Individual #00000133

Reference	Sharifah Nurain Syed Zanaruddin et al. (2013)
Gender	?
Geographic origin	Malaysia
Ethnic origin	-
Population	-
Remarks	-
Microattribution	-
Panel size	1
Diseases	OSCC
Owner name	Nuur Athirah Binti Mohd Daud
Database submission license
Created by	Nuur Athirah Binti Mohd Daud

No phenotypes found for this individual!

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

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Example	Matches
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Screening ID	Template	Technique	Genes screened	Variants found	Owner
0000000148	DNA	PCR;SEQ	TP53	27	Nuur Athirah Binti Mohd Daud

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 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

27 entries on 1 page. Showing entries 1 - 27.

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How to query

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
17	Unknown	+/.	g.7670685G>A	R342*	Sharifah Nurain Syed Zanaruddin et al. (2013), dbSNP, ClinVar	TP53_000027	rs730882029	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	10	NM_000546.5:c.1024C>T	-	r.(?)	p.(Arg342*)	-	ClinVar
17	Unknown	+/.	g.7670695_7670696insA	F338fs*8	Sharifah Nurain Syed Zanaruddin et al. (2013),	TP53_000026	-	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	10	NM_000546.5:c.1013_1014insT	-	r.(?)	p.(Glu339Argfs*8)	-	-
17	Unknown	+/.	g.7670703C>A	E336*	Sharifah Nurain Syed Zanaruddin et al. (2013)	TP53_000025	rs1553769428	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	10	NM_000546.5:c.1006G>T	-	r.(?)	p.(Glu336*)	-	-
17	Unknown	+/.	g.7673568del	960delG	Sharifah Nurain Syed Zanaruddin et al. (2013)	TP53_000024	rs1555524370	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	9	NM_000546.5:c.960del	-	r.(?)	p.(Lys321Asnfs*24)	-	-
17	Unknown	+/.	g.7673704G>A	R306*	Sharifah Nurain Syed Zanaruddin et al. (2013), dbSNP, ClinVar	TP53_000023	rs121913344	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	8	NM_000546.5:c.916C>T	-	r.(?)	p.(Arg306*)	-	ClinVar
17	Unknown	+/.	g.7673744del	876delA	Sharifah Nurain Syed Zanaruddin et al. (2013)	TP53_000022	rs1557136332	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	8	NM_000546.5:c.876del	-	r.(?)	p.(Glu294Serfs*51)	-	-
17	Unknown	+/.	g.7673763_7673789del	831_857del24	Sharifah Nurain Syed Zanaruddin et al. (2013)	TP53_000018	-	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	8	NM_000546.5:c.831_857del	-	r.(?)	p.(Cys277*)	-	-
17	Unknown	+/.	g.7673764C>T	E286K	Sharifah Nurain Syed Zanaruddin et al. (2013), dbSNP, ClinVar	TP53_000021	rs786201059	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	8	NM_000546.5:c.856G>A	-	r.(?)	p.(Glu286Lys)	-	ClinVar
17	Unknown	./.	g.7673776G>A	R282W	Sharifah Nurain Syed Zanaruddin et al. (2013), dbSNP, (OMIM 0018), ClinVar	TP53_000020	rs28934574	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	8	NM_000546.5:c.844C>T	-	r.(?)	p.(Arg282Trp)	-	ClinVar
17	Unknown	./.	g.7673788G>A	P278S	Sharifah Nurain Syed Zanaruddin et al. (2013), dbSNP, ClinVar	TP53_000019	rs17849781	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	8	NM_000546.5:c.832C>T	-	r.(?)	p.(Pro278Ser)	-	ClinVar
17	Unknown	./.	g.7673803G>A	R273C	Sharifah Nurain Syed Zanaruddin et al. (2013), dbSNP, ClinVar	TP53_000017	rs121913343	3/31	-	Nuur Athirah Binti Mohd Daud	TP53	8	NM_000546.5:c.817C>T	-	r.(?)	p.(Arg273Cys)	-	ClinVar
17	Unknown	+/.	g.7674220C>T	R248Q	Sharifah Nurain Syed Zanaruddin et al. (2013), dbSNP, ClinVar	TP53_000015	rs11540652	2/31	-	Nuur Athirah Binti Mohd Daud	TP53	7	NM_000546.5:c.743G>A	-	r.(?)	p.(Arg248Gln)	-	ClinVar
17	Unknown	+/.	g.7674221G>A	R248W	Sharifah Nurain Syed Zanaruddin et al. (2013), dbSNP, (OMIM 0001), ClinVar	TP53_000016	rs121912651	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	7	NM_000546.5:c.742C>T	-	r.(?)	p.(Arg248Trp)	-	ClinVar
17	Unknown	./.	g.7674232C>T	G244D	Sharifah Nurain Syed Zanaruddin et al. (2013), dbSNP, ClinVar	TP53_000014	rs985033810	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	7	NM_000546.5:c.731G>A	-	r.(?)	p.(Gly244Asp)	-	ClinVar
17	Unknown	+/.	g.7674252C>T	M237I	Sharifah Nurain Syed Zanaruddin et al. (2013), dbSNP, ClinVar	TP53_000012	rs587782664	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	7	NM_000546.5:c.711G>A	-	r.(?)	p.(Met237Ile)	-	ClinVar
17	Unknown	+?/.	g.7674253A>T	M237K	Sharifah Nurain Syed Zanaruddin et al. (2013), dbSNP, ClinVar	TP53_000013	rs765848205	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	7	NM_000546.5:c.710T>A	-	r.(?)	p.(Met237Lys)	-	ClinVar
17	Unknown	+/.	g.7674261G>C	Y234*	Sharifah Nurain Syed Zanaruddin et al. (2013)	TP53_000011	-	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	7	NM_000546.5:c.702C>G	-	r.(?)	p.(Tyr234*)	-	-
17	Unknown	./.	g.7674262T>C	Y234C	Sharifah Nurain Syed Zanaruddin et al. (2013), dbSNP, ClinVar	TP53_000010	rs587780073	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	7	NM_000546.5:c.701A>G	-	r.(?)	p.(Tyr234Cys)	-	ClinVar
17	Unknown	+?/.	g.7674917T>C	Y205C	Sharifah Nurain Syed Zanaruddin et al. (2013), dbSNP, ClinVar	TP53_000009	rs1057520007	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	6	NM_000546.5:c.614A>G	-	r.(?)	p.(Tyr205Cys)	-	ClinVar
17	Unknown	+/.	g.7675064G>C	S183*	Sharifah Nurain Syed Zanaruddin et al. (2013), dbSNP, ClinVar	TP53_000008	rs1555525970	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	5	NM_000546.5:c.548C>G	-	r.(?)	p.(Ser183*)	-	ClinVar
17	Unknown	./.	g.7675076T>C	H179R	Sharifah Nurain Syed Zanaruddin et al. (2013), dbSNP, ClinVar	TP53_000007	rs1057519991	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	5	NM_000546.5:c.536A>G	-	r.(?)	p.(His179Arg)	-	ClinVar
17	Unknown	+?/.	g.7675085C>A	C176F	Sharifah Nurain Syed Zanaruddin et al. (2013), dbSNP, ClinVar	TP53_000006	rs786202962	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	5	NM_000546.5:c.527G>T	-	r.(?)	p.(Cys176Phe)	-	ClinVar
17	Unknown	+/.	g.7675088C>T	R175H	Sharifah Nurain Syed Zanaruddin et al. (2013), dbSNP, (OMIM 0030), ClinVar	TP53_000005	rs28934578	2/31	-	Nuur Athirah Binti Mohd Daud	TP53	5	NM_000546.5:c.524G>A	-	r.(?)	p.(Arg175His)	-	ClinVar
17	Unknown	+/.	g.7675142A>C	V157G	Sharifah Nurain Syed Zanaruddin et al. (2013)	TP53_000004	-	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	5	NM_000546.5:c.470T>G	-	r.(?)	p.(Val157Gly)	-	-
17	Unknown	?/.	g.7675158G>A	P152S	Sharifah Nurain Syed Zanaruddin et al. (2013), dbSNP, ClinVar	TP53_000003	rs767328513	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	5	NM_000546.5:c.454C>T	-	r.(?)	p.(Pro152Ser)	-	ClinVar
17	Unknown	+/.	g.7675999A>G	C124R	Sharifah Nurain Syed Zanaruddin et al. (2013)	TP53_000002	rs121909223	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	4	NM_000546.5:c.370T>C	-	r.(?)	p.(Cys124Arg)	-	-
17	Unknown	+/.	g.7676030_7676032del	F113del	Sharifah Nurain Syed Zanaruddin et al. (2013)	TP53_000001	rs587777801	1/31	-	Nuur Athirah Binti Mohd Daud	TP53	4	NM_000546.5:c.337_339del	-	r.(?)	p.(Phe113del)	-	-

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