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

Polymorphism Information

NameALFRED UIDLocus NameLocus Symbol
exon 4 Val158Met (NlaIII codon 158)SI000155LCatechol-O-methyltransferaseCOMT
FstAvg Het# Populations Typed
0.0850.40987
Synonyms: rs4680 ;
Frequency on Map:    
Frequency Display Formats:     
Estimated Heterozygosity: 
Frequency Download:   
External Resources: HGVbase Site Definition Record   Typing Protocol Record  GenBank sequence Record  dbSNP ss# Record  PharmGKB Variant Information Record  
References: See References
Polymorphism Description:  A single base pair change (G to A) in exon 4 of the COMT gene, at position 472 in the long mRNA, and 322 in the short mRNA, results in an amino acid change (Val to Met), at codon 158 of MB-COMT and codon 108 of S-COMT, that decreases the activity level of COMT enzyme 3 to 4 fold. In addition to being a functional polymorphism, this SNP also creates a polymorphic NlaIII restriction site in the DNA sequence of the gene. The two alleles are referred to as COMT*H, the site-absent (G; Val) allele that encodes the thermostable, high activity enzyme and COMT*L, the site-present (A; Met) allele that encodes the low activity enzyme.
Some frequencies vary from those in the manuscript as a few related individuals are included.
Ancestral Allele:  Site Absent
Ancestral Allele Determine by: Sequence on primate DNA
Alleles:
Allele NameAllele SymbolDescription
AACutting allele codes for low activity enzyme:           5'-ggatttcgctgg C A TG aaggacaaggt-3'
GGNon-cutting allele codes for high activity enzyme: 5'-ggatttcgctgg C G TG aaggacaaggt-3'

References:
- Chen CH, Lee YR, Wei FC, Koong FJ, Hwu HG, Hsiao KJ. "Association study of NlaIII and MspI genetic polymorphisms of catechol-O-methyltransferase gene and susceptibility to schizophrenia". Biol Psychiatry 41:985-7. (1997) Online citation.

- Daniels JK, Williams NM, Williams J, Jones LA, Cardno AG, Murphy KC, Spurlock G, Riley B, Scambler P, Asherson P, McGuffin P, Owen MJ. "No evidence for allelic association between schizophrenia and a polymorphism determining high or low catechol O-methyltransferase activity". Am J Psychiatry 153:268-70. (1996) Online citation.

- DeMille MM, Kidd JR, Ruggeri V, Palmatier MA, Goldman D, Odunsi A, Okonofua F, Grigorenko E, Schulz LO, Bonne-Tamir B, Lu RB, Parnas J, Pakstis AJ, Kidd KK. "Population variation in linkage disequilibrium across the COMT gene considering promoter region and coding region variation". Human Genetics 111:521-537. (2002) Online citation.

- Palmatier MA, Kang AM, Kidd KK. "Global variation in the frequencies of functionally different catechol-O-methyltransferase alleles". Biol. Psychiatry. 46:557-67. (1999) Online citation.

© 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