Individual #00000242

Reference	Siti Aishah Zainal et al. (2012)
Gender	-
Geographic origin	Malaysia
Ethnic origin	Malay
Population	Kelantan
Remarks	-
Microattribution	-
Panel size	1
Diseases	NSHL
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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Screening ID	Template	Technique	Genes screened	Variants found	Owner
0000000257	DNA	DHPLC;SEQ	GJB2	13	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

13 entries on 1 page. Showing entries 1 - 13.

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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
13	Parent #2	+/.	g.20189202C>T	-	Siti Aishah Zainal et al. (2012), dbSNP, ClinVar	GJB2_000007	rs111033196	2/32	-	Nuur Athirah Binti Mohd Daud	GJB2	-	NM_004004.6:c.380G>A	-	r.(?)	p.(Arg127His)	-	ClinVar
13	Parent #2	./.	g.20189214G>T	-	Siti Aishah Zainal et al. (2012), dbSNP, ClinVar	GJB2_000006	rs111033188	1/32	-	Nuur Athirah Binti Mohd Daud	GJB2	-	NM_004004.6:c.368C>A	-	r.(?)	p.(Thr123Asn)	-	ClinVar
13	Parent #2	-/.	g.20189241T>C	-	Siti Aishah Zainal et al. (2012), dbSNP, ClinVar	GJB2_000005	rs2274083	6/32	-	Nuur Athirah Binti Mohd Daud	GJB2	-	NM_004004.6:c.341A>G	-	r.(?)	p.(Glu114Gly)	-	ClinVar
13	Parent #1	+/.	g.20189241T>C	-	Siti Aishah Zainal et al. (2012), dbSNP, ClinVar	GJB2_000005	rs2274083	1/32	-	Nuur Athirah Binti Mohd Daud	GJB2	-	NM_004004.6:c.341A>G	-	r.(?)	p.(Glu114Gly)	-	ClinVar
13	Unknown	+/.	g.20189323_20189325del	-	Siti Aishah Zainal et al. (2012)	GJB2_000010	-	1/32	-	Nuur Athirah Binti Mohd Daud	GJB2	-	NM_004004.6:c.257_259delCGC	-	r.(?)	p.(Pro87del)	-	-
13	Parent #1	+/.	g.20189473C>T	-	Siti Aishah Zainal et al. (2012), dbSNP, (OMIM 0023), ClinVar	GJB2_000001	rs72474224	6/32	-	Nuur Athirah Binti Mohd Daud	GJB2	-	NM_004004.6:c.109G>A	-	r.(?)	p.(Val37Ile)	-	ClinVar
13	Both (homozygous)	+/.	g.20189473C>T	-	Siti Aishah Zainal et al. (2012), dbSNP, (OMIM 0023), ClinVar	GJB2_000001	rs72474224	2/32	-	Nuur Athirah Binti Mohd Daud	GJB2	-	NM_004004.6:c.109G>A	-	r.(?)	p.(Val37Ile)	-	ClinVar
13	Unknown	?/.	g.20189482T>A	-	Siti Aishah Zainal et al. (2012), dbSNP, ClinVar	GJB2_000009	rs564084861	1/32	-	Nuur Athirah Binti Mohd Daud	GJB2	-	NM_004004.6:c.100A>T	-	r.(?)	p.(Met34Leu)	-	ClinVar
13	Both (homozygous)	+/.	g.20189487C>T	-	Siti Aishah Zainal et al. (2012), dbSNP, ClinVar	GJB2_000008	rs111033190	1/32	-	Nuur Athirah Binti Mohd Daud	GJB2	-	NM_004004.6:c.95G>A	-	r.(?)	p.(Arg32His)	-	ClinVar
13	Parent #1	-/.	g.20189503C>T	-	Siti Aishah Zainal et al. (2012), dbSNP, ClinVar	GJB2_000004	rs2274084	8/32	-	Nuur Athirah Binti Mohd Daud	GJB2	-	NM_004004.6:c.79G>A	-	r.(?)	p.(Val27Ile)	-	ClinVar
13	Unknown	+/.	g.20189511C>T	-	Siti Aishah Zainal et al. (2012), dbSNP, (OMIM 0003), ClinVar	GJB2_000002	rs104894396	2/32	-	Nuur Athirah Binti Mohd Daud	GJB2	-	NM_004004.6:c.71G>A	-	r.(?)	p.(Trp24*)	-	ClinVar
13	Both (homozygous)	+/.	g.20189511C>T	-	Siti Aishah Zainal et al. (2012), dbSNP, (OMIM 0003), ClinVar	GJB2_000002	rs104894396	1/32	-	Nuur Athirah Binti Mohd Daud	GJB2	-	NM_004004.6:c.71G>A	-	r.(?)	p.(Trp24*)	-	ClinVar
13	Unknown	./.	g.20189571C>T	-	Siti Aishah Zainal et al. (2012), dbSNP, ClinVar	GJB2_000003	rs111033222	9/32	-	Nuur Athirah Binti Mohd Daud	GJB2	-	NM_004004.6:c.11G>A	-	r.(?)	p.(Gly4Asp)	-	ClinVar

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