Details

OrganismHuman
Sequence NameIGKV1D-8*i01
IMGT Name
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 MK308861A007A007 VKIGKV1D-8*01_S8780

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 IDA00052
CuratorMats Ohlin
Curator addressDept. of Immunotechnology, Lund University, Medicon Village building 406, S-22381 Lund, Sweden
Version1
Release Date2020-08-01 00:00:00
Release Notes

Published by IARC on 1/8/2020.

LocusIGK
Sequence TypeV
Gene Subgroup1D
Gene Designation8
Allele Designationi01

Acknowledgements

Individuals acknowledged as contributing to this sequence:

NameInstitutionORCID ID
Néstor Vázquez BernatKarolinska Institutet SE-171 77 Stockholm

Notes

Notes are added by IARC reviewers.

This inference was considered at IARC Meeting 49 on February 4th 2020, at which it was noted:

The sequence was seen in 0.3% of all unmutated rearrangements, with 747 sequences including 538 perfect matches to the inferred allele. There was abundant variation in the CDR3 regions of the aligned sequences, though relatively large numbers of sequences were clonally related (42 “Unique CDR3s with unmutated”). The IGKV1D-8*01 allele was also present in the genotype, at a similar frequency (0.4% of all unmutated sequences; 976 sequences; 758 unmutated sequences). It was noted that the select set available in SRA/ENA is very limited in size (essentially only representing 2 different rearrangements, either involving IGKJ1 or IGKJ2) as only full-length sequences (covering all bases of the V gene up to and including base 335) had been included in the submitted set. IGKV1-8*01 was also present at high frequency (7743 sequences), but this sequence has 12 nucleotide differences to the inference under consideration. Haplotype data is unavailable. Plots of the final 3’ nucleotides showed a high level of variability, making it impossible to determine the final three nucleotides with certainty. The sequence, up to and including nucleotide 332, was affirmed as a Level 1 sequence. Uncertainty regarding nucleotides 333-335 will be indicated in IARC and OGRDB publications by three dots at the end of the affirmed 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
2020-08-01 13:31:50
Version 1 published

Published by IARC on 1/8/2020.