IMGT Repertoire (IG and TR)


Gene table: human (Homo sapiens) IGLC

"+" or "-" indicates if the gene sequences have been found (+) or not been found (-) transcribed (T) and/or translated into protein (Pr). Arbitrarily that information is shown on the first line of each gene when the data have been confirmed by several studies.

Functionality is shown between parentheses, (F) and (P), when the accession number refers to rearranged genomic DNA or cDNA and the corresponding germline gene has not yet been isolated.
Functionality is shown between brackets, [F] and [P], when the accession number refers to genomic DNA, but not known as being germline or rearranged.

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Polymorphism by duplication of the IGLC2 and/or IGLC3 genes has been described [11,13]. The RFLP (Restriction Fragment Length Polymorphism) alleles correspond to polymorphic 8-, 13-, 18-, 23-, 28-kb EcoRI fragments [11-13,18], which contain 2, 3, 4, 5, 6 genes, respectively. So far, only the IGLC2 and IGLC3 genes of the 8-kb EcoRI fragment have been sequenced [9].

IMGT gene name IMGT allele name Fct Chromosomal localization T Pr Positions in the locus IMGT/LIGM-DB reference sequences IMGT/LIGM-DB sequences from the literature
Clone names Exons Accession numbers Positions in the sequence Secondary accession numbers Clone names Accession numbers Positions in the sequence
IGLC1 IGLC1*01 (6,14) ORF (18) 22q11.2 J00252 [9] (1)
IGLC1*02 (6,14) F 22q11.2 X51755 [6] (19) D87023 [2] (19)
IGLC2 [11-13][1] IGLC2*01 (6,15) F 22q11.2 J00253 [9]
IGLC2*02 (6,15) F 22q11.2 X06875 [5] X51754 [6]
X51755 [6] (19)
D87023 [2] (19)
IGLC2*03 (6,15) F 22q11.2 AJ491317 [3] (6)
IGLC3 [11-13][1] IGLC3*01 (6,16) F 22q11.2 J00254 [9] (1)
IGLC3*02 (6,16) F 22q11.2 K01326 [10]
IGLC3*03 (6,16) F 22q11.2 X06876 [5] X51755 [6] (19)
IGLC3*04 (6,15) F 22q11.2 D87017 [2] D87023 [2] (19)
IGLC4 IGLC4*01 P (2) 22q11.2 J03009 [12] (3)
IGLC4*02 P (2) 22q11.2 X51755 [6] (19) D87017 [2]
IGLC5 IGLC5*01 P (4) 22q11.2 J03010 [12]
IGLC5*02 P (4) 22q11.2 X51755 [6] (19) X57808 [8]
D87017 [2]
IGLC6 IGLC6*01 (6,17) F 22q11.2 J03011 [12]
IGLC6*02 (13) P (5) 22q11.2 X51755 [6] (12)(19)
IGLC6*03 (13) P (5) 22q11.2 M61769 [7]
IGLC6*04 (13) P (5) 22q11.2 X57808 [8]
IGLC6*05 (13) P (5) 22q11.2 D87017 [2]
IGLC7 IGLC7*01 (6,9) F 22q11.2 X51755 [6] (19) X57808 [8]
D87017 [2]
IGLC7*02 (6,9) F 22q11.2 M61771 [7]
IGLC7*01 (6,9) F 22q11.2 X51755 [6] X57808 [8]
D87017 [2]
IGLC7*02 (6,9) F 22q11.2 M61771 [7]
IGLC7*03 (6,9) F 22q11.2 KM455557 [14]

Homo sapiens IGLC copy number variation (CNV) polymorphism

One, two, three or four additional IGLC genes (IGLC2A, IGLC2B, IGLC2C, IGLC2D), each one probably preceded by one IGLJ (IGLJ2A, IGLJ2B, IGLJ2C, IGLJ2D), have been shown to characterize IGLC haplotypes with eight, nine, 10 or 11 genes [1, 13], but these genes have not yet been sequenced.

IMGT notes:
  1. (1) Partial C-GENE in 5': 5 nucleotides missing.
  2. (2) Pseudogene due to DELETIONs leading to frameshifts.
  3. (3) Partial C-GENE in 5': 2 nucleotides missing.
  4. (4) Pseudogene due to a DELETION of 11 bp leading to a frameshift.
  5. (5) Pseudogene due to INSERTIONs leading to frameshifts.
  6. (6) Click here to see Correspondence between serological lambda isotypes and IGLC gene and alleles names.
  7. (7) Amino acid residue positions correspond to the IMGT unique numbering for C-DOMAIN and C-LIKE-DOMAIN (in bold), to the IMGT numbering for coding regions (between parentheses) and to the Kabat numbering (in italics).
  8. (8) In most haplotypes IGLC6 is a pseudogene.
  9. (9) IGLC7 encodes four of the five characteristic amino acids of the Ke+ Oz- isotype. However, it encodes a Lys at position 82 whereas all Ke+ Oz- myeloma proteins described to date contain a Thr at this position [4].
  10. (10) The IGLC3 Ke- Oz- isotype has not been assigned serologically but on the presence of the characteristic amino acids.
  11. (11) Partial C-GENE: sequence partial in 5'.
  12. (12) The additional nucleotide g between 372 and 373 is probably a typing error.
  13. (13) The translation of the alleles *02 to *05 give a truncated lambda protein (premature STOP-CODON at position 88 as a result of the insertion (duplication) of 4 nucleotides which leads to a frameshift).
  14. (14) Serological marker: Mcg.
  15. (15) Serological markers: Ke- Oz-.
  16. (16) Serological markers: Ke- Oz+.
  17. (17) Serological markers: Ke+ Oz-.
  18. (18) ORF because of none cDNA found.
  19. (19) The IGLC1*02 is the EX3 of the conventional IGLL5*01 gene and allele (IGLL5 is a RPI gene that comprises three exons as identified in the X51755 and D87023 genomic sequences) (Gene and allele table: Human (Homo sapiens) IGLL)
IMGT references:
  1. [1] Kay, P.H. et al., Immunogenetics, 35, 341-343 (1992). doi: 10.1007/BF00189897. PMID:1348496
  2. [2] Kawasaki, K. et al., Genome Res., 7, 250-261 (1997). PMID:9074928
  3. [3] Naud, J.F. and Gibson D.M., Eur. J. Immunogenet., 28, 97-99 (2001). PMID:11251692
  4. [4] Fett, J.W. and Deutsh, H.F., Immunochemistry, 12, 643-652 (1975). PMID:812801
  5. [5] Udey, J. A. and Blomberg, B., Nucleic Acids Res., 16, 2959-2969 (1988). PMID:3130611
  6. [6] Vasicek, T.J. and Leder, P., J. Exp. Med., 172, 609-620 (1990). PMID:2115572
  7. [7] Bauer, T.R. et al., J. Immunol., 146, 2813-2820 (1991). PMID:1901886
  8. [8] Combriato, G. and Klobeck, H.G., Eur. J. Immunol., 21, 1513-1522 (1991). PMID:1904362
  9. [9] Hieter, P. A. et al., Nature, 294, 536-540 (1981). PMID:6273747
  10. [10] Hollis, G. F. et al., Nature, 296, 321-325 (1982). PMID:6801526
  11. [11] Taub, R.A. et al., Nature, 304, 172-174 (1983). PMID:6306474
  12. [12] Dariavach, P. et al., Proc. Natl. Acad. Sci. USA., 84, 9074-9078 (1987). PMID:3122211
  13. [13] Ghanem, N. et al., Exp. Clin. Immunogenet., 5, 186-195 (1988). PMID:2908491
  14. [14] Watson C.T. et al., Genes and Immunity, 16, 24-34 (2015). PMID:25338678

Chromosomal orphon set IGLC

IMGT gene name IMGT allele name Fct Chromosomal localization T Pr Positions in the locus IMGT/LIGM-DB reference sequences IMGT/LIGM-DB sequences from the literature
Clone names Exons Accession numbers Positions in the sequence Secondary accession numbers Clone names Accession numbers Positions in the sequence
IGLC/OR22-1 P 16.1 Mb from the centromere of chr 22 [1,2] dJ90G24.3 (1) MAP AL008723 [1,2]
IGLC/OR22-2 P 16.26 Mb from the centromere of chr 22 [1,2] dJ149A16.1 (2) MAP AL021937 [1,2]
IGLJ-C/OR18 (4) IGLJ-C/OR18*01 ORF Shortarm p of the chr 18 RP11-838N2 MAP AP001025 [1,2] 130863-131211
IGLJ-C/OR18*02 P Shortarm p of the chr 18 J00255 [3] (3)

MAP: Mapped reference sequences.

IMGT notes:
  1. (1) dJ90G24.3 [2] isolated from AL008723.8 has 82.7 % identity with J00252 (IGLC1*01).
  2. (2) dJ149A16.1 [2] isolated from AL021937.1 has 51.0 % identity with J00252 (IGLC1*01). The 5' end is telomeric whereas the 3' end is centromeric.
  3. (3) J00255 has several stop codons whereas AP001025 is an ORF.
  4. (4) IGLJ-C/OR18 is the only known processed immunoglobulin gene, with IGHEP2.
IMGT references:
  1. [1] Dunham, I. et al., Nature, 402, 489-495 (1999). PMID:10591208
  2. [2] The Sanger Center: Human chromosome 22 Home.
  3. [3] Hollis, G.F. et al., Nature, 296, 321-325 (1982). PMID:6801526
Created:
09/03/2000
Last updated:
22/09/2023
Authors:
Nathalie Bosc