Changes in bd28246: Updated IKZF3 (markdown)

				IKZF3.md
			
          @@ -1,6 +1,6 @@

           # IKZF3

           ## Overview

          -IKZF3 (IKAROS family zinc finger 3, also known as AIOLOS) is a transcription factor involved in regulating B-cell development and function. Mutations in IKZF3 can lead to transcriptional dysregulation and contribute to the pathogenesis of B-cell neoplasms. IKZF3 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. 

          +IKZF3 (IKAROS family zinc finger 3, also known as AIOLOS) is a transcription factor involved in regulating B-cell development and function. Mutations in IKZF3 can lead to transcriptional dysregulation and contribute to the pathogenesis of B-cell neoplasms. IKZF3 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. IKZF3 has multiple hot spot mutations in DLBCL. The most common, L162R, has been identified as a driver in CLL. In that context, it alters DNA binding specificity and causes hyperactivation of B-cell receptor (BCR) signaling and overexpression of NF-κB target genes.<sup>1</sup> While primarily studied in CLL, the functional effects of IKZF3 mutations could have implications for other B-cell malignancies, including DLBCL 

           ## Relevance tier by entity

          @@ -43,8 +43,23 @@ IKZF3 (IKAROS family zinc finger 3, also known as AIOLOS) is a transcription fac

           | Chromosome |Coordinate (hg19) | ref>alt | HGVSp | 

            | :---:| :---: | :--: | :---: |

          -| chr17 | 37947782 | T>C | N160S |

          -| chr17 | 37947776 | A>C | L162R |

          +|chr17|37948968|T>C|I128V| 

          +|chr17|37948958|T>C|N131S| 

          +|chr17|37948950|T>C|M134V| 

          +|chr17|37948949|A>T|M134K| 

          +|chr17|37947783|T>G|N160H| 

          +|chr17|37947782|T>C|N160S| 

          +|chr17|37947776|A>C|L162R| 

          +|chr17|37944583|G>T|Q213K| 

          +|chr17|37944582|T>C|Q213R| 

          +|chr17|37944577|T>G|S215R| 

          +|chr17|37944575|A>T|S215R| 

          +|chr17|37944575|A>C|S215R| 

          +|chr17|37944568|C>T|E218K| 

          +|chr17|37944565|C>T|E219K| 

          +|chr17|37944564|T>A|E219V| 

          +|chr17|37944556|C>T|E222K| 

          +

           View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IKZF3_protein.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IKZF3_protein_hg38.html)

          @@ -53,3 +68,6 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM

           View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IKZF3.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IKZF3_hg38.html)

           ![image](images/proteinpaint/IKZF3.svg)

          +

          +## References

          +1. *Lazarian, G., Yin, S., Hacken, E., Sewastianik, T., Uduman, M., Font-Tello, A., Gohil, S., Li, S., Kim, E., Joyal, H., Billington, L., Witten, E., Zheng, M., Huang, T., Severgnini, M., Lefebvre, V., Rassenti, L., Gutierrez, C., Georgopoulos, K., Ott, C., Wang, L., Kipps, T., Burger, J., Livak, K., Neuberg, D., Baran-Marszak, F., Cymbalista, F., Carrasco, R., & Wu, C. (2021). A hotspot mutation in transcription factor IKZF3 drives B cell neoplasia via transcriptional dysregulation.. Cancer cell, 39 3, 380-393.e8 . https://doi.org/10.1016/j.ccell.2021.02.003.*

...	...	@@ -1,6 +1,6 @@
1	1	# IKZF3
2	2	## Overview
3		-IKZF3 (IKAROS family zinc finger 3, also known as AIOLOS) is a transcription factor involved in regulating B-cell development and function. Mutations in IKZF3 can lead to transcriptional dysregulation and contribute to the pathogenesis of B-cell neoplasms. IKZF3 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
	3	+IKZF3 (IKAROS family zinc finger 3, also known as AIOLOS) is a transcription factor involved in regulating B-cell development and function. Mutations in IKZF3 can lead to transcriptional dysregulation and contribute to the pathogenesis of B-cell neoplasms. IKZF3 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. IKZF3 has multiple hot spot mutations in DLBCL. The most common, L162R, has been identified as a driver in CLL. In that context, it alters DNA binding specificity and causes hyperactivation of B-cell receptor (BCR) signaling and overexpression of NF-κB target genes.<sup>1</sup> While primarily studied in CLL, the functional effects of IKZF3 mutations could have implications for other B-cell malignancies, including DLBCL
4	4
5	5	## Relevance tier by entity
6	6
...	...	@@ -43,8 +43,23 @@ IKZF3 (IKAROS family zinc finger 3, also known as AIOLOS) is a transcription fac
43	43
44	44	\| Chromosome \|Coordinate (hg19) \| ref>alt \| HGVSp \|
45	45	\| :---:\| :---: \| :--: \| :---: \|
46		-\| chr17 \| 37947782 \| T>C \| N160S \|
47		-\| chr17 \| 37947776 \| A>C \| L162R \|
	46	+\|chr17\|37948968\|T>C\|I128V\|
	47	+\|chr17\|37948958\|T>C\|N131S\|
	48	+\|chr17\|37948950\|T>C\|M134V\|
	49	+\|chr17\|37948949\|A>T\|M134K\|
	50	+\|chr17\|37947783\|T>G\|N160H\|
	51	+\|chr17\|37947782\|T>C\|N160S\|
	52	+\|chr17\|37947776\|A>C\|L162R\|
	53	+\|chr17\|37944583\|G>T\|Q213K\|
	54	+\|chr17\|37944582\|T>C\|Q213R\|
	55	+\|chr17\|37944577\|T>G\|S215R\|
	56	+\|chr17\|37944575\|A>T\|S215R\|
	57	+\|chr17\|37944575\|A>C\|S215R\|
	58	+\|chr17\|37944568\|C>T\|E218K\|
	59	+\|chr17\|37944565\|C>T\|E219K\|
	60	+\|chr17\|37944564\|T>A\|E219V\|
	61	+\|chr17\|37944556\|C>T\|E222K\|
	62	+
48	63
49	64	View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IKZF3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IKZF3_protein_hg38.html)
50	65
...	...	@@ -53,3 +68,6 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM
53	68	View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/IKZF3.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/IKZF3_hg38.html)
54	69
55	70	![image](images/proteinpaint/IKZF3.svg)
	71	+
	72	+## References
	73	+1. Lazarian, G., Yin, S., Hacken, E., Sewastianik, T., Uduman, M., Font-Tello, A., Gohil, S., Li, S., Kim, E., Joyal, H., Billington, L., Witten, E., Zheng, M., Huang, T., Severgnini, M., Lefebvre, V., Rassenti, L., Gutierrez, C., Georgopoulos, K., Ott, C., Wang, L., Kipps, T., Burger, J., Livak, K., Neuberg, D., Baran-Marszak, F., Cymbalista, F., Carrasco, R., & Wu, C. (2021). A hotspot mutation in transcription factor IKZF3 drives B cell neoplasia via transcriptional dysregulation.. Cancer cell, 39 3, 380-393.e8 . https://doi.org/10.1016/j.ccell.2021.02.003.