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FAM107B (family with sequence similarity 107, member B)

Written2015-01Hideo Nakajima, Keita Koizumi
Department of Oncology, Ageo Central General Hospital, Ageo, Saitama, Department of Surgery, Saitama Medical Center, Saitama Medical University, Kawagoe, Saitama, nakajima.h@ach.or.jp (HN); Center for Child Mental Development, Kanazawa University, Kanazawa, Ishikawa, kkoizumi@med.kanazawa-u.ac.jp (KK) Japan.

Abstract FAM107 members contain an N-terminal domain of unknown function (DUF1151) that is conserved across species. Mammals have two genes, FAM107A and FAM107B, which expressions are strong in neural cells, whereas their expressions are mostly down-regulated in cancer cells. Both proteins appear to alter cytoskeleton rearrangements and are involved in cell migration and invasion. The molecular mechanisms underlying the diverse biological functions of FAM107 remain unclear, while it shows functional similarity with heat-shock proteins (HSPs) as well as reactions to cellular stress.

Keywords tumor suppressor gene, heat-shock protein, neuron

(Note : for Links provided by Atlas : click)

Identity

Alias_namesC10orf45
chromosome 10 open reading frame 45
family with sequence similarity 107, member B
Alias_symbol (synonym)FLJ45505
MGC11034
Other aliasHITS
HGNC (Hugo) FAM107B
LocusID (NCBI) 83641
Atlas_Id 53778
Location 10p13  [Link to chromosome band 10p13]
Location_base_pair Starts at 14518557 and ends at 14774897 bp from pter ( according to hg19-Feb_2009)  [MappiÓg FA 105B.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
EIF3B (7p22.3) / FAM107B (10p13)FAM107B (10p13) / DGKG (3q27.2)FAM107B (10p13) / GCNT7 (20q13.31)
FAM107B (10p13) / MXI1 (10q25.2)FAM107B (10p13) / PHF11 (13q14.2)FAM107B (10p13) / UBALD2 (17q25.1)
FAM168B (2q21.1) / FAM107B (10p13)LOC100507412 (-) / FAM107B (10p13)MLEC (12q24.31) / FAM107B (10p13)
TXNDC12 (1p32.3) / FAM107B (10p13)USP6NL (10p14) / FAM107B (10p13)WDR37 (10p15.3) / FAM107B (10p13)
Note The FAM107B protein is encoded by FAM107B gene.

DNA/RNA

Description FAM107B gene is located on the minus strand of chromosome 10, p13, which is on the short arm of the chromosome.
Transcription FAM107B has ten transcript variants. Variant 1 and 3 through 10 encode the same isoform (a: 131 aa) with coding DNA sequence consisting of 396 bps on three exons. Variant 2 lacks an exon and initiates translation at an alternate start codon, which encodes longer isoform (b: 306 aa) with a distinct N-terminus.

Protein

Note FAM107 members contain an N-terminal domain of unknown function (DUF1151) that is conserved across species, including mammalian, xenopus, fish, and drosophila, and show no homologous matches to other functionally conserved domains. Mammals have two genes, FAM107A and FAM107B, which encode for proteins of 144 amino acids (aa) and 131 aa, respectively.
 
Description 131 amino acids, 15.6 kDa. FAM107B protein includes an N-terminal (aa 1-66) conserved domain DUF1151, a nuclear localization signal (NLS) and a C-terminal (aa 61-112) variable coiled-coil domain (Nakajima et al., 2010; Nakajima et al., 2014).
Expression FAM107B is expressed in most tissues and found in all stages of human development. FAM107B gene has a promoter region with heat-shock transcription factor 1 (HSF1) binding sites, and FAM107B expression is increased after heat-shock or hyperthermia treatment (Nakajima et al., 2010).
Localisation Nucleus (Nakajima et al., 2010)
Function FAM107B is regarded as a candidate tumor suppressor gene because a loss of FAM107B expression was observed to be a common phenomenon in cancers of various organs, resulting in tumor development and proliferation. Forced expression of FAM107B inhibited cancer cell proliferation in response to growth factors in vitro and tumor xenograft growth in vivo (Nakajima et al., 2010; Nakajima et al., 2012).
Homology FAM107B protein sequence is nearly 98% identical with mouse and rat homologues. FAM107A and FAM107B proteins have 65% sequence similarity in their DUF1151 regions (Nakajima et al., 2010; Nakajima et al., 2014).

Mutations

Note A point mutation in the C-terminal region (chromosome 10:14603968 CïG?TïA transition) is frequently observed in basal-like breast cancer (Ding et al., 2010).

Implicated in

Note
  
Entity Breast cancer
Note A point mutation in the C-terminal region was frequently observed in basal-like breast cancer (Ding et al., 2010), and mutated amino acid sequence of FAM107B in breast cancer was identified as a unique tumor antigen predicted to bind to HLA-A2 (Li et al., 2011). Copy number aberrations (CNA) of FAM107B are found specifically in basal-like breast cancer (Weigman et al., 2012). In addition, genome-wide DNA methylation study was performed to identify differentially methylated sites between monozygotic twins discordant for breast cancer. FAM107B was identified as a hypermethylated region in breast cancer blood samples (Heyn et al., 2013). In analysis for FAM107B expression and the clinico-pathological parameters, FAM107B expression intensity was positively correlated with the expressions of HER2 and Ki-67, but it was inversely correlated with PR expression. Accordingly, FAM107B expression was mostly lost in HER2 negative, Ki-67 negative, PR positive, and desmoplastic reaction-negative type breast cancer, which is believed to be a non-aggressive or indolent phenotype (Nakajima et al., 2012).
  
  
Entity Stomach Cancer
Note FAM107B expression is decreased in intestinal-type gastric adenocarcinomas but not in diffuse type or mucinous adenocarcinomas (Nakajima et al., 2010).
  
  
Entity Colon Cancer
Note FAM107B expression is decreased during the processes in the colorectal adenoma-to-carcinoma transition (Nakajima et al., 2010).
  
  
Entity Uterine Cervical Cancer
Note In uterine cervical diseases, FAM107B expression is lost in invasive squamous cell carcinoma but not in cervical intraepithelial neoplasia (CIN) (Nakajima et al., 2012).
  
  
Entity Autism Spectrum Disorder
Note Six genome-wide association studies (GWASs) were integrated to figures out genetic networks of candidate genes associated with autism spectrum disorders (ASD). SNP close to FAM107B is mentioned as one of the ASD associated candidates (Poelmans et al., 2013).
  
  
Entity Major Depression
Note Genome-wide DNA methylation study using post mortem frontal cortex of healthy and major depression subjects figured out FAM107B region is differentially methylated in neural cells of major depression (Guintivano et al., 2013).
  

Bibliography

Genome remodelling in a basal-like breast cancer metastasis and xenograft
Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, Harris CC, McLellan MD, Fulton RS, Fulton LL, Abbott RM, Hoog J, Dooling DJ, Koboldt DC, Schmidt H, Kalicki J, Zhang Q, Chen L, Lin L, Wendl MC, McMichael JF, Magrini VJ, Cook L, McGrath SD, Vickery TL, Appelbaum E, Deschryver K, Davies S, Guintoli T, Lin L, Crowder R, Tao Y, Snider JE, Smith SM, Dukes AF, Sanderson GE, Pohl CS, Delehaunty KD, Fronick CC, Pape KA, Reed JS, Robinson JS, Hodges JS, Schierding W, Dees ND, Shen D, Locke DP, Wiechert ME, Eldred JM, Peck JB, Oberkfell BJ, Lolofie JT, Du F, Hawkins AE, O'Laughlin MD, Bernard KE, Cunningham M, Elliott G, Mason MD, Thompson DM Jr, Ivanovich JL, Goodfellow PJ, Perou CM, Weinstock GM, Aft R, Watson M, Ley TJ, Wilson RK, Mardis ER
Nature 2010 Apr 15;464(7291):999-1005
PMID 20393555
 
A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression
Guintivano J, Aryee MJ, Kaminsky ZA
Epigenetics 2013 Mar;8(3):290-302
PMID 23426267
 
DNA methylation profiling in breast cancer discordant identical twins identifies DOK7 as novel epigenetic biomarker
Heyn H, Carmona FJ, Gomez A, Ferreira HJ, Bell JT, Sayols S, Ward K, Stefansson OA, Moran S, Sandoval J, Eyfjord JE, Spector TD, Esteller M
Carcinogenesis 2013 Jan;34(1):102-8
PMID 23054610
 
Cancer genome sequencing and its implications for personalized cancer vaccines
Li L, Goedegebuure P, Mardis ER, Ellis MJ, Zhang X, Herndon JM, Fleming TP, Carreno BM, Hansen TH, Gillanders WE
Cancers (Basel) 2011 Nov 25;3(4):4191-211
PMID 24213133
 
Family with sequence similarity 107: A family of stress responsive small proteins with diverse functions in cancer and the nervous system (Review)
Nakajima H, Koizumi K
Biomed Rep 2014 May;2(3):321-325
PMID 24748967
 
AKAPs integrate genetic findings for autism spectrum disorders
Poelmans G, Franke B, Pauls DL, Glennon JC, Buitelaar JK
Transl Psychiatry 2013 Jun 11;3:e270
PMID 23756379
 
Basal-like Breast cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival
Weigman VJ, Chao HH, Shabalin AA, He X, Parker JS, Nordgard SH, Grushko T, Huo D, Nwachukwu C, Nobel A, Kristensen VN, Børresen-Dale AL, Olopade OI, Perou CM
Breast Cancer Res Treat 2012 Jun;133(3):865-80
PMID 22048815
 

Citation

This paper should be referenced as such :
Hideo Nakajima, Keita Koizumi
FAM107B (family with sequence similarity 107, member B)
Atlas Genet Cytogenet Oncol Haematol. 2016;20(2):71-73.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/FAM107BID53778ch10p13.html


External links

Nomenclature
HGNC (Hugo)FAM107B   23726
Cards
AtlasFAM107BID53778ch10p13
Entrez_Gene (NCBI)FAM107B  83641  family with sequence similarity 107 member B
AliasesC10orf45; HITS
GeneCards (Weizmann)FAM107B
Ensembl hg19 (Hinxton)ENSG00000065809 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000065809 [Gene_View]  chr10:14518557-14774897 [Contig_View]  FAM107B [Vega]
ICGC DataPortalENSG00000065809
TCGA cBioPortalFAM107B
AceView (NCBI)FAM107B
Genatlas (Paris)FAM107B
WikiGenes83641
SOURCE (Princeton)FAM107B
Genetics Home Reference (NIH)FAM107B
Genomic and cartography
GoldenPath hg38 (UCSC)FAM107B  -     chr10:14518557-14774897 -  10p13   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)FAM107B  -     10p13   [Description]    (hg19-Feb_2009)
EnsemblFAM107B - 10p13 [CytoView hg19]  FAM107B - 10p13 [CytoView hg38]
Mapping of homologs : NCBIFAM107B [Mapview hg19]  FAM107B [Mapview hg38]
Gene and transcription
Genbank (Entrez)###############################################################################################################################################################################################################################################################
RefSeq transcript (Entrez)NM_001282695 NM_001282696 NM_001282697 NM_001282698 NM_001282699 NM_001282700 NM_001282701 NM_001282702 NM_001282703 NM_001320735 NM_001320736 NM_001320737 NM_001320738 NM_001320739 NM_001320740 NM_001320741 NM_031453
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)FAM107B
Cluster EST : UnigeneHs.446315 [ NCBI ]
CGAP (NCI)Hs.446315
Alternative Splicing GalleryENSG00000065809
Gene ExpressionFAM107B [ NCBI-GEO ]   FAM107B [ EBI - ARRAY_EXPRESS ]   FAM107B [ SEEK ]   FAM107B [ MEM ]
Gene Expression Viewer (FireBrowse)FAM107B [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)83641
GTEX Portal (Tissue expression)FAM107B
Human Protein AtlasENSG00000065809-FAM107B [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9H098   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9H098  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9H098
Splice isoforms : SwissVarQ9H098
PhosPhoSitePlusQ9H098
Domains : Interpro (EBI)DUF1151   
Domain families : Pfam (Sanger)DUF1151 (PF06625)   
Domain families : Pfam (NCBI)pfam06625   
Conserved Domain (NCBI)FAM107B
DMDM Disease mutations83641
Blocks (Seattle)FAM107B
SuperfamilyQ9H098
Human Protein Atlas [tissue]ENSG00000065809-FAM107B [tissue]
Peptide AtlasQ9H098
HPRD12575
IPIIPI00871831   IPI00027799   IPI00646308   IPI00947154   IPI00945456   IPI00946222   IPI00945668   IPI01012864   IPI01012351   IPI00946163   IPI00945357   IPI00514363   
Protein Interaction databases
DIP (DOE-UCLA)Q9H098
IntAct (EBI)Q9H098
FunCoupENSG00000065809
BioGRIDFAM107B
STRING (EMBL)FAM107B
ZODIACFAM107B
Ontologies - Pathways
QuickGOQ9H098
Ontology : AmiGO
Ontology : EGO-EBI
NDEx NetworkFAM107B
Atlas of Cancer Signalling NetworkFAM107B
Wikipedia pathwaysFAM107B
Orthology - Evolution
OrthoDB83641
GeneTree (enSembl)ENSG00000065809
Phylogenetic Trees/Animal Genes : TreeFamFAM107B
HOVERGENQ9H098
HOGENOMQ9H098
Homologs : HomoloGeneFAM107B
Homology/Alignments : Family Browser (UCSC)FAM107B
Gene fusions - Rearrangements
Fusion : MitelmanWDR37/FAM107B [10p15.3/10p13]  [t(10;10)(p13;p15)]  
Fusion: TCGA_MDACCUSP6NL 10p14 FAM107B 10p13 LUAD
Fusion: TCGA_MDACCWDR37 10p15.3 FAM107B 10p13 BLCA
Tumor Fusion PortalFAM107B
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerFAM107B [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)FAM107B
dbVarFAM107B
ClinVarFAM107B
1000_GenomesFAM107B 
Exome Variant ServerFAM107B
ExAC (Exome Aggregation Consortium)ENSG00000065809
GNOMAD BrowserENSG00000065809
Genetic variants : HAPMAP83641
Genomic Variants (DGV)FAM107B [DGVbeta]
DECIPHERFAM107B [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisFAM107B 
Mutations
ICGC Data PortalFAM107B 
TCGA Data PortalFAM107B 
Broad Tumor PortalFAM107B
OASIS PortalFAM107B [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICFAM107B  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDFAM107B
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch FAM107B
DgiDB (Drug Gene Interaction Database)FAM107B
DoCM (Curated mutations)FAM107B (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)FAM107B (select a term)
intoGenFAM107B
NCG5 (London)FAM107B
Cancer3DFAM107B(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM
Orphanet
DisGeNETFAM107B
MedgenFAM107B
Genetic Testing Registry FAM107B
NextProtQ9H098 [Medical]
TSGene83641
GENETestsFAM107B
Target ValidationFAM107B
Huge Navigator FAM107B [HugePedia]
snp3D : Map Gene to Disease83641
BioCentury BCIQFAM107B
ClinGenFAM107B
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD83641
Chemical/Pharm GKB GenePA134902915
Clinical trialFAM107B
Miscellaneous
canSAR (ICR)FAM107B (select the gene name)
Probes
Litterature
PubMed19 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineFAM107B
EVEXFAM107B
GoPubMedFAM107B
iHOPFAM107B
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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