IMGT Repertoire (IG and TR)

120kb upstream from JH region
135Kb upstream from JH region
150Kb upstream from JH region
Inferred functionality:(F)
truncated pseudogene not assigned to subgroups with functional genes, no V-RS, several STOP-CODON in V-REGION
because frameshifts in V-REGION
no L-PART1, no L-PART2, frameshifts in V-REGION: several insertions and deletions
no L-PART1, no L-PART2, frameshifts in V-REGION: deletion of 2 nt and deletion of 1 nt in FR1-IMGT
frameshifts and stop-codon in V-exon
because of deletion of a nucleotide in FR2-IMGT, leading to frameshift in CDR2-IMGT
frameshift in V-REGION: deletion of 1 nt in FR2-IMGT
non canonical DONOR-SPLICE nga instead of ngt and 2nd-CYS is replaced by Tyr
noncanonical DONOR-SPLICE ngc instead of ngt, however this V-GENE has been seen rearranged in vivo
INSERTION of 4 nucleotides (TACC) between codons 28 and 29 in the CDR1-IMGT leading to a frameshift
frameshift in V-REGION: insertion of 4 nt in CDR1-IMGT
because of frameshift in L-PART1
frameshift in L-PART1
frameshift in L-PART1 causing defectuous DONOR-SPLICE
frameshift in L-PART1: deletion of 1 nt causing defectuous DONOR-SPLICE
previously IGHV1-e*01
175Kb upstream from JH region
several STOP-CODON in V-REGION, no CONSERVED-TRP: STOP-CODON instead of Trp, no INIT-CODON: Val instead of Met, frameshift in L-PART1 causing defectuous DONOR-SPLICE
ORF, 1st_Cys is replaced by Arg
no CONSERVED-TRP: Gly instead of Trp
frameshifts in V-REGION: deletion of 1 nt in FR1-IMGT
frameshift in V-REGION: deletion of 1 nt in FR1-IMGT
frameshift in V-REGION: deletion of 2 nt in FR1-IMGT
STOP-CODON in L-PART1, several STOP-CODON in V-REGION, frameshift in V-REGION: insertion of 1 nt in FR3-IMGT
In the ID line RNA should be replaced by DNA, correction asked to EMBL on the 10/01/2001.
In the current annotation, only the new genes alleles and the new reference sequences are annotated
unmapped
noncanonical V-HEPTAMER: tcctgtg instead of cacagtg
because no usual V-HEPTAMER, TCCTGTG instead of CACAGTG
no L-PART2
1st-CYS is replaced by Phe
no 1st-CYS: Phe instead of Cys
The CDR2 length (7) of this allele differs from the CDR2 length of other IGHV3-21 alleles (8), first described in Corcoran MM et al., Nat Commun. 2016. PMID: 27995928; PMCID: PMC5187446.
In frame STOP-CODON in FR3-IMGT, CONSERVED-TRP (tgg) residue at the beginning of FR2 is replaced by GLY (ggg).
"IGHV3-23*04" being assigned to AJ879486 in IMGT/GENE-DB, the sequence AY757302 was assigned to IGHV3-23*05 by IMGT-NC and represents the IMGT reference sequence for the IGHV3-23*05 allele.
because of in frame STOP-CODON, CONSERVED_TRP (tgg) residue at the beginning of FR2 is replaced by CYS (tgt).
in frame STOP-CODON in FR3-IMGT
ORF,C41 instead of W.(other alleles are Pseudo owing to a codon stop in 103.In HM855898 the codon stop is replaced by a Y)
STOP-CODON in V-REGION: position 103
In frame STOP-CODON in L-PART1 and V-REGION, and unusual V-HEPTAMER sequence.
several STOP-CODON in V-REGION, STOP-CODON in L-PART1
1 nt deletion compared to the one displayed in figure 3 of Olee et al., J. Clin. Invest., 88, 193-203 (1991). As the gene is described as functional in the manuscript, one missing nt 'g' has been added at position 286 (codon 96) in the IMGT/GENE-DB reference sequence
previously IGHV3-30-5*01
previously IGHV3-30-5
frameshift in V-REGION: deletion of 10 nt in FR3-IMGT
because of STOP-CODONs in V-EXON
STOP-CODON in L-PART2, several STOP-CODON in V-REGION
in frame STOP-CODON in L-PART1 and V-REGION
in frame STOP-CODON in V-EXON
in frame STOP-CODON in V-REGION
several STOP-CODON in V-REGION
in frame STOP-CODON in V-EXON and no V-RS
because of STOP-CODONs in L-PART1 and V-REGION
in frame STOP-CODONs in V-REGION at positions AA 38, 52 and 106
because of STOP-CODON in V-REGION, no recombination signals
frameshifts and STOP-CODON's in V-REGION, no recombination signals
this gene has not been found rearranged
non canonical DONOR-SPLICE: nat instead of ngt
noncanonical DONOR-SPLICE: nat instead of ngt
STOP-CODON in V-REGION: position 52
because of STOP CODONs in L-PART1 and frameshifts in V-REGION
frameshift in V-REGION: insertion of 1 nt in FR1-IMGT
STOP-CODON in L-PART1 and frameshifts and STOP-CODON in V-REGION
STOP-CODON in L-PART1, frameshift in V-REGION: insertion of 1 nt in FR1-IMGT
no INIT-CODON: Arg instead of Met
because no INIT-CODON in L-PART1
STOP-CODON in L-PART2 and frameshifts in L-PART1 and V-REGION
STOP-CODON in V-REGION: position 9
Pseudogene because of in frame stop_codon and unusual recombination signals
frameshift in V-REGION: insertion of 8 nt in FR1-IMGT
because STOP-CODON in V-REGION
no L-PART1, frameshifts in V-REGION: several insertions and deletions
no L-PART1, frameshifts in V-REGION: several insertions ans deletions
frameshifts in V-REGION: several insertions and deletions
because insertion of one nucleotide (g) around position 17 in FR1-IMGT,and STOP-CODON at position 75 in FR3-IMGT
frameshift in V-REGION: insertion of 1 in FR1-IMGT
because of STOP-CODON in V-REGION
frameshift in V-REGION: deletion of 1 nt in FR3-IMGT
STOP-CODON in V-REGION: position 51
frameshift in V-REGION: deletion of 1 in FR3-IMGT
STOP-CODON in V-REGION: positions 38, 106
frameshift in V-REGION: insertion of 1 nt in CDR1-IMGT
Frameshift in V-REGION
because of STOP-CODON in FR3-IMGT
STOP-CODON in V-REGION: position 67
no DONOR-SPLICE, frameshifts in V-REGION: several insertions
frameshift in L-PART1 causing defectuous DONOR-SPLICE, frameshifts in V-REGION: several insertions and deletions
no DONOR-SPLICE, frameshifts in V-REGION: several insertions and deletions
Pseudogene because of in frame STOP-CODON and a DELETION causing a frameshift in V-REGION
several STOP-CODON in V-REGION, no CONSERVED-TRP: STOP-CODON instead of Trp, frameshift in V-REGION: deletion of 2 nt in FR2-IMGT
STOP-CODON in V-REGION: position 3, frameshifts in V-REGION: several insertions and deletions
frameshift in L-PART1 causing defectuous DONOR-SPLICE, frameshift in V-REGION: deletion of 2 nt
frameshift in L-PART1: deletion of 1 nt causing defectuous DONOR-SPLICE, frameshift in V-REGION: deletion of 1 nt in FR1-IMGT
frameshift in V-REGION: deletion of 1 nt in FR1-IMGT, frameshift in L-PART1 causing defectuous DONOR-SPLICE
155Kb upstream form JH region
previously IGHV4-30-1*02
previously IGHV4-30-1*03
previously IGHV4-31*04
previously IGHV4-30-1*05
previously IGHV4-30-1*06
previously IGHV4-31*07
previously IGHV4-30-1*08
G00-128-528, in frame stop codon in CDR1
The CDR1 length (8) of this allele differs from the CDR1 length of other IGHV4-61 alleles (10), first described in Parks T et al., Nat Commun. 8,14946 (2017).PMID: 28492228.
STOP-CODON in V-REGION: position 75
STOP-CODON in V-REGION: position 75, no V-RS
The absence of nt in codon 96 (c288>del compared with X92227) is a sequencing error because of an expressed cDNA (U00543) has been described with 99.65% identity in V-REGION. Therefore, the functionality of IGHV5-a*02 has been changed from pseudogene (P) to functional (F).
unspliced
160Kb upstream from JH region
STOP-CODON in V-REGION: position 43, no V-RS
in frame STOP-CODON in L-PART1, in frame STOP-CODONs in V-REGION at positions AA 43, 44 and 54
STOP-CODON in L-PART1, STOP-CODON in V-REGION: position 43, 44, 54
no L-PART1, no L-PART2, frameshifts in V-REGION: several insertions
not yet fully annotated.
no L-PART1, no L-PART2, STOP-CODON in V-REGION
in frame stop-codon, deletion and insertion of nucleotides leading to frameshifts
because non usual V-HEPTAMER, CACCATG instead of CACAGTG
noncanonical V-HEPTAMER:caccatg instead of cacagtg, noncanonical V-NONAMER:tcagaaatc instead of acacaaacc
STOP-CODON in FR1-IMGT
noncanonical V-HEPTAMER: catcgtg instead of cacagtg, noncanonical V-NONAMER: agacagact instead of acacaaacc
STOP-CODON in V-REGION: position 15
noncanonical V-HEPTAMER: catcgtg instead of cacagtg and noncanonical V-NONAMER: agacagact instead of acacaaacc
May be defective on structural grounds [Chothia et al., J. Mol. Biol., 227, 799-817 (1992)].
Arbitrary limits of the DNA sequence assigned to the different IGHV genes. V-GENE positions are those in the Accession numbers AB019437, AB019438, AB019439, AB019440, AB019441.
Submitted to the INSDC (18-FEB-2019) by Rodriguez O.L., Watson C.T. in department of Genetics and Data Science, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
Inferred allele: IMGT-NC_Report_2019-11-0418_Homsap_IGHV.
Truncated V-GENE with completely divergent 3' region.
This sequence has been assigned by IMGT to a previously described gene by sequence alignment.
Absence of the conventional DONOR-SPLICE site (ngc instead of ngt) at the 5' end of the L-PART1, however this V-GENE has been seen rearranged in vivo.
Owing to a sequence gap and an assembly error, IGHV1-38-4 and IGHV(III)-38-1D positions appear downstream of IGHV4-38-2, whereas they should be located upstream of the IGHV(II)-43-1D - IGHV3-43D - IGHV3-42D -IGHV7-40D duplication.
It is not possible to assign these sequences to a single allele (owing, for example, to their partiality).
The DELETION of nucleotides 208 to 248 in M99645 EMBL flat file is probably a typing error. This DELETION does not exist in the paper.
The IMGT000054, IMGT000055, IMGT000056, IMGT000057 and IMGT000058 sequences are in direct orientation relative to the IMGT Homo sapiens IGH locus. These IMGT accession number sequences are reverse-complement respectively, of the GEDI (GenBank/ENA/DDBJ/IMGT/LIGM-DB) AC279151, AC279152, AC279153, AC279154 and AC279155, which are in opposite orientation relative to the IMGT Homo sapiens IGH locus.
The INSERTION of one nucleotide between position 195 and 196 in M99646 EMBL flat file is probably a typing error. This insertion does not exist in the paper.
Inferred allele: IMGT-NC_Report_2019-18-1218_Homsap_IGHV.
Inferred allele: IMGT-NC_Report_2021-3-1117_Homsap_IGHV.
The sequence described in the manuscript is different from the one submitted to the EMBL data library. We refer to the sequence published in the original manuscript .
Unusual V-HEPTAMER and V-NONAMER sequences (cacaaag and acaaaaccc instead of cacagtg and acaaaaacc). g100>del ,g107>del, g117>del may result from sequencing errors in X62108. The sequence is probably identical to allele *02 with a CDR1-IMGT of 10 aminoacids, like the other IGHV2 subgroup genes.
In frame STOP-CODON and recombination signal sequences not conserved.
Unusual V-HEPTAMER sequence (cacagag instead of cacagtg) but this V-GENE has been seen rearranged.
MN337621 previously assigned to IGHV3-9*01 (sequence from the literature) have been now assigned to IGHV3-9*04 (IMGT reference sequence). Authors change in EMBL flat file the nucleotide sequence version 1 T307>C in version 2.
Germline transcript.
Unusual V-HEPTAMER sequence : cactgtg instead of cacagtg, ACCEPTOR-SPLICE site at the 5' side of the V-EXON and second part of the leader exon (L-PART2) are missing.
V-NONAMER sequence (acacaaacg) differs from the family consensus: acacaaacc but this V-GENE has been seen rearranged.
Inferred allele: IMGT-NC_Report_2019-17-1118_Homsap_IGHV.
IARC committee confirms the allele sequence up to and including nucleotide 319 (according to IMGT numbering).
In frame STOP-CODON at position 67 in FR3-IMGT, CONSERVED-TRP (tgg) residue at the beginning of FR2 is replaced by GLY (ggg).
VH26 [J00236, Matthyssens and Rabbitts, P.N.A.S U.S.A, 77, 6561-6565 (1980)] corrected by Chen et al. (M83136).
in frame STOP-CODON in FR3-IMGT, CONSERVED_TRP (tgg) residue at the beginning of FR2 is replaced by CYS (tgt).
The M77323 sequence (Baj clone) has 1 nt deletion compared to the one displayed in figure 3 of Olee et al., J. Clin. Invest., 88, 193-203 (1991) [27]. As the gene is described as functional in the manuscript, one missing nt has been added at position 286 (codon 96) in the IMGT/GENE-DB reference sequence and in Alignment of alleles to maintain the reading frame.
In EMBL/GenBank flat file, intron is missing. Request has been done by IMGT/LIGM-DB annotators for sequence correction.
Except for the IGHV3-30-5*01 (AC244456 and KC162925) and the IGHV3-30-5*02 (AC245243), sequences of the polymorphic IGHV3-30-5 gene cannot be differenciated from those of the IGHV3-30 gene. All sequences are described therefore as "IGHV3-30 alleles" by comparison to the allele *01 of IGHV3-30 (M83134).However, it is not excluded that some of these "alleles" belong exclusively to the IGHV3-30-5 gene.
Unusual V-HEPTAMER sequence : cactgtg instead of cacagtg, may be defective on structural grounds [Chothia et al., J. Mol. Biol., 227, 799-817 (1992)].
Translational frameshift in FR1 and STOP-CODON, no recombination signal sequences.
DELETION of 2 nucleotides in CDR2 leading to a frameshift after residue 61 and STOP-CODON.
In frame STOP-CODON in FR2 and 1 bp DELETION leading to a frameshift after residue 70 in FR3-IMGT.
One nucleotide INSERTION between codons 15, 16 in the FR1 leading to a frameshift and STOP-CODON.
Missing translation initiation codon and frameshift after residue 80 in the FR3 due to one nucleotide DELETION.
V-NONAMER sequence (acacagacc) differs from the subgroup consensus: acacaaacc.
In frame STOP-CODON in the FR1.
In frame STOP-CODON and unusual recombination signal sequences.
Submitted to the INSDC (27-OCT-1992) by Tomlinson M. in MRC Centre for Protein Engineering, Hills Road, Cambridge, CB2 2QH, U.K.
The sequence described in the manuscript is different from the one submitted to the EMBL data library. We refer to the sequence published in the original manuscript. STOP-CODON at position 46 and mutation in the V-HEPTAMER recombination signal.
In frame STOP-CODONs and not canonical recombination signal sequences.
V-NONAMER differs from the subgroup consensus: acacaaacc but this V-GENE has been seen rearranged.
Unusual V-HEPTAMER recombination signal sequence: cacagcg instead of cacagtg this V-GENE has been seen rearranged.
The two substitutions c46>t (P16>S) and g308>a (C103>Y) in the X56363 EMBL flat file are probably typing errors. These substitutions do not exist in the publication (VH4.19, Figure 1, Sanz I. et al. EMBO J. 1989, 8(12): 3741-3748. PMID: 2511001. The codon R106 (aga) also missing in the flat file has been added in the Alignment of alleles.
In frame STOP-CODON and DELETION of 2 nucleotides at the end of FR2 leading to a translational frameshift.
IMGT note: The sequence HM855939 obtained by Next Generation Sequencing (NGS) has the features of a chimeric sequence between two different genes belonging to the Homo sapiens IGHV3 subgroup (IGHV3-30*02 in 5' and IGHV3-23 or IGHV3-66 in 3'). Five other sequences obtained from NGS reads, HM855685, HM855784, HM855853, HM855863 and HM855880, are most probably duplicate copies of the same unique chimeric sequence. These chimeric sequences (HM855939 and the five duplicates) need therefore to be confirmed by analysis of other genomic and mapped germline clones (M-P. Lefranc, 17/12/10).
Sequences of the polymorphic IGHV4-30-1 gene cannot be differenciated from those of the IGHV4-31 gene.All sequences are described therefore as "IGHV4-31 alleles" by comparison to the allele *01 of IGHV4-31 (L10098).However, it is not excluded that some of these "alleles" belong exclusively to the IGHV4-30-1 gene.
The sequence described in the manuscript is different from the one submitted to the EMBL data library. We refer to the sequence submitted to the EMBL data library (X56359).
VH32 (X92279, Humphries et al.) corrected by Sanz et al. (X92227). The absence of nt in codon 96 in the sequence X92279 (c288>del compared with X92227) is a sequencing error because of an expressed cDNA (U00543) has been described. Therefore, the functionality of IGHV5-a*02 has been changed from pseudogene (P) to functional (F).
VH251 (M18806, Shen et al.) corrected by Sanz et al (X92226). The sequence (X92226) described in the manuscript is different from the one submitted to the EMBL data library : one nucleotide (g) inserted in the file compared to the publication. Correction asked to EMBL by IMGT and the authors (Capra, D.). Corrected 6th December 1996.
25 bp DELETION in the immediate 3' flank resulting in loss of the V-HEPTAMER and part of the spacer region [J. Exp. Med., 173, 1529-1535 (1991)]In addition in X92213, but not in the other sequences, there is an incorrect translation frame due to the INSERTION of two nucleotides (a730 and a732) in L-PART2, but these insertions may represent sequencing errors.
One nucleotide INSERTION in L-PART1 and two nucleotides DELETIONS in CDR2 leading to a frameshift; 25 bp DELETION resulting in loss of the V-HEPTAMER and part of the spacer region [J. Exp. Med., 173, 1529-1535 (1991)].
Or VI-4.1b: extraordinary polymorphic allele [EMBO J., 10, 3641-3645 (1991)]. V-NONAMER sequence differs from the subgroup consensus: tctaaaacc.
The sequences Z12320 and L10059 previously designated as IGHV7-40*03 have been shown to correspond to allele IGHV7-34-1*01 (06/03/2014).
Wong et al., Autoimmunity, 20, 191-199 (1995)
In frame STOP-CODON at position 27.
Partial sequence whose functionality has been assigned by comparison to another sequence of the gene.
The allele IGHV1-2*08 has been permanently removed due to its similarity to an orphon of chromosome 15 (IGHV1/OR15-1*01) and the existence of a gap in the sequence that could imply its misplacement on the locus.
The definitive IMGT gene name IGHV1-38-4 has been assigned to IGHV1-c owing to its localization in AC241995 and AC234225 [Watson C.T. et al., Am. J. Hum. Genet., 92, 1-17 (2013)].
The definitive IMGT gene name IGHV1-69-2 has been assigned to IGHV1-f owing to its localization in AC245023 and AC245094 [Watson C.T. et al., Am. J. Hum. Genet., 92, 1-17 (2013)].
The definitive IMGT gene name IGHV3-38-3 has been assigned to IGHV3-d owing to its localization in AC241995 and AC234225 [Watson C.T. et al., Am. J. Hum. Genet., 92, 1-17 (2013)].
The IGHV5-10-1 (F) and IGHV3-64D (F) genes have been described as a CNV and localized as an alternative to the presence of IGHV2-10 (P), IGHV3-9 (F) and IGHV1-8 (F) in one haplotype [Watson C.T. et al., Am. J. Hum. Genet., 92, 1-17 (2013)].
The definitive IMGT gene name IGHV3-69-1 has been assigned to IGHV3-h owing to its localization in AC245023 and AC245094 [Watson C.T. et al., Am. J. Hum. Genet., 92, 1-17 (2013)].
Missing translation initiation codon, (atg) is replaced by (aag)
The definitive IMGT gene name IGHV4-38-2 has been assigned to IGHV4-b owing to its localization in AC233755 and KC162926 [Watson C.T. et al., Am. J. Hum. Genet., 92, 1-17 (2013)].
The definitive IMGT gene name IGHV5-10-1 has been assigned to IGHV5-a owing to its localization in AC245085 and AC247036 [Watson C.T. et al., Am. J. Hum. Genet., 92, 1-17 (2013)].

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IMGT Repertoire (IG and TR)

Dynamic gene tables per IMGT group and per species (IMGT/GeneTables)

Gene table legend:

IMGT notes: ↑

IMGT references: ↑

IMGT Repertoire (IG and TR)

Dynamic gene tables per IMGT group and per species (IMGT/GeneTables)

Version 1.4

Version 1.3

Version 1.2

Version 1.1

Version 1.0

Gene table legend:

IMGT notes: ↑

IMGT references: ↑