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
CD4 antigen (p55)	LO000169Q	CD4	12	12pter-p12

Synonyms:
Sites List: See Sites List
External Resources: Entrez Gene Locus Information OMIM description GenBank sequence PharmGKB Gene Information Genopedia (HuGE Navigator)
References: See References
Locus Description: The CD4 gene encodes the T4 antigen, a glycoprotein of approximately 55 kDa, expressed on the surface of helper T lymphocytes. CD4 is the official designation for T-cell antigen T4/leu3. CD stands for "cluster of differentiation". The number that follows is arbitrarily assigned but sequential in time. The CD4 gene spans at least 33 kb and is composed of 10 exons (Maddon et al., 1987) [PubMed ID: 3501122]. With genetic blotting experiments and in situ hybridization, CD4 has been located on chromosome 12 at 12pter-p12 (Isobe et al., 1986 [PubMed ID: 3086883] and Kozbor et al., 1986 [PubMed ID: 3080518]). Thus, the CD4 gene is not linked to any known member of the immunoglobulin gene family, including its counterpart gene, T8, which resides on human chromosome 2 immediately distal to the immunoglobulin kappa locus (Isobe et al., 1986) [PubMed ID: 3086883]. The overall structure of T4 consists of an N-terminal variable (V)-like domain, a joining (J)-like region, a third extracellular domain, a membrane-spanning region homologous to class II major histocompatibility complex (MHC) beta-chains, and a highly charged cytoplasmic domain (Maddon et al., 1985) [PubMed ID: 2990730]. In spite of the role in immune response, CD4 also serves as human immunodeficiency virus (HIV) receptors, binding directly to the envelope protein gp120 on HIV (Lyerly et al., 1987) [PubMed ID: 3037522]. The cytoplasmic part of CD4 is known to be essential for interaction with the HIV-1 proteins Vpu and Nef (Willbold and Rosch, 1996) [PubMed ID: 11725124]
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	Status	# Populations typed
C___1217691_10	rs10774447	6894449		55
rs1922452	rs1922452	6896194		50
rs11064386	rs11064386	6896318		51
rs11064391	rs11064391	6897527		50
rs7956804	rs7956804	6898460		51
G-784C	rs2855534	6898521		42
rs2857227	rs2857227	6899528		50
rs2707212	rs2707212	6901134		51
rs2707210	rs2707210	6902002		51
C___2184681_10	rs2857234	6905181		47
C___2184682_10	rs2707209	6905264		78
Alu Ins/Del	rs4646985	6907384		85
C__11338582_10	rs2255301	6909442		51
rs7957426	rs7957426	6915906		87
rs11064404	rs11064404	6915963		50
C___2184696_10	rs7299900	6917832		57
rs11064410	rs11064410	6919569		50
D12S1623	rs111982299	6921814		32
rs10774451	rs10774451	6923018		78
rs3782736	rs3782736	6924718		51
rs1055141	rs1055141	6926363		86
C___2184703_1_	rs3213427	6928747		43
TaqI	rs2071081	6935631	Now associated with GPR162	73
CD4 (CTTTT)_n pentanucleotide repeat (version 2)				27
2-site haplotype (CTTTT pentanucleotide STRP, Alu deletion)				42
CD4 (CTTTT) _n pentanucleotide repeat (version 1)				57

References:
- Bogdawa HM, Hutz MH, Salzano FM, Weimer TA. "Diversity of Two Short Tandem Repeat Loci (CD4 and F13A1) in Three Brazilian Ethnic Groups". Hum. Biol. 72:1045-1053. (2000) Online citation.

- Isobe M, Huebner K, Maddon PJ, Littman DR, Axel R, Croce CM. "The gene encoding the T-cell surface protein T4 is located on human chromosome 12". Proc. Natl. Acad. Sci. U. S. A. 83:4399-402. (1986) Online citation.

- Kozbor D, Finan J, Nowell PC, Croce CM. "The gene encoding the T4 antigen maps to human chromosome 12". J. Immunol. 136:1141-3. (1986) Online citation.

- Lyerly HK, Matthews TJ, Langlois AJ, Bolognesi DP, Weinhold KJ. "Human T-cell lymphotropic virus IIIB glycoprotein (gp120) bound to CD4 determinants on normal lymphocytes and expressed by infected cells serves as target for immune attack". Proc. Natl. Acad. Sci. U. S. A. 84:4601-5. (1987) Online citation.

- Maddon PJ, Littman DR, Godfrey M, Maddon DE, Chess L, Axel R. "The isolation and nucleotide sequence of a cDNA encoding the T cell surface protein T4: a new member of the immunoglobulin gene family". Cell 42:93-104. (1985) Online citation.

- Maddon PJ, Molineaux SM, Maddon DE, Zimmerman KA, Godfrey M, Alt FW, Chess L, Axel R. "Structure and expression of the human and mouse T4 genes". Proc. Natl. Acad. Sci. U. S. A. 84:9155-9. (1987) Online citation.

- Tishkoff SA, Dietzsch E, Speed W, Pakstis AJ, Cheung K, Kidd JR, Bonne-Tamir B, Santachiara-Benerecetti AS, Moral P, Watson E, Krings M, Paabo S, Risch N, Jenkins T, Kidd KK. "Global patterns of linkage disequilibrium at the CD4 locus and modern human origins". Science 271:1380-7. (1996) Online citation.

- Willbold D, Rosch P. "Solution Structure of the Human CD4 (403-419) Receptor Peptide". J. Biomed. Sci. 3:435-441. (1996) Online citation.

Top

© 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