-linked
Maternal, mitochondrial
Isolated (sporadic)
Complex

Subtype: Subtype

Phenotype ID	Age of onset	Phenotype details	Inheritance	Subtype	Owner
0000012736	34y	-	-	-	Despoina Kalfakakou

Screenings

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DNA
RNA = RNA (cDNA)
Protein
? = unknown

Technique: Technique(s) used to identify the sequence variant.
All options:

? = Unknown
arrayCGH = array for Comparative Genomic Hybridisation
arraySEQ = array for resequencing
arraySNP = array for SNP typing
arrayCNV = array for Copy Number Variation (SNP and CNV probes)
BESS = Base Excision Sequence Scanning
CMC = Chemical Mismatch Cleavage
CSCE = Conformation Sensitive Capillary Electrophoresis
DGGE = Denaturing-Gradient Gel-Electrophoresis
DHPLC = Denaturing High-Performance Liquid Chromatography
DOVAM = Detection Of Virtually All Mutations (SSCA variant)
ddF = dideoxy Fingerprinting
DSCA = Double-Strand DNA Conformation Analysis
EMC = Enzymatic Mismatch Cleavage
HD = HeteroDuplex analysis
MCA = high-resolution Melting Curve Analysis (hrMCA)
IHC = Immuno-Histo-Chemistry
MAPH = Multiplex Amplifiable Probe Hybridisation
MLPA = Multiplex Ligation-dependent Probe Amplification
SEQ-NG = Next-Generation Sequencing
SEQ-NG-H = Next-Generation Sequencing - Helicos
SEQ-NG-I = Next-Generation Sequencing - Illumina/Solexa
SEQ-NG-R = Next-Generation Sequencing - Roche/454
SEQ-NG-S = Next-Generation Sequencing - SOLiD
Northern = Northern blotting
PCR = Polymerase Chain Reaction
PCRdig = PCR + restriction enzyme digestion
PCRlr = PCR, long-range
PCRm = PCR, multiplex
PCRq = PCR, quantitative
PAGE = Poly-Acrylamide Gel-Electrophoresis
PTT = Protein Truncation Test
PFGE = Pulsed-Field Gel-Electrophoresis (+Southern)
RT-PCR = Reverse Transcription and PCR
SEQ = SEQuencing
SBE = Single Base Extension
SSCA = Single-Strand DNA Conformation polymorphism Analysis (SSCP)
SSCAf = SSCA, fluorescent (SSCP)
Southern = Southern blotting
TaqMan = TaqMan assay
Western = Western Blotting

Type: Screening Type

Screening ID	Template	Technique	Type	Genes screened	Variants found	Owner
0000006792	DNA	SEQ	1	MEN1	1	Despoina Kalfakakou

Variants

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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.

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.

Effect: The variant's effect on a protein's function, in the format 'R/C' where R is the value reported by the source and C is the value concluded by the curator; '+' indicating the variant affects function, '+?' probably affects function, '+*' affects function, not associated with individual's disease phenotype, '#' affects function, not associated with any known disease phenotype, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect not classified.

DNA change (genomic) (hg19): Description of variant at DNA level, based on the genomic DNA reference sequence (following HGVS recommendations).

g.12345678C>T
g.12345678_12345890del
g.12345678_12345890dup

Reference: Reference to publication describing the variant, including links to OMIM (when available), PubMed or or other source, e.g. "den Dunnen ASHG2003 P2346".

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.

dbSNP ID: The dbSNP ID.

Variant remarks: Remarks regarding the variant described, e.g. germline mosaicism in mother, 345 kb deletion, muscle RNA analysed, not in 200 control chromosomes tested, on founder haplotype, etc.

Genetic origin: Origin of variant; unknown, germline, somatic, de novo, from parental disomy (maternal or paternal) or in vitro (cloned) when tested for functional consequences.
All options:

Unknown
Germline
Somatic
De novo
Uniparental disomy
Uniparental disomy, maternal allele
Uniparental disomy, paternal allele
In vitro (cloned)

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

Also Known As: Non-HGVS names of the variant. (Useful for LGRs)

Geographic Origin (for founder variants): Where is the founder variant located?

Is Greek Founder: Is the variant a Greek Founder Mutation?
All options:

Exon: Number of exon/intron containing variant; 2 = exon 2, 12i = intron 12, 2i_7i = exons 3 to 7, 8i_9 = border intron 8/exon 9.

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.

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

1 entry on 1 page. Showing entry 1.

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Chr	Allele	Effect	DNA change (genomic) (hg19)	Reference	DB-ID	dbSNP ID	Variant remarks	Genetic origin	Segregation	Also Known As	Geographic Origin (for founder variants)	Is Greek Founder	Owner	Gene	Exon	DNA change (cDNA)	RNA change	Protein
11	Parent #2	+/+	g.64577581T>G	-	MEN1_000039	-	-	Germline	?	-	-	-	Despoina Kalfakakou	MEN1	-	NM_000244.3:c.1A>C, NM_130799.2:c.1A>C, NM_130800.2:c.1A>C, NM_130801.2:c.1A>C, NM_130802.2:c.1A>C, NM_130803.2:c.1A>C, NM_130804.2:c.1A>C	r.?	p.?

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