ALFRED: allele frequency database

The ALlele FREquency Database
ALFRED is a resource of gene frequency data on human populations
supported by the U. S. National Science Foundation.

ALFRED detailed record information

Locus Information

Name	ALFRED UID	Locus Symbol	Chromosome	Band Position
Apolipoprotein B (including Ag(x) antigen)	LO000199T	APOB	2	2p24-p23

Synonyms:
Sites List: See Sites List
External Resources: Entrez Gene Locus Information HGMD polymorphism OMIM description GenBank Sequence GenBank Sequence The University of Manitoba (Animated lipoprotein metabolic cycle in the liver) UniGene PharmGKB Gene Information Genopedia (HuGE Navigator)
References: See References
Locus Description: APOB comprises 43 kb divided into 29 exons (Ludwig et al., 1987) [PubMed ID: 3652907] and encodes apolipoprotein B, which is a key protein that controls cholesterol metabolism in the liver and intestine as apolipoprotein B attaches to cholesterol to form low-density lipoproteins (LDL). The gene is located at 2p24-p23. Apolipoprotein B occurs in the plasma in two main isoforms: first is apoB-48, which is synthesized exclusively by the intestine, and second is apoB-100 synthesized by the liver (Knott et al., 1985) [PubMed ID: 2994225]. Due to this characteristic, APOB gene represents a good model for the understanding of tissue-specific gene control by using transgenic animals as research models (Kim and Young, 1998) [PubMed ID: 9555937]. Elevated plasma concentrations of apoB-100 and LDL are recognized causation factors for atherosclerotic coronary disease, which is a leading cause of death in the United States (American Heart Association, 1998).
Sites within this locus ordered by their chromosomal position in the 37.3 NCBI build:

Site Name (Navigates to ALFRED description)	dbSNP rs# (Navigates to dbSNP reference page)	Chr-Position	# Populations typed
exon 29 Glu4154Lys (also known as AG*T,Z )	rs1042031	21079258	2
exon 26 MspI	rs1801701	21082332	9
exon 14 Val591Ala (also known as AG*A1, D)	rs679899	21104419	2
SP 24,27	rs11279109	21120282	7
9 bp_Ins/Del (version 1)	rs11279109	21120282	6
AG*X,Y	rs1042034	21225281	5
exon 29 EcoRI	rs1042031	21225753	42
rs12720851	rs12720851	21227331	50
exon 26 Gln3611Arg (also known as AG*H,I)	rs1801701	21228827	1
exon 26 Arg3500Gln	rs5742904	21229160	3
C___3216558_10	rs676210	21231524	79
2-site haplotype (XbaI, EcoRI)		21232195	32
exon 26 XbaI	rs693	21232195	87
rs673548	rs673548	21237544	51
rs11126598	rs11126598	21240364	50
C___2072479_10	rs10199768	21244000	43
C___1026583_10	rs679899	21250914	74
rs550619	rs550619	21260601	51
rs12720794	rs12720794	21262375	50
exon 4 Thr71Ile (also knowm as AG*C,G)	rs1367117	21263900	5
6-site haplotype		21266777	1
9 bp_Ins/Del (version 2)	rs11279109	21266777	2
C-265T	rs1800481	21267210	2
C___2072465_10	rs589566	21269809	42
rs1713222	rs1713222	21271323	70
3' VNTR (version 3)			9
3' VNTR (version 1)			3
3' VNTR (version 2)			12

References:
- Alonso S, Fernandez-Fernandez I, Castro A, De Pancorbo MM. "Genetic characterization of APOB and D17S5 AFLP loci in a sample from the Basque Country (northern Spain)". Hum. Biol. 70:491-505. (1998) Online citation.

- Anderson JL, Bunker CH, Aston CE, Kamboh MI. "Relationship of Two Apolipoprotein B Polymorphisms with Serum Lipoprotein and Lipid Levels in African Blacks". Hum. Biol. 69:793-807. (1997) Online citation.

- Da Silva WA Jr, Bortolini MC, Meyer D, Salzano FM, Elion J, Krishnamoorthy R, Schneider MP, De Guerra DC, Layrisse Z, Castellano HM, Weimer TD, Zago MA. "Genetic diversity of two African and sixteen South American populations determined on the basis of six hypervariable loci.". Am. J. Phys. Anthropol. 109:425-437. (1999) Online citation.

- Gajra B, Candlish JK, Heng CK, Mak JW, Saha N. "Genotype Associations among Seven Apolipoprotein B Polymorphisms in a Population of Orang Asli of Western Malaysia". Hum. Biol. 69:629-40. (1997) Online citation.

- Kim E, Young SG. "Genetically modified mice for the study of apolipoprotein B". J. Lipid Res. 39:703-23. (1998) Online citation.

- Knott TJ, Rall SC Jr, Innerarity TL, Jacobson SF, Urdea MS, Levy-Wilson B, Powell LM, Pease RJ, Eddy R, Nakai H, et al. "Human apolipoprotein B: structure of carboxyl-terminal domains, sites of gene expression, and chromosomal localization". Science 230:37-43. (1985) Online citation.

- Ludwig EH, Blackhart BD, Pierotti VR, Caiati L, Fortier C, Knott T, Scott J, Mahley RW, Levy-Wilson B, McCarthy BJ. "DNA sequence of the human apolipoprotein B gene". DNA 6:363-72. (1987) Online citation.

- Machado MO, Hirata MH, Bertolami MC, Hirata RD. "Apo B gene haplotype is associated with lipid profile of higher risk for coronary heart disease in Caucasian Brazilian men". J. Clin. Lab. Anal. 15:19-24. (2001) Online citation.

- Mastana SS, Reddy PH, Das MK, Reddy P, Das K. "Molecular Genetic Diversity in 5 Populations of Madhya Pradesh, India". Hum. Biol. 72:499-510. (2000) Online citation.

- Scacchi R, Corbo RM, Rickards O, Mantuano E, Guevara A, De Stefano GF. "Apolipoprotein B and E genetic polymorphisms in the Cayapa Indians of Ecuador". Hum. Biol. 69:375-382. (1997) Online citation.

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© 2012 Kenneth K Kidd, Yale University. All rights reserved. The full Copyright Notification is also available.
Originally prototyped by Michael Osier with the aid of Kei Cheung
Upgrades and maintenance since 2002 by Haseena Rajeevan