IGKV2-29 gene
IGKV2D-29 gene

Human IGKV2-29 gene

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Method: PCR and restriction enzyme mapping. Primers AF68 (IPP700002) and AF76 (IPP700000) (IMGT/PRIMER-DB).

IGKV
gene name		 IGKV
allele name		 Fct Enzymes (1) Fragments (bp) (1) Polym. type (2) Frequencies (3)
Swedish Caucasians
[1] n=206		 Chinese Hong Kong
[1] n=232
IGKV2-29 IGKV2-29*01 P BsmI
+
AgeI		 846 + 109 RS 0.92 0.50
IGKV2-29*02 F 955 RS 0.08 0.50
IGKV2D-29   F/ORF 742 + 214   1.00 1.00

IMGT notes:

(1) The amplified band is of the same size for the IGKV2-29 and IGKV2D-29 genes (955 bp and 956 bp respectively). The double digest allows to remove the IGKV2D-29 band (cut by AgeI) and to identify the polymorphic IGKV2-29*01 band (cut by BsmI) [1].
The AgeI site (A CCGGT) is present at positions 197-202 (codons 66-68) in the IGKV2D-29 gene (according to the IMGT unique numbering for V-REGION). The BsmI recognition site (GAATGC) is present at positions 311-316 (codons 104-106) of the IGKV2-29*01. Interestingly this site corresponds to the stop codon (codon 104) which makes IGKV2-29*01 a pseudogene. The polymorphic nucleotide substitution a312>c in IGKV2-29*02 suppresses the stop codon and restores the 2nd-CYS 104. The absence of the BsmI site allows therefore to identify the functional IGKV2-29*02 allele including, if present, the *03 and *04 alleles, as in Black Africans [2].
(2) Polymorphism type: RS, polymorphic Restriction Sites.
(3) n= number of alleles
Alleles IGKV2-29*03 and *04 identified in Mozambique Black Africans [2] cannot be detected by this restriction enzyme mapping.

Method: PCR and restriction enzyme mapping. Primers 5'A183 (IPP800004) and 3'A182 (IPP800005) (IMGT/PRIMER-DB).

IGKV
gene name		 IGKV
allele name		 Fct Enzymes (1) Fragments (bp) Polym. type (2) Enzymes (3) Fragments (bp) Polym. type (2) Frequencies (4)
Danish
Caucasians [2]		 Greenland
Eskimos [2]		 Mozambique
Black Africans [2]
IGKV2-29 IGKV2-29*01 P MboI 175 + 220 RS SphI 395 RS 0.92 0.55 0.57
IGKV2-29*02 F 395 RS 300 + 95 RS 0.08 0.45 0.23
IGKV2-29*03 (4) F 175 + 220 RS 300 + 95 RS     0.19

IMGT notes:

(1) The MboI site ( GATC) is present at positions 159-162 (codons 53-54) of the IGKV2-29*01 and *03 alleles.
(2) Polymorphism type: RS, polymorphic Restriction Sites.
(3) The SphI site (GCATG C) is present at positions 311-316 (codons 104-105) of the IGKV2-29*02 and *03 alleles. The presence of the SphI site, that corresponds to the codon of 2nd-CYS 104, allows to identify the functional IGKV2-29 alleles, whereas the absence of the SphI site, that corresponds to a stop codon, allows to identify the pseudogene IGKV2-29*01 allele.
(4) The IGKV2-29*03 (L-PART2 g12>a) allele is probably not amplified with primer 5'A183 (IPP800004).

References:

[1] Padyukov, L. et al., Immunogenetics, 53, 22-30 (2001) PMID:11261927
[2] Juul, L. et al., Tissue antigens, 49, 595-604 (1997) PMID:9234481

Human IGKV2D-29 gene

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Method: PCR and restriction enzyme mapping. Primers AF103 (IPP800001) and AF68 (IPP700002) (IMGT/PRIMER-DB).

IGKV
gene name		 IGKV
allele name		 Fct Enzymes (1) Fragments (bp) (1) Polym. type (2) Enzymes (3) Fragments (3) Polym. type (2) Frequencies (4)
Swedish Caucasians
[1] n=206		 Chinese Hong Kong
[1] n=232
IGKV2D-29 IGKV2D-29*01 F BsmAI (or isoschizomer Alw261) 555 RS Tsp4CI 472 + 87 RS 0.90 0.53
IGKV2D-29*02 F 309 + 246 RS 472 + 87 RS 0.05 0.43
ORF 555 RS 0.05 0.04

IMGT notes:

(1) The BsmAI recognition site GTCTC is present at positions 144-148 (codons 48-50) of the IGKV2D-29*02 alleles (F and ORF). The c145>t polymorphic nucleotide substitution corresponds to the P49>S in the IGKV2D-29*02 alleles.
(2) Polymorphism type: RS, polymorphic Restriction Sites.
(3) The Tsp4CI site ACN GT is present at positions 2-6 of the V-HEPTAMER (CACAGTG) of the functional IGKV2D-29*01 and *02 alleles, but absent of the IGKV2D-29*02 ORF allele due to a mutation at position 6 (CACAGAG).
(4) n= number of alleles.

Reference:

[1] Padyukov, L. et al., Immunogenetics, 53, 22-30 (2001) PMID:11261927

Created: 01/12/2003
Author: Marie-Paule Lefranc Marie-Paule.Lefranc@igh.cnrs.fr
Editor: Chantal Ginestoux