As indicated in the updated "C-M217" thread, C-P39 is likely to have eastern coastal North Asian backgrounds. The y hg C branches in eastern coastal North Asia belong to the same macro-branch. Apart from that, the estimated age of C-"IMS-JST645622+13" as a whole is particularly high there. Among those North Asian lineages which are most closely related to C-P39+ there are C-B77+, the lineage of an eastern coastal North Asian aborigine, and C-B78+, the lineage of a Turkic-speaker from a region geographically close to territories formerly inhabited by Yeniseian-speakers.
Linguists have been pointing to a possible relationship between Yeniseian and Na-Dene languages for a while. I cannot comment on that since I'm not a linguist. Apart from that, authors repeatedly claimed to have observed physical anthropological similarities between Yeniseians and Amerindians. But statistics seem to indicate very signficant physiological differences between the last surviving Yeniseian-speakers of the 20th century and Amerindians. Even more, ...
- people in hg C-P39+ are mostly in North America, where the aborigines statistically resembled Mongols in terms of facial width and maybe also build in general
- the last surviving Yeniseians, the Kets, mostly belong to y hg Q and might have been on average very different from North American aborigines according to biometric statistics (with Mongols possibly having been intermediate in between Yeniseians and Amerindians)
These differences can be explained by long-term consequences of the migration of the supposedly Amerindian-like ancestors of the Kets to the west, such as...
- adoption of inland continental Asian ways of life and selection processes in favour of the according body types
- adoption of patrilineal identities with Yeniseian men having taken wives from inland North Eurasian peoples
In this sense, most Yeniseian ethnic groups having gone extinct can be compared with relatively many North American aboriginal ethnic groups having survived until the 20th century. And one peculiar question could be whether any side effects of patrilineal social organisation could have contributed to the extinction of Yeniseian ethnic groups. Indeed, there is the statement that matrilineal aborigines managed to maintain relatively high levels of demographic continuity when compared with patrilineal aborigines in North America.
There's also a lineage found among pre-Russian Empire ethnic groups in Northeast Siberia, C2b1a2b-B90, that is slightly more closely related to C2b1a2a-M86/M77 than either of those is related to other subclades of C-L1373.
Another branch of C-L1373 has been found in at least one Japanese person (I suspect that it might be one of the HGDP Japanese sampled in the USA).
There is also a deeply bifurcated branch attested in Jammu-Kashmir, in Slovakia, and recently in an archaeological specimen from the steppe or southern Siberia IIRC, with the modern Slovakian being closely related to the archaeological specimen, and the northern Indian being very distant from those two.
As you have noted, C-P39 has been observed in people with indigenous North American ancestry.
The other extant branches of C-L1373 all seem to be found in populations with connections to the steppe, from Central Europe (e.g. West Slavs) to Manchuria and the basin of the Amur River. These "Altaic" branches do not seem to share a common ancestor any more recently than they share a common ancestor with the more geographically outlying subclades of C-L1373 in Northeast Siberia, North America, North India, Japan, etc.
I wonder whether the North Indian/Slovakian(+Scythian?) subclade might have accompanied female members of mtDNA haplogroup C in the Mesolithic western steppe.