Details


Species	Human
Species subgroup
Subgroup type
Sequence Name	IGHV1-69*i04
IUIS Name
Alternative names
Affirmation Level	1
Full Sequence
Coding Sequence
Functionality	ORF
Inference Type	Rearranged Only
Mapped	False
Paralogs
Paralog Rep	False

Evidence

The table below lists submissions to IARC , and the inferences within them, on which this IARC-affirmed sequence is based.

'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 ID	Accession No	Subject ID	Genotype Name	Sequence Name	Sequence Match
S00037	OW151137	S45	P1_I48_S1_ogrdb_report	IGHV1-69*06_G240A

Observations in VDJbase

Inferred sequences in VDJbase that match this sequence:

VDJbase Allele Name	Subjects	Sequence Match
IGHV1-69*06_g240a	1

Un-rearranged Observations

Un-rearranged sequence observations that support this sequence:

No Items

CDR delineation


CDR1 Start	76
CDR1 End	99
CDR2 Start	151
CDR2 End	174
CDR3 Start	289

Extension


3' Extension	A
3' start
3' end

Additional Information


Sequence ID	A02559
Curator	William Lees
Curator address	Birkbeck College, University of London, Malet Street, London
Version	3
Release Date	2023-07-10
Release Notes	Bulk upload of sequences for the AIRR-C Human IG germline sets
Locus	IGH
Sequence Type	V
Gene Subgroup	1
Gene Designation	69
Allele Designation	i04

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. IGHV1-6906_G240A was inferred in subject S45 (VDJ-base: P1_I48_S1). The genotype also carried IGHV1-6901 and IGHV1-6906. Given the common duplication of IGHV1-69 in the human IGHV locus, this is not an unexpected finding. The inference was supported by a relative large number of sequences (680) and unmutated sequences (627), a high overall frequency in the unmutated population (2.4%) and a large and diverse set of unique CDR3s (607) in the unmutated sequence set. Its allelic ratio was 22%. Haplotyping based on allelic diversity in IGHJ6 was not possible. IARC affirms the sequence at level 1 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 one additional 3’-nucleotides for which there is insufficient evidence to make an affirmation. The allele is given the name IGHV1-69(D)i04. This name highlights the uncertainty of which of the two duplicated genes the allele is most likely associated with. Additional information for this sequence was imported into OGRDB via bulk update with the following notes: Sequence annotation is based on VDJbase sample(s) VDJbase example haplotype: P1_I48

This inferred allele was assessed at IARC meeting 100 on June 8th, 2022. IGHV1-69*06_G240A was inferred in subject S45 (VDJ-base: P1_I48_S1). The genotype also carried IGHV1-69*01 and IGHV1-69*06. Given the common duplication of IGHV1-69 in the human IGHV locus, this is not an unexpected finding. The inference was supported by a relative large number of sequences (680) and unmutated sequences (627), a high overall frequency in the unmutated population (2.4%) and a large and diverse set of unique CDR3s (607) in the unmutated sequence set. Its allelic ratio was 22%. Haplotyping based on allelic diversity in IGHJ6 was not possible. IARC affirms the sequence at level 1 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 one additional 3’-nucleotides for which there is insufficient evidence to make an affirmation. The allele is given the name IGHV1-69(D)*i04. This name highlights the uncertainty of which of the two duplicated genes the allele is most likely associated with.

Additional information for this sequence was imported into OGRDB via bulk update with the following notes:
Sequence annotation is based on VDJbase sample(s)
VDJbase example haplotype: P1_I48

Attachments

No Items

History

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


Mats Ohlin 2022-07-25 10:52:55	Version 1 published The allele was published by IARC on July 25th, 2022.


William Lees 2023-07-10 11:20:54	Version 2 published (D) removed from name as this designation is not used in the AIRR-C human germline sets


William Lees 2023-07-10 11:24:36	Version 3 published Bulk upload of sequences for the AIRR-C Human IG germline sets

Changes from previous version

	v2	v3
Curator	Mats Ohlin	William Lees
Curator address	Dept. of Immunotechnology, Lund University, Medicon Village building 406, S-22381 Lund, Sweden	Birkbeck College, University of London, Malet Street, London
Alternative names	IGHV1-6906 G240A,IGHV1-69(D)i04
Chromosome		14
Functionality	F	ORF
Inference Type	Rearranged	Rearranged Only
Subgroup type	none
Gene Designation	1-69(D)	69
Full Sequence
Codon Frame	1
Extension?	False	True
3' Extension		A
5' Extension
Notes		changed

Versions

All published versions of this sequence.

Sequence Name	IMGT Name	Alternative names	Inference Type	Affirmation Level	Species subgroup	Subgroup type	Gene start	Gene end	UTR 5' Start	UTR 5' End	L-PART1 Start	L-PART1 End	L-PART2 Start	L-PART2 End	CDR1 Start	CDR1 End	CDR2 Start	CDR2 End	CDR3 Start	v_rs_start	v_rs_end	d_rs_3_prime_start	d_rs_3_prime_end	d_rs_5_prime_start	d_rs_5_prime_end	j_rs_start	j_rs_end	Codon Frame	Version	Date
IGHV1-69*i04		IGHV1-6906 G240A,IGHV1-69(D)i04	Rearranged	1		none	1	295							76	99	151	174	289									1	2	2023-07-10
IGHV1-69*i04			Rearranged Only	1			1	295							76	99	151	174	289										3	2023-07-10