Genetics: Chromosome 6 BTN2A2 and BTN3A3

[forestglip]

Could you explain why I get the following associations in STRING :

I am particularly interested for the relations of MFGE8 (Milk Fat Globule - existing below in the figure describing efferocytosis) with BTN2A2, MERTK and GAS6.

I don't know anything about these proteins, but if you want to see how they're related, you should be able to click the lines between proteins on the STRING plot, and it'll give you all the evidence it based the relationships on.

 

[jnmaciuch]

Could you explain why I get the following associations in STRING :

If you select the BNT2A2 node you can go to the “Edges” tab and get details about the connection. Here is seems that the connection is just driven by both being mentioned in abstracts together, in the specific context of milk secretion:

https://string-db.org/cgi/textmining?taskId=bqNdhdUHCbuy&sessionId=bGTquoSxCF58

 

[Andy]

Butyrophilin 2A2 promotes T cell immunoregulation via CD45 phosphatase activation and protects against murine autoimmune glomerulonephritis and pregnancy loss, 2025, Karumanchi et al

Open access

 

[ChronicallyOverIt]

Perusing therapies for antagonism of BTN3A and saw this:

About ICT01

Imcheck Therapeutics : Opening new spaces in Immuno-Oncology.

www.imchecktherapeutics.com

 

[forestglip]

I used the Open GWAS API to retrieve traits associated with the lead variants at each of the 8 DecodeME loci. I wrote more details on the CA10 locus thread.

Keep in mind that multiple traits being significant for the same variant doesn't necessarily mean the same variant is causal for all of the traits, since a variant can be significant just because it is correlated to (in LD with) another variant which is actually causal.

Here are traits associated with rs9358913/6:26239176:A:G (the lead DecodeME variant near BTN2A2). This is just the 20 most significant:

For all rows:
chr = 6
position (GRCh37) = 26239404
ea (effect allele) = G
nea (non-effect allele) = A

id	trait	eaf (effect allele frequency)	beta	se	p	n
eqtl-a-ENSG00000158373	ENSG00000158373 (HIST1H2BD)	0.301641	-0.38993	0.0125454	4.2658e-212	31033
ebi-a-GCST90002322	Mean corpuscular hemoglobin	0.261606	-0.060347	0.00217	4.02717e-170	486823
ebi-a-GCST90002390	Mean corpuscular hemoglobin	0.26022	-0.0629517	0.00234383	6.69885e-159	408112
ukb-b-10787	Standing height	0.260314	-0.0387569	0.00147479	3.3037e-152	461950
ebi-a-GCST90025962	Mean corpuscular hemoglobin concentration	0.260132	-0.0569232	0.0022403	1.09901e-148	443081
ebi-a-GCST90018959	Height	0.449299	-0.0404	0.0016	9.1622e-143	360388
ebi-a-GCST90028995	Mean corpuscular hemoglobin	0.260263	-0.0541398	0.00224492	4.79733e-134	572863
ebi-a-GCST90002334	Mean corpuscular volume	0.263375	-0.049689	0.00204	5.97035e-131	544127
ebi-a-GCST90029008	Height	0.260236	-0.0440775	0.00191716	6.69885e-124	673878
ebi-a-GCST90025949	Height	0.260121	-0.0441507	0.00191887	1.30017e-123	458235
ebi-a-GCST90002392	Mean corpuscular volume	0.260242	-0.0542473	0.00231531	2.09894e-121	408112
eqtl-a-ENSG00000158406	ENSG00000158406 (HIST1H4H)	0.301641	-0.278695	0.0127537	7.4131e-106	30819
ebi-a-GCST90025963	Mean corpuscular volume	0.260169	-0.0470034	0.00221907	1.59956e-101	444035
ukb-d-30050_irnt	Mean corpuscular haemoglobin	0.258524	-0.0575702	0.00269485	3.41979e-101	350472
ebi-a-GCST90013979	Mean corpuscular volume (UKB data field 30040)	nan	-0.0492092	0.00236811	6.57355e-96	396624
ukb-a-389	Standing height	0.257995	-0.0400524	0.00196926	6.62827e-92	336474
ukb-d-30040_irnt	Mean corpuscular volume	0.258522	-0.0494931	0.00270167	6.27191e-75	350473
ebi-a-GCST90018964	Mean corpuscular hemoglobin	0.420983	-0.044	0.0024	8.47032e-75	350472
ebi-a-GCST90095038	Height	0.2728	-0.0498	0.0028	5.89794e-71	350741
ieu-a-89	Height	0.267	-0.057	0.0033	6.29941e-67	251412

The trait most significantly associated with this variant is expression of the HIST1H2BD gene.

The G allele at this variant is associated with increased risk of ME/CFS (odds ratio greater than 1/beta greater than 0 in DecodeME) and decreased expression of HIST1H2BD (beta less than 0 above).

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There were too many traits associated at p<1e-6 to include them all in the post, so I'll just attach a spreadsheet that has all traits associated with the 8 DecodeME variants.