Details

SpeciesHuman
Species subgroup
Subgroup type
Sequence NameIGHV4-39*08
IUIS NameIGHV4-39*08
Alternative namesIGHV4-39*i01
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
IGHV4-39*01_c66g 1

Un-rearranged Observations

Un-rearranged sequence observations that support this sequence:

AccessionTypeRepositoryStartEnd
OU596110InferredGenBank1298

Extension

3' ExtensionA
3' start
3' end

Additional Information

Sequence IDA00070
CuratorWilliam Lees
Curator addressBirkbeck College, University of London, Malet Street, London
Version2
Release Date2023-07-10
Release Notes

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

LocusIGH
Sequence TypeV
Gene Subgroup4
Gene Designation39
Allele Designation08

Acknowledgements

Individuals acknowledged as contributing to this sequence:

No Items

Notes

Notes are added by IARC reviewers.

IARC meeting 62 (Nov 3rd, 2020):
The meeting considered the inference of the variant IGHV4-39*01_c66g, in the VDJbase dataset of sample P1_I90_S1. The sequence was seen in 2.74% of all unmutated rearrangements, with 1217 sequences including 1098 perfect matches to the inferred allele. There was abundant variation in the CDR3 regions of the aligned sequences. IGHV4-39*01 was also present in the genotype, at a similar frequency (3.09% of all unmutated sequences,
1360 sequences, 1239 unmutated sequences). Haplotyping data showed almost perfect separation of the assigned alleles. Plots of the final 3’ nucleotides of the inference were unavailable. The inferred sequence was tentatively affirmed as a Level 1 sequence. The final 3’ nucleotides will be considered at a later date, at which time the affirmed sequence will be noted in the IARC minutes.

IARC meeting 83 (Oct 18th, 2021):
IGHV4-39*01_C66G was inferred in subject S86 (VDJbase: P1_I90_S1), a genotype that also carries IGHV4-39*01. This inference has previously been pre-assessed at IARC meeting 62 (https://www.antibodysociety.org/wordpress/wp-content/uploads/2021/04/Meeting-62-3_11_20-minutes.pdf). IGHV4-39*01_C66G was well expressed, represented by 1305 sequences, 1135 unmutated sequences, 1131 unique CDR3s in the unmutated sequence set, showed an allelic frequency of 48%, and represented 3.3% of all unmutated reads of the genotype. Haplotyping based on allelic diversity in IGHJ6 was possible and the alleles distributed well between haplotypes (IGHV4-39*01_C66G: 2:98; IGHV4-39*01: 100:0). IARC affirms the sequence as a level 1 sequence up to and including base 319 in agreement with past practice. It is acknowledged that the allele most likely carries one additional base, typically A at base position 320. A trailing “.” 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. It is known that the second last base of alleles of IGHV4-39 may be either C or G. The data describing the final bases of this inferred allele strongly supports that this base (319) is a C. The inference of IGHV4-39*07_C288A in data set VDJbase: P1_I29_S1 in contrast suggests that this allele features a G as the penultimate residue, illustrating that the inference process can pick up a difference at the second last base of alleles. The allele representing IGHV4-39*01_C66G is given the name IGHV4-39*i01.

>IGHV4-39*i01
CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACGTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGAC.

Additional information for this sequence was imported into OGRDB via bulk update with the following notes:
Sequence annotation is based on Genbank sample OU596110
VDJbase example haplotype: P1_I90 (*01_c66g)
VDJbase example haplotype: P1_I90 (*01_c66g)
Mapped by P1_I90 haplotype

Attachments

No Items

History

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

Mats Ohlin
2021-11-01 22:50:18
Version 1 published

Submission published by IARC on November 1st, 2021

Mats Ohlin
2021-11-17 15:25:25
IMGT Name updated to IGHV4-39*08

IMGT Name updated.

William Lees
2023-07-10 11:24:41
Version 2 published

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

Changes from previous version

v1v2
CuratorMats OhlinWilliam Lees
Curator addressDept. of Immunotechnology, Lund University, Medicon Village building 406, S-22381 Lund, SwedenBirkbeck College, University of London, Malet Street, London
Sequence NameIGHV4-39*i01IGHV4-39*08
Alternative namesIGHV4-39*i01
Chromosome14
MappedTrue
FunctionalityFORF
Subgroup typenone
Allele Designationi0108
Full Sequence
Gene start1
Gene end298
Codon Frame1
Paralog RepFalse
Extension?FalseTrue
3' ExtensionA
5' Extension
curational_tagsnonelikely_full-length
Noteschanged

Versions

All published versions of this sequence.

Sequence NameIMGT NameAlternative namesInference TypeAffirmation LevelSpecies subgroupSubgroup typeVersionDate
IGHV4-39*i01IGHV4-39*08Rearranged Only1none12021-11-01
IGHV4-39*08IGHV4-39*08IGHV4-39*i01Rearranged Only122023-07-10