Question about gens name starting "LOC~"

Question

[mangfu100]

Greeting all.

I am searching novel somatic mutations using various public software and annotation tools such as annovar.

I have been using my own cancer exome data not public data 'just real patient data' and finally I completed running calling program(MuTect and annovar) and I got to discover some genes that looks disease-like to me.

One of my genes is starting with LOC and its full name is LOC100129697 and it has variation in nonsynonymous region.

I hope that this gene are related to the disease and with this hope in mind, I ran the IGV to analyze this variation more deeply.

However, when I looked up IGV , I was surprised to see that gene name which IGV shows me is totally different from LOC100129697.

How can I interpret this gene LOC100129697?

Is there a gene which have another nick-name?

[cdsouthan]

If you still come across these IDs they are unlikely to be real proteins. Transcripts of some description probably, genes maybe (but not by HGNC's definition). Ensembl/Havana call this out as antisense, not ORF

http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000205018;r=16:88939789-88951524;t=ENST00000378347

Answer 1

[iraun]

From NCBI:

Symbols beginning with LOC. When a published symbol is not available, and orthologs have not yet been determined, Gene will provide a symbol that is constructed as 'LOC' + the GeneID. This is not retained when a replacement symbol has been identified, although queries by the LOC term are still supported. In other words, a record with the symbol LOC12345 is equivalent to GeneID = 12345. So if the symbol changes, the record can still be retrieved on the web using LOC12345 as a query, or from any file using GeneID = 12345.