Details

SpeciesHuman
Species subgroup
Subgroup typenone
Sequence NameIGHV3-43D*05
IUIS NameIGHV3-43D*05
Alternative namesIGHV3-43D*i02
Affirmation Level1
Full Sequence
Coding Sequence
FunctionalityORF
Inference TypeRearranged Only
MappedTrue
Paralogs
Paralog RepFalse

Observations in VDJbase

Inferred sequences in VDJbase that match this sequence:

VDJbase Allele NameSubjectsSequence Match
IGHV3-43D*04_g4a 1

Un-rearranged Observations

Un-rearranged sequence observations that support this sequence:

AccessionTypeRepositoryStartEnd
OW151136InferredGenBank1297

Additional Information

Sequence IDA02558
CuratorWilliam Lees
Curator addressBirkbeck College, University of London, Malet Street, London
Version3
Release Date2024-01-11
Release Notes

First published version.

LocusIGH
Sequence TypeV
Gene Subgroup3
Gene Designation43D
Allele Designationi02

Acknowledgements

Individuals acknowledged as contributing to this sequence:

No Items

Notes

Notes are added by IARC reviewers.

This inferred allele was assessed at IARC meeting 100 on June 8th, 2022. IGHV3-43D*04_G4A was inferred in subject S10 (VDJ-base: P1_I10_S1). The genotype also carried IGHV3-43*01 but no other allele of IGHV3-43D. The inference was supported by a relatively small number of sequences (104) and unmutated sequences (93), a low overall frequency in the unmutated population (0.3%) and a small but diverse set of unique CDR3s (89) in the unmutated sequence set. Its allelic ratio was 100%. Haplotyping based on allelic diversity in IGHJ6 was possible and the alleles distributed to one haplotype, a haplotype different from that associated with the allele IGHV3-43 (IGHV3-43D*04_G4A: 100:0; IGHV3-43*01: 0:100). Reads of IGHV3-43D*04_G4A were associated to the same haplotype as those of IGHV4-38-2, a common duplication combination. Reads of IGHV3-43D*04_G4A were associated to an upstream region similar to that of other alleles of IGHV3-43D (but not similar to alleles of IGHV3-43) (doi: 10.3389/fimmu.2021.730105). Altogether, the association of this allele to IGHV3-43D is reasonable. IARC affirms the sequence at level 1 up to and including base 321 in agreement with past practice. It is acknowledged that the allele most likely carries one additional base, typically A at base position 322. A trailing “.” indicates IARC’s opinion that the sequence is likely to contain one additional 3’-nucleotides for which there is insufficient evidence to make an affirmation. The allele is given the name IGHV3-43D*i02.

Additional information for this sequence was imported into OGRDB via bulk update with the following notes:
Sequence annotation is based on Genbank sample OW151136
VDJbase example haplotype: Y
Mapped by IARC haplotype

TR-IG NRC Report (2023-1a) allocated the IUIS name IGHV3-43D*05 to this allele

The report stated:

The TR-IG NRC have determined that the IARC-affirmed inferred sequence IGHV3-43D*i02 should be confirmed as IGHV3-43D*05. The missing terminal nucleotide of the sequence can be confirmed as ‘A’ by reference to recent genomic sequences of Rodriguez and colleagues that are reported in the VDJbase database from three individuals. This evidence is accessible via the VDJbase genomic data gene table (https://vdjbase.org/genetable ). The location of the sequence was well described in the IARC report, and is demonstrated by good haplotypable AIRR-seq data. Data strongly suggests that the novel allele is at the IGHV3-43D locus rather than the IGHV3-43 locus, and IGHV3-43 and IGHV3-43D are at least 22 nucleotides different from other IGHV genes.

Attachments

No Items

History

History logs the times and reasons for the publication of each version of this sequence.

Mats Ohlin
2022-07-25 10:53:31
Version 1 published

The allele was published by IARC on July 25th, 2022.

William Lees
2023-07-10 11:24:39
Version 2 published

Bulk upload of sequences for the AIRR-C Human IG germline sets

William Lees
2024-01-11 09:58:38
Version 3 published

First published version.

Changes from previous version

v2v3
IUIS NameIGHV3-43D*05
Sequence NameIGHV3-43D*i02IGHV3-43D*05
Alternative namesIGHV3-43D*i02
Subgroup typenone
Coding Sequence
Gene end297298
Codon Frame1
Extension?TrueFalse
3' ExtensionA
5' Extension
Noteschanged

Versions

All published versions of this sequence.

Sequence NameIMGT NameAlternative namesInference TypeAffirmation LevelSpecies subgroupSubgroup typeVersionDate
IGHV3-43D*i02IGHV3-43D*04 G4ARearranged1none12022-07-25
IGHV3-43D*i02Rearranged Only122023-07-10
IGHV3-43D*05IGHV3-43D*05IGHV3-43D*i02Rearranged Only1none32024-01-11