Details

OrganismHuman
Sequence NameIGHV4-59*i02
IMGT NameIGHV4-59*11
Affirmation Level1
Full Sequence
Coding Sequence
FunctionalTrue
Inference TypeRearranged Only
Alternative names
Paralogs

Evidence

The table below lists the submissions, and the inferences within them, on which this published sequence is based. The list may be short when the sequence is first published, containing, for example, reference to just a single submission, but is expected to grow over time as additional inferences are submitted.

'Sequence Match' indicates whether the inference exactly matches the sequence, and clicking on the tick or cross will provide an alignment. Mismatches may be caused, for example, by the inclusion of leader sequences, or nucleotides in the inference which do not in IARC's opinion have sufficient evidence for inclusion in the sequence.

Submission IDAccession NoSubject IDGenotype NameSequence NameSequence Match
S00010 MK471385B16B16IGHV4-59*01_S8652

Supporting Observations

Sequences in other published genotypes which have been identified by IARC and support the inference:

No Items

Observations in VDJbase

Inferred sequences in VDJbase that match this sequence:

No Items

Additional Information

Sequence IDA00048
CuratorMats Ohlin
Curator addressDept. of Immunotechnology, Lund University, Medicon Village building 406, S-22381 Lund, Sweden
Version1
Release Date2019-12-12 00:00:00
Release Notes

Submission published by IARC on Dec 13, 2019.

LocusIGH
Sequence TypeV
Gene Subgroup4
Gene Designation59
Allele Designationi02

Acknowledgements

Individuals acknowledged as contributing to this sequence:

NameInstitutionORCID ID
Davide Bagnaradavide.bagnara@edu.unige.it
Martin CorcoranDepartment of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institute, Stockholm Sweden.

Notes

Notes are added by IARC reviewers.

Assessed by IARC on December 2, 2019 during meeting 46.

The committee considered IGHV4-59*01_S8652 (T109C) of Genotype B16 of submission S00010, which was previously evaluated as IGHV4-59*01_S5140 of submission S00006 at Meeting 12. It was affirmed as a Level 0 sequence at that time.

The sequence was seen in 3.03% of all unmutated rearrangements, with 18133 sequences including 8545 perfect matches to the inferred allele. There was abundant variation in the CDR3 regions of the aligned sequences. One other IGHV4-59 allele was present in the genotype, as well as two IGHV4-4 sequences and one IGHV4-61 sequences. Haplotype data is supportive of the inference, though the haplotype ratios likely reflect the presence of some chimeric sequences within the dataset. The ratios for the two IGHV4-59 sequences were 77:23 for the inference and 19:81 for the *01 allele, suggesting that the sequences are carried on different chromosomes. The sequence, up to and including nucleotide 319, was affirmed as a Level 1 sequence, but was subsequently identified as the recently reported allele IGHV4-59*11. The sequence submitted to Genbank lacked the 320th nucleotide that is noted in the IMGT sequence. In IARC and OGRDB communications, a dot at the 3’ end of the sequence shows that the IARC believes there is a nucleotide missing from the sequence. The affirmed sequence will be submitted to IMGT as IGHV4-59*i02, as a record of the rearrangability (and therefore likely functionality) of the sequence.

Attachments

Attachment File Name
 

History

History records log the times and reasons for the publication of each version of this sequence record.

Andrew Collins
2019-12-12 22:51:38
Version 1 published

Submission published by IARC on Dec 13, 2019.