Chromosome 9

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ENTITIES: by Chromosome band

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Chromosome 9

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Band 9p12

chr9:39000000-40000000 (1000 Kb)

Chromosomal abnormalities in band 9p12

Genes in band 9p12 (reference hg38)

External links

References

Chromosomal abnormalities in band 9p12

(click on headers to reorder columns)

Band 1	Band 2	Class	Entity	Partner 1	Partner 2	Links	Topography	Morphology	[PubMed]	[Study]
9p12		Cosmic_SV	del(9)(p12)			Cosmic_SV [COST142591]	ovary__NS	carcinoma__mixed_adenosquamous_carcinoma		[COSU585]
9p12		Cosmic_SV	del(9)(p12)			Cosmic_SV [COST142591]	pancreas__NS	carcinoid-endocrine_tumour__NS		[COSU586]
9p12		Cosmic_SV	del(9)(p12)			Cosmic_SV [COST151195]	ovary__NS	carcinoma__mixed_adenosquamous_carcinoma		[COSU585]
9p12		Cosmic_SV	del(9)(p12)			Cosmic_SV [COST160470]	ovary__NS	carcinoma__mixed_adenosquamous_carcinoma		[COSU585]
9p12		Cosmic_SV	del(9)(p12)			Cosmic_SV [COST195630]	bone__NS	Ewings_sarcoma-peripheral_primitive_neuroectodermal_tumour__NS		[COSU645]
		Mitelman	del(9)(p12)			Mitelman (ISB-CGC)		Acute lymphoblastic leukemia/lymphoblastic lymphoma
		Mitelman	del(9)(p12)			Mitelman (ISB-CGC)		Acute myeloid leukemia, NOS
		Mitelman	del(9)(p12)			Mitelman (ISB-CGC)		Bilineage or biphenotypic leukemia
		Mitelman	del(9)(p12)			Mitelman (ISB-CGC)	Brain	Astrocytoma, grade III-IV/Glioblastoma
		Mitelman	del(9)(p12)			Mitelman (ISB-CGC)		Chronic lymphocytic leukemia
		Mitelman	del(9)(p12)			Mitelman (ISB-CGC)		Diffuse large B-cell lymphoma
		Mitelman	del(9)(p12)			Mitelman (ISB-CGC)		Follicular lymphoma
		Mitelman	del(9)(p12)			Mitelman (ISB-CGC)		Mantle cell lymphoma
		Mitelman	del(9)(p12)			Mitelman (ISB-CGC)		Mature B-cell neoplasm, NOS
		Mitelman	del(9)(p12)			Mitelman (ISB-CGC)	Pleura	Mesothelioma
		Mitelman	del(9)(p12p22)			Mitelman (ISB-CGC)		Acute lymphoblastic leukemia/lymphoblastic lymphoma
		Mitelman	del(9)(p12p24)			Mitelman (ISB-CGC)		Acute lymphoblastic leukemia/lymphoblastic lymphoma
9p12	9q12	Cosmic_SV	del(9)(p12q12)			Cosmic_SV [COST166089]	pancreas__NS	carcinoid-endocrine_tumour__NS		[COSU586]
9p24	9p12	Cosmic_SV	del(9)(p24p12)			Cosmic_SV [COST118994]	pancreas__NS	carcinoma__ductal_carcinoma		[COSU328]
		Mitelman	der(9)del(9)(p12)t(9;20)(p12;p11)			Mitelman (ISB-CGC)		Acute lymphoblastic leukemia/lymphoblastic lymphoma
		Mitelman	dic(9;12)(p12;p12)			Mitelman (ISB-CGC)		Acute lymphoblastic leukemia/lymphoblastic lymphoma
		Mitelman	dic(9;20)(p12;q11)			Mitelman (ISB-CGC)		Acute lymphoblastic leukemia/lymphoblastic lymphoma
9p12	9p12	Cosmic_SV	dup(9)(p12p12)			Cosmic_SV [COST123586]	pancreas__NS	carcinoma__ductal_carcinoma		[COSU328]
9p12	9p12	Cosmic_SV	dup(9)(p12p12)			Cosmic_SV [COST153400]	ovary__NS	carcinoma__mixed_adenosquamous_carcinoma		[COSU585]
9p24	9p12	Cosmic_SV	dup(9)(p24p12)			Cosmic_SV [COST125724]	pancreas__NS	carcinoma__ductal_carcinoma		[COSU328]
		Mitelman	idic(9)(p12)			Mitelman (ISB-CGC)		Acute lymphoblastic leukemia/lymphoblastic lymphoma
9p12		Cosmic_SV	ins(9)(p12)			Cosmic_SV [COST188666]	prostate__NS	carcinoma__adenocarcinoma		[COSU538]
		Mitelman	inv(9)(p12q13)			Mitelman (ISB-CGC)		Acute lymphoblastic leukemia/lymphoblastic lymphoma
		Mitelman	inv(9)(p12q13)			Mitelman (ISB-CGC)		Acute myeloid leukemia, NOS
		Mitelman	inv(9)(p12q13)			Mitelman (ISB-CGC)		Bilineage or biphenotypic leukemia
		Mitelman	inv(9)(p12q13)			Mitelman (ISB-CGC)	Breast	Adenocarcinoma
		Mitelman	inv(9)(p12q13)			Mitelman (ISB-CGC)		Chronic lymphocytic leukemia
		Mitelman	inv(9)(p12q13)			Mitelman (ISB-CGC)		Myelodysplastic syndrome, NOS
9p21	9p21	Cosmic_SV	inv(9)(p21p21)			Cosmic_SV [COST116539]	pancreas__NS	carcinoma__ductal_carcinoma		[COSU328]
9p22	9p22	Cosmic_SV	inv(9)(p22p22)			Cosmic_SV [COST125716]	pancreas__NS	carcinoma__ductal_carcinoma		[COSU328]
1p13	9p12	Atlas - Leukemia	t(1;9)(p13;p12) PAX5/HIPK1	PAX5	HIPK1	t0109p13p12ID1557		B-ALL	[Biblio]
7q11	9p12	ChiTaRS	t(7;9)(q11;p12)			ChiTaRS		-	[PubMed]
7q11	9p12	Atlas - Leukemia	t(7;9)(q11;p12) PAX5/POM121	PAX5	POM121	t0709q11p12ID1558		B-ALL	[Biblio]
9p12	13q21	Atlas - Leukemia	t(9;13)(p12;q21) PAX5/DACH1	PAX5	DACH1	t0913p12q21ID1560		B-ALL	[Biblio]
9p12	13q21	ChiTaRS	t(9;13)(p12;q21)			ChiTaRS		-	[PubMed]
		Mitelman	t(9;14)(p12;q32)			Mitelman (ISB-CGC)		Chronic lymphocytic leukemia
		Mitelman	t(9;20)(p12;p11)			Mitelman (ISB-CGC)		Acute lymphoblastic leukemia/lymphoblastic lymphoma
4q28	9p12	Cosmic_SV	u(4;9)(q28;p12)			Cosmic_SV [COST380862]	breast__NS	carcinoma__ductal_carcinoma		[COSU652]
5q14	9p12	Cosmic_SV	u(5;9)(q14;p12)			Cosmic_SV [COST720889]	prostate__NS	carcinoma__adenocarcinoma		[COSU538]
5q14	9p12	Cosmic_SV	u(5;9)(q14;p12)			Cosmic_SV [COST773374]	prostate__NS	carcinoma__adenocarcinoma		[COSU538]
5q23	9p12	Cosmic_SV	u(5;9)(q23;p12)			Cosmic_SV [COST765170]	prostate__NS	carcinoma__adenocarcinoma		[COSU538]
6p11	9p12	Cosmic_SV	u(6;9)(p11;p12)			Cosmic_SV [COST326940]	breast__NS	carcinoma__ductal_carcinoma		[COSU652]
6p12	9p12	Cosmic_SV	u(6;9)(p12;p12)			Cosmic_SV [COST171423]	adrenal_gland__adrenal_gland	adrenal_cortical_carcinoma__virilizing_syndrome_producing
8p11	9p12	Cosmic_SV	u(8;9)(p11;p12)			Cosmic_SV [COST228306]	haematopoietic_and_lymphoid_tissue__NS	lymphoid_neoplasm__adult_T_cell_lymphoma-leukaemia
8p21	9p12	Cosmic_SV	u(8;9)(p21;p12)			Cosmic_SV [COST375315]	breast__NS	carcinoma__ductal_carcinoma		[COSU652]
8q12	9p12	Cosmic_SV	u(8;9)(q12;p12)			Cosmic_SV [COST354788]	breast__NS	carcinoma__ductal_carcinoma		[COSU652]
8q22	9p12	Cosmic_SV	u(8;9)(q22;p12)			Cosmic_SV [COST737476]	prostate__NS	carcinoma__adenocarcinoma		[COSU537]
9p12	10p15	Cosmic_SV	u(9;10)(p12;p15)			Cosmic_SV [COST214868]	pancreas__NS	carcinoma__ductal_carcinoma		[COSU382]
9p12	12p13	Cosmic_SV	u(9;12)(p12;p13)			Cosmic_SV [COST151402]	ovary__NS	carcinoma__mixed_adenosquamous_carcinoma		[COSU585]
9p12	12q21	Cosmic_SV	u(9;12)(p12;q21)			Cosmic_SV [COST347460]	breast__NS	carcinoma__ductal_carcinoma		[COSU652]
9p12	14p13	Cosmic_SV	u(9;14)(p12;p13)			Cosmic_SV [COST391285]	breast__NS	carcinoma__ductal_carcinoma		[COSU652]
9p12	18p11	Cosmic_SV	u(9;18)(p12;p11)			Cosmic_SV [COST371167]	breast__NS	carcinoma__ductal_carcinoma		[COSU652]
9p12	1p36	Cosmic_SV	u(9;1)(p12;p36)			Cosmic_SV [COST462648]	pancreas__NS	carcinoma__NS		[COSU382]
9p12	6p12	Cosmic_SV	u(9;6)(p12;p12)			Cosmic_SV [COST171440]	adrenal_gland__adrenal_gland	adrenal_cortical_carcinoma__virilizing_syndrome_producing
9p12	8p23	Cosmic_SV	u(9;8)(p12;p23)			Cosmic_SV [COST563692]	prostate__NS	carcinoma__adenocarcinoma		[COSU537]
9p12	8q22	Cosmic_SV	u(9;8)(p12;q22)			Cosmic_SV [COST739131]	prostate__NS	carcinoma__adenocarcinoma		[COSU537]
9p12	9p12	Cosmic_SV	u(9)(p12;p12)			Cosmic_SV [COST326752]	breast__NS	carcinoma__ductal_carcinoma		[COSU652]
9p12	9p12	Cosmic_SV	u(9)(p12;p12)			Cosmic_SV [COST757425]	prostate__NS	carcinoma__adenocarcinoma		[COSU537]
9p12	9p12	Cosmic_SV	u(9)(p12;p12)			Cosmic_SV [COST765957]	prostate__NS	carcinoma__adenocarcinoma		[COSU537]
9p13	9p12	Cosmic_SV	u(9)(p13;p12)			Cosmic_SV [COST176098]	central_nervous_system__brain	glioma__astrocytoma_Grade_IV
9p13	9p12	Cosmic_SV	u(9)(p13;p12)			Cosmic_SV [COST333600]	breast__NS	carcinoma__ductal_carcinoma		[COSU652]
9p13	9p12	Cosmic_SV	u(9)(p13;p12)			Cosmic_SV [COST379079]	breast__NS	carcinoma__lobular_carcinoma		[COSU652]
9p13	9p12	Cosmic_SV	u(9)(p13;p12)			Cosmic_SV [COST564917]	prostate__NS	carcinoma__adenocarcinoma		[COSU537]
9p21	9p12	Cosmic_SV	u(9)(p21;p12)			Cosmic_SV [COST335364]	breast__NS	carcinoma__ductal_carcinoma		[COSU652]
9p23	9p12	Cosmic_SV	u(9)(p23;p12)			Cosmic_SV [COST347359]	breast__NS	carcinoma__ductal_carcinoma		[COSU652]
9p12	Xp22	Cosmic_SV	u(9;X)(p12;p22)			Cosmic_SV [COST376109]	breast__NS	carcinoma__ductal_carcinoma		[COSU652]

Genes in band 9p12

(click on headers to reorder columns)

GoldenPath hg38	Band 1	Band 2	Class	Fusion	Partner 1	Partner 2	Links	Topography	Morphology	Pubmed	Omim	Accession
chr9:39072767-39288167 -	9p12		Gene [G]		CNTNAP3		[Cosmic]				[Omim]	[Entrez]
chr9:39072767-39288167 -	9p12	11q13	Gene [GDB]	NUMA1/CNTNAP3	CNTNAP3	NUMA1	[Cosmic] [FusionGDB]				[Omim]	[Entrez]
chr9:39072767-39288167 -	9p12	11q13	Gene [M]	NUMA1/CNTNAP3	CNTNAP3	NUMA1	[Cosmic] [Mitelman]	Skin	Malignant melanoma	[PubMed]	[Omim]	[Entrez]
chr9:39355669-39361962 +	9p12		Gene [G]		SPATA31A1		[Cosmic]				[Omim]	[Entrez]
chr9:39873853-39876242 +	9p12		Gene [G]		LOC102724238						[Omim]	[Entrez]
chr9:39873857-39875395 +	9p12		Gene [G]		LOC554249						[Omim]	[Entrez]

[ Bold normal : A; Italic normal :G; Italic small : E ]

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External links

Mitelman Database [NCI] : Breakpoint 9p12

[ UCSC ][ enSembl ][ MapView - NCBI ][ 1000Genomes ][ EVS ][ CGWB ][ DGV ][ DBVar ][ OMIM ][ HapMap ][ DECIPHER ] [ ECARUCA ]
Gene Expression (MSigDB) in 9p12 [ HTC ] [ NCI ] [ INV ]

Global tables

Anomalies list (tabulated txt file)

Genes list (tabulated txt file)

Anomalies list - limited to abnormalities with gene fusions(tabulated txt file)

Genes list - limited to genes fusions (tabulated txt file)

list of gene fusions for each gene (with origins of the data)

list of gene fusions by origin (with topography and morphology)

The human genome used in these documents corresponds to the hg38 (Build GRCh38). A more precise informtion about assemby can be found at Human genome Overview.
The limits of cytogenetic bands correspond to data from UCSC : cytoBand.txt.gz

ISCN Abbreviated Terms and Symbols

[A]Atlas - Annotated genes

[G]Atlas - Other Genes

[F] fishClones (hg38)

[M] Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer [ Jan 2021 ]
and "Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer" (2012). Mitelman F, Johansson B and Mertens F (Eds.)" [Sept 2016]

[N] Mitelman Database of Chromosome Aberrations (/number)

[COS] Catalogue Of Somatic Mutations In Cancer [v92]

[COF] Catalogue Of Somatic Mutations In Cancer : Gene Fusions [v92] [PubMed 2017]

[CSV] Catalogue Of Somatic Mutations In Cancer : Structural variations (extracted frorm CosmicStructExport.tsv) [v92) [PubMed 2014]

[CEN] Cancer Gene Census [v92]

[TF] [PubMed 2014]TCGA Fusions (MDAndersson) TCGA Fusions (Jackson Lab) [PubMed 2014] (the fusions are limited to tiers 1 and 2)

[TIC] [PubMed 2007] TicDB

[H2] [PubMed 2006] ChimerDB_2.0

[H3] [PubMed 2010] [PubMed 2017] ChimerDB_3.0

[H4] ChimerDB4 [PubMed 2017]

[K] [PubMed 2011] dbCRID

[CT] [PubMed 2011] [PubMed 2012] [PubMed 2014] ChiTARS-2.1 [PubMed 2016] ChiTARS-3.1

[LAI] [PubMed 2015] Fusion transcript loci share many genomic Features with non-fusion loci. Lai et al. BMC Genomics 2015

[PM] Gene Fusions from Pubmed abstract mining

[L] [PubMed 2011] Fusion gene microarray reveals cancer type-specificity among fusion genes. Lovf M et al.Genes Chromosomes Cancer. 2011 May;50(5):348-57.

[S] [PubMed 21009] A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis. Skotheim RI, et al. Mol Cancer. 2009 Jan 19;8:5.

[V][PubMed 2012] ETV6 fusion genes in hematological malignancies: A review. De Braekeleer E. et al. Leuk Res. 2012 May 12.

[GT] [Pubmed 2015] Cell Lines (Genentech) Nature Biotech Suppl.Table8

[FC] [PubMed 2015] Fusion cancer (Beijing) (the fusions are limited to class A and B)

[NOR] [PubMed 2016] Babiceanu M et al. Recurrent chimeric fusion RNAs in non-cancer tissues and cells. Nucleic Acids Res. 2016 Feb 2 (Table S3)

[URK] [PubMed 2016] Urakami et al. Next generation sequencing approach for detecting 491 fusion genes from human cancer. Biomed Res. 2016;37(1):51-62.

[AM] [PubMed 2016] Global analysis of somatic structural genomic alterations and their impact on gene expression in diverse human cancersAlaei-Mahabadi B. et al.,Proc Natl Acad Sci U S A. 2016 Nov 16. pii: 201606220.

[FM] [PubMed 2018] Genomic hotspots but few recurrent fusion genes in breast cancer, Fimereli et al., Genes Chromosomes Cancer. (SupplTableS2.xls) 2018 Feb 13

[MA] [PubMed 2018] Pan-cancer genome and transcriptome analyses of1,699 paediatric leukaemias and solid tumours, Ma et al, Nature (March 2018) Table S3

[GAO] [PubMed 2018] Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Gao et al, Cell Reports (April 2018) Table S2

[MAY] [PubMed 2018] Development and Verification of an RNA Sequencing (RNA-Seq) Assay for the Detection of Gene Fusions in Tumor, Winters et al (July 2018) Table S7

[GDB] [PubMed 2019] Fusion gene annotation DataBase. Kim P t Zhou X. Nucleic Acids Res. 2019 Jan 8;47(D1):D994-D1004 [site FusionGDB]

[DDR][DDG] [PubMed 2019] Improved detection of gene fusions by applying statistical methods reveals oncogenic RNA cancer drivers, Dehghannasiri R et al, Proc Natl Acad Sci U S A. 2019 Jul 15. pii: 201900391. doi: 10.1073/pnas.1900391116

[DDR] TGCA novel recurrent fusions - Sup. Table 1

[DDG] GTEx (normal tissus) recurrent fusions - Sup. Table 1

[PC] PCAWG : Pan-cancer analysis of whole genomes. ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Nature. 2020 Feb;578(7793):82-93. doi: 10.1038/s41586-020-1969-6. [PubMed 2020] gene fusion data on synapse syn10003873)

Contributor(s)

Written may 2012 Philippe Dessen

Updated fevr. 2021 Philippe Dessen and Jean-Loup Huret

Citation

This paper should be referenced as such :
Dessen P and Huret JL. Chromosomal band 9p12. Atlas Genet Cytogenet Oncol Haematol. July 2012.
URL : http://atlasgeneticsoncology.org/Bands/9p12.html

© Atlas of Genetics and Cytogenetics in Oncology and Haematology

indexed on : sam. fevr. 20 15:30:32 CET 2021

Home Genes Leukemias Solid Tumors Cancer-Prone Deep Insight Case reports Journals Portal Teaching

Written	may 2012	Philippe Dessen

Updated	fevr. 2021	Philippe Dessen and Jean-Loup Huret