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
Phenylalanine Hydroxylase	LO000210D	PAH	12	12q22-q24.2

Synonyms:
Sites List: See Sites List
External Resources: Entrez Gene Locus Information OMIM description GenBank sequence GenBank sequence Phenylalanine Hydroxylase Locus Knowledgebase (PAHdb) NCBI Genes and disease PharmGKB Gene Information Genopedia (HuGE Navigator)
References: See References
Locus Description: The PAH gene encodes the enzyme phenylalanine hydroxylase, which is a liver-specific enzyme that converts phenylalanine to tyrosine and is the rate-limiting step in phenylalanine catabolism. The human PAH gene was cloned by DiLella et al. (1986) [PubMed ID: 3008810]. The coding region of the PAH gene is about 90 kb in length and contains 13 exons, with intron sizes ranging from 1 to 23 kb. By in situ hybridization, the assignment of the PAH locus was narrowed to 12q22-q24.1 (Lidsky et al., 1985) [PubMed ID: 3862128]. Two clusters of polymorphic sites have been reported by use of the PAH cDNA as the probe: one cluster consists of BglII, PvuII (a), and PvuII (b) at the 5' end of the gene and the second cluster consists of EcoRI, XmnI, MspI (a), MspI (b), EcoRV, and HindIII at the 3' end of the gene (Woo et al., 1983 [PubMed ID: 6316140] and Lidsky et al., 1985 [PubMed ID: 3862128]). Deficiency of this enzyme activity results in the autosomal recessive disorder phenylketonuria (PKU), which is one of the most common genetic diseases in people of northern-European descent (Bickel et al., 1981)
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
PAH Tetranucleotide STRP		0	49
intron 8 XmnI	rs869916	101768143	57
C___1402591_10	rs10860925	103228225	43
rs4764916	rs4764916	103229978	87
C___1402599_10	rs1801153	103232766	77
rs2245360	rs2245360	103234544	87
rs2242381	rs2242381	103237160	86
rs12580432	rs12580432	103238017	50
C___1402610_1_	rs2270729	103240452	78
rs940528	rs940528	103243355	50
PAH gene LI SNPs 3-site haplotype	rs869916	103244013	0
intron 7 MspI	rs1722383	103245802	90
exon 7 AluI	rs1042503	103246700	55
C___1402626_10	rs1722381	103247836	45
C___1402631_10	rs2251905	103249164	43
rs2251897	rs2251897	103249327	51
intron 5 EcoRI	rs4646988	103253157	37
rs1718306	rs1718306	103257308	50
rs1498694	rs1498694	103257876	77
C___1402638_10	rs4764918	103258923	57
C___1402642_1_	rs2133298	103260634	86
rs3817446	rs3817446	103260819	87
rs1522304	rs1522304	103264904	50
C___1402657_10	rs1617090	103267770	42
rs1718301	rs1718301	103271193	51
C__11703182_1_	rs2037639	103271350	44
rs7964033	rs7964033	103271466	50
rs1718302	rs1718302	103272686	50
rs1718303	rs1718303	103273310	50
A/G SNP	rs1718304	103275882	53
C/T SNP	rs1722390	103275901	37
C___1402673_10	rs11111414	103277428	45
C___8342426_10	rs1522305	103280756	42
rs10860936	rs10860936	103282952	86
C___1402683_10	rs11111419	103285043	42
intron 3 PvuII B	rs4646987	103287067	32
rs7131709	rs7131709	103293223	85
C___1402699_10	rs1522307	103298517	87
intron 2 PvuII A	rs4646986	103305409	29
rs1498688	rs1498688	103307021	51
C____250158_10	rs3805122	103307583	43
C___1402712_10	rs7970836	103308646	42
6-site haplotype (BglII, PvuII A, PvuII B, EcoRI, MspI, XmnI)		103310787	37
7-site haplotype (BglII, PvuII A, PvuII B, EcoRI, AluI, MspI, XmnI)		103310787	37
4-site haplotype (BglII, PvuII A, MspI, XmnI)		103310787	29
intron 1 BglII	rs1522296	103310787	34
6-site haplotype (BglII, PvuII A, PvuII B, AluI, MspI, XmnI)		103310787	32
C__11753051_10	rs1522299	103312108	42
rs1807839	rs1807839	103315529	14
C___1402744_10	rs34068029	103318089	37
3' VNTR			9

References:
- Bickel H, Bachmann C, Beckers R. "Neonatal mass screening for metabolic disorders: a collaborative study". Eur. J. Pediatr. 137:133-39. (1981)

- 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.

- DiLella AG, Kwok SC, Ledley FD, Marvit J, Woo SL. "Molecular structure and polymorphic map of the human phenylalanine hydroxylase gene". Biochemistry 25:743-9. (1986) Online citation.

- Kidd JR, Pakstis AJ, Zhao H, Lu RB, Okonofua FE, Odunsi A, Grigorenko E, Bonne-Tamir B, Friedlaender J, Shulz LO, Parnas J, Kidd KK. "Haplotypes and linkage disequilibrium at the phenylalanine hydroxylase locus (PAH) in a global representation of populations". Am. J. Hum. Genet. 66:1882-1899. (2000) Online citation.

- Kidd JR. "Population genetics and population history of Amerindians as reflected by nuclear DNA variation". Ph.D. dissertation, Yale University (1993)

- Lidsky AS, Law ML, Morse HG, Kao FT, Rabin M, Ruddle FH, Woo SL. "Regional mapping of the phenylalanine hydroxylase gene and the phenylketonuria locus in the human genome". Proc. Natl. Acad. Sci. U. S. A. 82:6221-5. (1985) Online citation.

- Woo SL, Lidsky AS, Guttler F, Chandra T, Robson KJ. "Cloned human phenylalanine hydroxylase gene allows prenatal diagnosis and carrier detection of classical phenylketonuria". Nature 306:151-5. (1983) 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