Details

OrganismHuman
Sequence NameIGHV3-53*i01
IMGT NameIGHV3-53*05
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
S00028 MK308860A007A007 VHIGHV3-53*02_S0744

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:

VDJbase Allele NameSubjectsSequence Match
IGHV3-53*02_c288t 2

Additional Information

Sequence IDA00038
CuratorAndrew Collins
Curator addressSchool of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney Australia
Version2
Release Date2019-11-26 00:00:00
Release Notes

Updated with IMGT namne.

LocusIGH
Sequence TypeV
Gene Subgroup3
Gene Designation53
Allele Designationi01

Acknowledgements

Individuals acknowledged as contributing to this sequence:

No Items

Notes

Notes are added by IARC reviewers.

The 40th meeting of the IARC on August 7th 2019 considered the sequence IGHV3-53*02_S0744. The sequence represents IGHV3-53*02 C288T in the IMGT numbering system. The committee noted a rearrangement frequency of 0.7%, with 5149 alignments including 2426 perfect matches to the inferred allele. Alignments were also seen to three other IGHV3-53 sequences, though only one of these sequences was abundant (IGHV3-53*04: 3448 alignments, 2149 unmutated alignments). Haplotyping based on IGHJ6 alleles confirmed the segregation of reads associated with these two alleles to the different haplotypes Alignments to the two other alleles shown in the genotype were at trivial levels (<0.01% of ‘unmutated’ alignments, in each case). There were 742 different CDR3s associated with the inference, including 292 different CDR3s associated with unmutated alignments. The committee agreed that the sequence should be accepted as a Level 1 sequence as IGHV3-53*i01. In line with previous policy, the submitted sequence was recognized up to and including nucleotide 319. A trailing “.” in the affirmed sequence indicates IARC’s opinion that the sequence is likely to contain an additional 3’ nucleotide for which there is insufficient evidence to make an affirmation.

Reanalysis of the original submission at Meeting 43 of the IARC on October 7, 2019 again identified the same novel allele IGHV3-53*02_S0744 (IGHV3-53*02 C288T) with 5425 sequences aand 2447 perfect matches and 300 Unique CDR3s with unmutated Seqs. In this analysis only one other allele of IGHV3-53 was seen (as very rare inferences had been removed by IgDiscover filtering), IGHV3-53*04 with 3551 sequences and 2163 perfect matches giving a 60:40 allelic ratio. These alleles were very well separated by IGHJ6-based haplotype analysis (1:99 and 99:1, respectively). The re-analysis thus confirmed the inference of IGHV3-53*i01 as a Level 1 sequence. In line with previous policy, the submitted sequence is recognized up to and including nucleotide 319. A trailing “.” in the affirmed sequence indicates IARC’s opinion that the sequence is likely to contain an additional 3’ nucleotide for which there is insufficient evidence to make an affirmation.

Attachments

Attachment File Name
 

History

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

Andrew Collins
2019-10-31 05:32:03
Version 1 published

This sequence was considered and affirmed at IARC Meetings 40 and 43.

Mats Ohlin
2019-11-26 21:03:51
Version 2 published

Updated with IMGT namne.