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  Chromosome X

Genes Linked with Cancer

How to use this data table Click on the gene name for detailed information. Type in the Search box e.g. 'germline' or 'Breast Cancer' to search within Chromosome X; or Sort by clicking on a column heading e.g. 'Gene'.

Gene Location Aliases Abnormalities Implicated in
KDM6A Xp11.2 UTX, KABUK2, bA386N14.2Somatic
ELK1 Xp11.2
TFE3 Xp11.22 TFEA, RCCP2, RCCX1, bHLHe33Somatic
Translocation
-Kidney Cancer
-Soft Tissue Sarcoma
SSX2 Xp11.22 SSX, HD21, CT5.2, CT5.2A, HOM-MEL-40Somatic
Translocation
-Synovial Sarcoma
KDM5C Xp11.22-p11.21 MRXJ, SMCX, MRXSJ, XE169, MRXSCJ, JARID1C, DXS1272ESomatic
SSX4 Xp11.23 CT5.4Somatic
Translocation
-Synovial Sarcoma
GATA1 Xp11.23 GF1, GF-1, NFE1, XLTT, ERYF1, NF-E1, XLANP, XLTDA, GATA-1Somatic
SSX1 Xp11.23 SSRC, CT5.1Somatic
Translocation
-Synovial Sarcoma
TIMP1 Xp11.3-p11.23 EPA, EPO, HCI, CLGI, TIMP
WAS Xp11.4-p11.21 THC, IMD2, SCNX, THC1, WASP
ARAF Xp11.4-p11.2 PKS2, A-RAF, ARAF1, RAFA1
BCOR Xp11.4 MAA2, ANOP2, MCOPS2Somatic
ZRSR2 Xp22.1 URP, U2AF1L2, U2AF1RS2, U2AF1-RS2Somatic
FANCB Xp22.2 FA2, FAB, FACB, FAAP90, FAAP95Germline-Fanconi Anaemia
CD99 Xp22.32 and Yp11.3 MIC2, HBA71, MIC2X, MIC2Y, MSK5XOverexpression-Ewing's Sarcoma
MSN Xq11.1 HEL70Somatic
AMER1 Xq11.2 WTX, OSCS, FAM123BSomatic-Wilms Tumour
AR Xq12 KD, AIS, TFM, DHTR, SBMA, HYSP1, NR3C4, SMAX1, HUMARA
CXCR3 Xq13 GPR9, MigR, CD182, CD183, Mig-R, CKR-L2, CMKAR3, IP10-R-Cervical Cancer
-Kidney Cancer
-Lung Cancer
-Stomach Cancer
MED12 Xq13 OKS, FGS1, HOPA, OPA1, OHDOX, ARC240, CAGH45, MED12S, TNRC11, TRAP230Somatic
NONO Xq13.1 P54, NMT55, NRB54, P54NRBSomatic
FOXO4 Xq13.1 AFX, AFX1, MLLT7Somatic
ATRX Xq21.1 JMS, SHS, XH2, XNP, ATR2, SFM1, RAD54, MRXHF1, RAD54L, ZNF-HXSomatic
SEPT6 Xq24 SEP2, SEPT2, RP5-876A24.2Somatic
ELF4 Xq26 MEF, ELFRSomatic
GPC3 Xq26.1 SGB, DGSX, MXR7, SDYS, SGBS, OCI-5, SGBS1, GTR2-2Germline-Breast Cancer
-Liver Cancer
-Lung Cancer
-Thyroid Cancer
-Wilms Tumour
PHF6 Xq26.3 BFLS, BORJ, CENP-31Somatic
HPCX Xq27-q28
TGCT1 Xq27 -Testicular Cancer
MCF2 Xq27 DBL, ARHGEF21
CTAG1B Xq28 CTAG, ESO1, CT6.1, CTAG1, LAGE-2, LAGE2B, NY-ESO-1
MAGEA1 Xq28 CT1.1, MAGE1
MAGEA2 Xq28 CT1.2, MAGE2, MAGEA2A
MAGEA3 Xq28 HIP8, HYPD, CT1.3, MAGE3, MAGEA6
MTCP1 Xq28 p8MTCP1, P13MTCP1Somatic

Structural Abnormalities

Selected list of common recurrent structural abnormalities - Chromosome X:

Abnormality Type Gene(s)
der(17)t(X;17) (p11.2;q25) in Alveolar Soft-Part SarcomaTranslocation
t(X;18)(p11.2;q11.2) SS18-SSX1 in Synovial SarcomaTranslocationSSX1 (Xp11.23)SS18 (18q11.2)
t(X;18)(p11.2;q11.2) SS18-SSX2 in Synovial SarcomaTranslocationSSX2 (Xp11.22)SS18 (18q11.2)
t(X;18)(p11.2;q11.2) SS18-SSX4 in Synovial SarcomaTranslocationSSX4 (Xp11.23)SS18 (18q11.2)
der(17)t(X;17)(p11.2;q25) in Alveolar Soft-Part SarcomaTranslocationTFE3 (Xp11.22)ASPSCR1 (17q25.3)
t(X;1)(p11;q21) in Papillary Renal Cell CarcinomaTranslocationTFE3 (Xp11.22)PRCC (1q21.1)

This is a highly selective list aiming to capture structural abnormalies which are frequesnt and/or significant in relation to diagnosis, prognosis, and/or characterising specific cancers. For a much more extensive list see the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer.


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