Genetics: Chromosome 12: SUDS3, TAOK3, PEBP1

[ME/CFS Science Blog]

Had a closer look at this locus. The credible set lies mostly inside the long gene TOAK3 but also SUDS3 and PEBP1.



Chromatin contacts also pointed to SSRM4 as an option on the east side, but it only has contact to the most easter side of the credible interval that doesn’t hold much probability of containing the causal variant.



The eQTL speaks in SUDS3’s favor because it colocalize well in multiple tissues.


The phewas results include neuroticism, anxiousness, depression, loneliness, irritability, tiredness, etc. No immune diseases show up.

 

[ME/CFS Science Blog]

Had a closer look at this locus. The credible set lies mostly inside the long gene TOAK3 but also SUDS3 and PEBP1.

FLAMES chose PEBP1 and was confident enough to claim it as the causal gene for this region.

Currently trying to decipher exactly why FLAMES made its evaluations, but it could be because PEBP1 fits into the synaptic pathwasy sthat show enrichment in ME/CFS. It came up in the SynGO analysis I did a while ago:
SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse, 2019, Koopmans et al. | Science for ME

 

[ME/CFS Science Blog]

Perhaps PEBP1 can be added to the name of this thread?

 

[forestglip]

Perhaps PEBP1 can be added to the name of this thread?

I added that.

 

[ME/CFS Science Blog]

I added that.

Thanks!