Individual #00000195

Reference	Alyaa Al-Khateeb et al. (2011)
Gender	-
Geographic origin	Malaysia
Ethnic origin	-
Population	-
Remarks	-
Microattribution	-
Panel size	1
Diseases	FH
Owner name	Nuur Athirah Binti Mohd Daud
Database submission license
Created by	Nuur Athirah Binti Mohd Daud

Phenotypes

Familial hypercholesterolemia (FH)

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

How to query this table

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Operator	Column type	Example	Matches
	Text	Arg	all entries containing 'Arg'
space	Text	Arg Ser	all entries containing 'Arg' and 'Ser'
\|	Text	Arg\|Ser	all entries containing 'Arg' or 'Ser'
!	Text	!fs	all entries not containing 'fs'
^	Text	^p.(Arg	all entries beginning with 'p.(Arg'
$	Text	Ser)$	all entries ending with 'Ser)'
=""	Text	=""	all entries with this field empty
=""	Text	="p.0"	all entries exactly matching 'p.0'
!=""	Text	!=""	all entries with this field not empty
!=""	Text	!="p.0"	all entries not exactly matching 'p.0?'
combination	Text	*\|Ter !fs	all entries containing '*' or 'Ter' but not containing 'fs'
	Date	2020	all entries matching the year 2020
\|	Date	2020-03\|2020-04	all entries matching March or April, 2020
!	Date	!2020-03	all entries not matching March, 2020
<	Date	<2020	all entries before the year 2020
<=	Date	<=2020-06	all entries in or before June, 2020
>	Date	>2020-06	all entries after June, 2020
>=	Date	>=2020-06-15	all entries on or after June 15th, 2020
combination	Date	2019\|2020 <2020-03	all entries in 2019 or 2020, and before March, 2020
	Numeric	23	all entries exactly matching 23
\|	Numeric	23\|24	all entries exactly matching 23 or 24
!	Numeric	!23	all entries not exactly matching 23
<	Numeric	<23	all entries lower than 23
<=	Numeric	<=23	all entries lower than, or equal to, 23
>	Numeric	>23	all entries higher than 23
>=	Numeric	>=23	all entries higher than, or equal to, 23
combination	Numeric	>=20 <30 !23	all entries with values from 20 to 29, but not equal to 23

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Example	Matches
Asian	all entries containing 'Asian', 'asian', including 'Caucasian', 'caucasian', etc.
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Asian\|African !Caucasian	all entries containing 'Asian' or 'African', but not containing 'Caucasian'
"South Asian"	all entries containing 'South Asian', but not containing 'South East Asian'

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Phenotype ID	Phenotype details	Inheritance	Owner
0000000092	-	-	Nuur Athirah Binti Mohd Daud

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

Screening ID	Template	Technique	Genes screened	Variants found	Owner
0000000210	DNA	DHPLC;MLPA;PCR	LDLR	29	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

29 entries on 1 page. Showing entries 1 - 29.

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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
19	Unknown	-/.	g.11100236C>T	-	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000002	rs2228671	1/147	-	Nuur Athirah Binti Mohd Daud	LDLR	2	NM_000527.4:c.81C>T	-	r.(=)	p.(=)	-	ClinVar
19	Unknown	./.	g.11100349A>T	-	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000023	rs769446356	1/147	-	Nuur Athirah Binti Mohd Daud	LDLR	2i	NM_000527.4:c.190+4A>T	-	r.spl?	p.?	-	ClinVar
19	Unknown	./.	g.11100401G>A	-	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000003	rs3745677	3/147	-	Nuur Athirah Binti Mohd Daud	LDLR	2i	NM_000527.4:c.190+56G>A	-	r.(=)	p.(=)	-	ClinVar
19	Unknown	+/.	g.11100403C>T	-	Alyaa Al-Khateeb et al. (2011), dbSNP	LDLR_000004	rs3745678	7/147	-	Nuur Athirah Binti Mohd Daud	LDLR	2i	NM_000527.4:c.190+58C>T	-	r.(=)	p.(=)	-	-
19	Unknown	-?/.	g.11102773C>T	-	Alyaa Al-Khateeb et al. (2011)dbSNP	LDLR_000005	rs766709484	1/147	-	Nuur Athirah Binti Mohd Daud	LDLR	3	NM_000527.4:c.300C>T	-	r.(=)	p.(=)	-	ClinVar
19	Unknown	./.	g.11102774G>A	-	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000024	rs144172724	11/147	-	Nuur Athirah Binti Mohd Daud	LDLR	3	NM_000527.4:c.301G>A	-	r.(?)	p.(Glu101Lys)	-	ClinVar
19	Unknown	+?/.	g.11105321G>C	-	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000025	rs879254517	1/147	-	Nuur Athirah Binti Mohd Daud	LDLR	4	NM_000527.4:c.415G>C	-	r.(?)	p.(Asp139His)	-	ClinVar
19	Unknown	+?/.	g.11105507G>A	-	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000026	rs879254589	9/147	-	Nuur Athirah Binti Mohd Daud	LDLR	4	NM_000527.4:c.601G>A	-	r.(?)	p.(Glu201Lys)	-	ClinVar
19	Unknown	+?/.	g.11106633T>A	-	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000027	rs879254668	10/147	-	Nuur Athirah Binti Mohd Daud	LDLR	5	NM_000527.4:c.763T>A	-	r.(?)	p.(Cys255Ser)	-	ClinVar
19	Unknown	./.	g.11107484G>A	-	Alyaa Al-Khateeb et al. (2011), dbSNP, (OMIM 0008), ClinVar	LDLR_000006	rs121908030	7/147	-	Nuur Athirah Binti Mohd Daud	LDLR	6	NM_000527.4:c.910G>A	-	r.(?)	p.(Asp304Asn)	-	ClinVar
19	Unknown	-/.	g.11107550G>A	-	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000007	rs13306513	3/147	-	Nuur Athirah Binti Mohd Daud	LDLR	6i	NM_000527.4:c.940+36G>A	-	r.(=)	p.(=)	-	ClinVar
19	Unknown	+/.	g.11110778C>A	c.1060+7T>C	Alyaa Al-Khateeb et al. (2011), dbSNP	LDLR_000008	rs2738442	18/147	-	Nuur Athirah Binti Mohd Daud	LDLR	7i	NM_000527.4:c.1060+7C>A	-	r.(=)	p.(=)	-	-
19	Unknown	+/.	g.11110781G>C	-	Alyaa Al-Khateeb et al. (2011), ClinVar	LDLR_000009	-	5/147	-	Nuur Athirah Binti Mohd Daud	LDLR	7i	NM_000527.4:c.1060+10G>C	-	r.(=)	p.(=)	-	-
19	Unknown	-?/.	g.11111680T>A	-	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000010	rs536387604	1/147	-	Nuur Athirah Binti Mohd Daud	LDLR	8i	NM_000527.4:c.1186+41T>A	-	r.(=)	p.(=)	-	ClinVar
19	Unknown	./.	g.11113285C>T	-	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000011	rs13306498	5/147	-	Nuur Athirah Binti Mohd Daud	LDLR	9	NM_000527.4:c.1194C>T	-	r.(=)	p.(=)	-	ClinVar
19	Unknown	-/.	g.11113505C>T	-	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000012	rs1003723	2/147	-	Nuur Athirah Binti Mohd Daud	LDLR	9i	NM_000527.4:c.1359-30C>T	-	r.(=)	p.(=)	-	ClinVar
19	Unknown	-?/.	g.11113587A>G	-	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000013	rs879254891	17/147	-	Nuur Athirah Binti Mohd Daud	LDLR	10	NM_000527.4:c.1411A>G	-	r.(?)	p.(Arg471Gly)	-	ClinVar
19	Unknown	-/.	g.11116124C>T	-	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000014	rs5929	6/147	-	Nuur Athirah Binti Mohd Daud	LDLR	11	NM_000527.4:c.1617C>T	-	r.(=)	p.(=)	-	ClinVar
19	Unknown	./.	g.11116268C>T	-	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000015	rs4508523	12/147	-	Nuur Athirah Binti Mohd Daud	LDLR	11i	NM_000527.4:c.1705+56C>T	-	r.(=)	p.(=)	-	ClinVar
19	Unknown	-?/.	g.11116324C>G	-	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000016	rs879254995	1/147	-	Nuur Athirah Binti Mohd Daud	LDLR	11i	NM_000527.4:c.1705+112C>G	-	r.(=)	p.(=)	-	ClinVar
19	Unknown	+/.	g.11116329T>G	-	Alyaa Al-Khateeb et al. (2011)	LDLR_000019	-	2/147	-	Nuur Athirah Binti Mohd Daud	LDLR	11i	NM_000527.4:c.1705+117T>G	-	r.(=)	p.(=)	-	-
19	Unknown	-/.	g.11116790G>T	-	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000018	rs7259278	1/147	-	Nuur Athirah Binti Mohd Daud	LDLR	11i	NM_000527.4:c.1706-69G>T	-	r.(=)	p.(=)	-	ClinVar
19	Unknown	-/.	g.11116804A>C	-	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000017	rs2738447	6/147	-	Nuur Athirah Binti Mohd Daud	LDLR	11i	NM_000527.4:c.1706-55A>C	-	r.(=)	p.(=)	-	ClinVar
19	Unknown	+/.	g.11116859_11116998dup	-	Alyaa Al-Khateeb et al. (2011)	LDLR_000028	-	2/147	-	Nuur Athirah Binti Mohd Daud	LDLR	12	NM_000527.4:c.1706_1845dup	-	r.(?)	p.(Asp616Ilefs*96)	-	-
19	Unknown	./.	g.11116926C>T	-	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000020	rs688	7/147	-	Nuur Athirah Binti Mohd Daud	LDLR	12	NM_000527.4:c.1773C>T	-	r.(=)	p.(=)	-	ClinVar
19	Unknown	./.	g.11120205T>C	-	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000021	rs5925	1/147	-	Nuur Athirah Binti Mohd Daud	LDLR	13	NM_000527.4:c.1959T>C	-	r.(=)	p.(=)	-	ClinVar
19	Unknown	+/.	g.11120378_11120394del	c.1996_2012del17	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000030	rs879255104	4/147	-	Nuur Athirah Binti Mohd Daud	LDLR	14	NM_000527.4:c.1996_2012del	-	r.(?)	p.(Trp666Profs*45)	-	ClinVar
19	Unknown	./.	g.11120482C>G	-	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000029	rs759858813	5/147	-	Nuur Athirah Binti Mohd Daud	LDLR	14	NM_000527.4:c.2100C>G	-	r.(?)	p.(Asp700Glu)	-	ClinVar
19	Unknown	-/.	g.11123265A>G	-	Alyaa Al-Khateeb et al. (2011), dbSNP, ClinVar	LDLR_000022	rs5927	5/147	-	Nuur Athirah Binti Mohd Daud	LDLR	15	NM_000527.4:c.2232A>G	-	r.(=)	p.(=)	-	ClinVar

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