Malaysian Node of the Human Variome Project Database
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Individual #00000191
Reference
Siti Aishah Abdul Wahab et al. (2016)
Gender
M
Geographic origin
Malaysia
Ethnic origin
Chinese
Population
-
Remarks
-
Microattribution
-
Panel size
1
Diseases
GA1
Owner name
Nuur Athirah Binti Mohd Daud
Database submission
license
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
Created by
Nuur Athirah Binti Mohd Daud
Phenotypes
Glutaric aciduria type 1 (
GA1
)
Add phenotype for this disease
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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
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Phenotype ID
Phenotype details
Inheritance
Owner
0000000089
-
Familial, autosomal recessive
Nuur Athirah Binti Mohd Daud
Screenings
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Template
: Template(s) used to detect the sequence variant; DNA = genomic DNA, RNA = RNA (cDNA).
All options:
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
Screening ID
Template
Technique
Genes screened
Variants found
Owner
0000000206
DNA
PCR;SEQ
GCDH
7
Nuur Athirah Binti Mohd Daud
Variants
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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 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.
DNA change (genomic) (hg38)
: 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
Published as
: Variant as originally reported (e.g. 521delT); listed only when different from "DNA change". Variants seen in animal models, tested in vitro, predicted from RNA analysis, etc. are described between brackets like c.(456C>G).
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.
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).
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.
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.
Published as
: Variant as originally reported (e.g. 521delT); listed only when different from "DNA change". Variants seen in animal models, tested in vitro, predicted from RNA analysis, etc. are described between brackets like c.(456C>G).
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
GVS function
: The functional annotation of this position from the Genome Variation Server.
All options:
intergenic
near-gene-5
utr-5
start-lost
coding
non-coding-exon
coding-near-splice
non-coding-exon-near-splice
coding-synonymous
coding-synonymous-near-splice
codingComplex
codingComplex-near-splice
frameshift
frameshift-near-splice
missense
missense-near-splice
splice-5
splice
non-coding-intron-near-splice
intron
splice-3
stop-gained
stop-gained-near-splice
stop-lost
stop-lost-near-splice
utr-3
near-gene-3
Clinical classification
: Clinical classification of variant
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Chr
Allele
Effect
DNA change (genomic) (hg38)
Published as
Reference
DB-ID
dbSNP ID
Frequency
Variant remarks
Owner
Gene
Exon
DNA change (cDNA)
Published as
RNA change
Protein
GVS function
Clinical classification
19
Unknown
+/.
g.12893530C>T
-
Siti Aishah Abdul Wahab et al. (2016)
,
dbSNP
,
ClinVar
GCDH_000007
rs752334462
1/8
-
Nuur Athirah Binti Mohd Daud
GCDH
-
NM_000159.3:c.382C>T
-
r.(?)
p.(Arg128*)
-
ClinVar
19
Unknown
+/.
g.12896949G>A
-
Siti Aishah Abdul Wahab et al. (2016)
,
dbSNP
,
ClinVar
GCDH_000001
rs761765983
1/8
-
Nuur Athirah Binti Mohd Daud
GCDH
9
NM_000159.3:c.892G>A
-
r.(?)
p.(Ala298Thr)
-
ClinVar
19
Unknown
./.
g.12897406G>A
-
Siti Aishah Abdul Wahab et al. (2016)
,
dbSNP
,
ClinVar
GCDH_000003
rs768925619
1/8
-
Nuur Athirah Binti Mohd Daud
GCDH
10
NM_000159.3:c.1060G>A
-
r.(?)
p.(Gly354Ser)
-
ClinVar
19
Unknown
./.
g.12897409C>T
-
Siti Aishah Abdul Wahab et al. (2016)
,
dbSNP
,
ClinVar
GCDH_000005
rs781477694
2/8
-
Nuur Athirah Binti Mohd Daud
GCDH
-
NM_000159.3:c.1063C>T
-
r.(?)
p.(Arg355Cys)
-
ClinVar
19
Unknown
+/.
g.12897788G>T
-
Siti Aishah Abdul Wahab et al. (2016)
GCDH_000004
rs876660106
1/8
-
Nuur Athirah Binti Mohd Daud
GCDH
-
NM_000159.3:c.1168G>T
-
r.(?)
p.(Gly390Trp)
-
-
19
Unknown
+/.
g.12899466A>C
-
Siti Aishah Abdul Wahab et al. (2016)
,
dbSNP
,
ClinVar
GCDH_000002
rs199999619
1/8
-
Nuur Athirah Binti Mohd Daud
GCDH
11i
NM_000159.3:c.1244-2A>C
-
r.spl?
p.?
-
ClinVar
19
Unknown
?/.
g.12899485G>A
-
Siti Aishah Abdul Wahab et al. (2016)
,
dbSNP
,
ClinVar
GCDH_000006
rs151201155
1/8
-
Nuur Athirah Binti Mohd Daud
GCDH
-
NM_000159.3:c.1261G>A
-
r.(?)
p.(Ala421Thr)
-
ClinVar
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