Aliases for TM9SF3 Gene

Aliases for TM9SF3 Gene

  • Transmembrane 9 Superfamily Member 3 2 3 4 5
  • SMBP 2 3 4
  • EP70-P-Iso 3 4
  • Dinucleotide Oxidase Disulfide Thiol Exchanger 3 Superfamily Member 3 3
  • Endomembrane Protein Emp70 Precursor Isolog 3
  • SM-11044 Binding Protein 3
  • SM-11044-Binding Protein 4
  • TM9SF3 5

External Ids for TM9SF3 Gene

Previous GeneCards Identifiers for TM9SF3 Gene

  • GC10M098267
  • GC10M091907

Summaries for TM9SF3 Gene

GeneCards Summary for TM9SF3 Gene

TM9SF3 (Transmembrane 9 Superfamily Member 3) is a Protein Coding gene. Diseases associated with TM9SF3 include Tumoral Calcinosis, Hyperphosphatemic, Familial, 1. An important paralog of this gene is TM9SF4.

Additional gene information for TM9SF3 Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TM9SF3 Gene

Genomics for TM9SF3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TM9SF3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TM9SF3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TM9SF3

Top Transcription factor binding sites by QIAGEN in the TM9SF3 gene promoter:
  • Bach2
  • Brachyury
  • Egr-4
  • FOXO4
  • GATA-1
  • HNF-1
  • HNF-1A
  • LUN-1
  • Max1
  • SRY

Genomic Locations for TM9SF3 Gene

Genomic Locations for TM9SF3 Gene
69,343 bases
Minus strand
69,344 bases
Minus strand

Genomic View for TM9SF3 Gene

Genes around TM9SF3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TM9SF3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TM9SF3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TM9SF3 Gene

Proteins for TM9SF3 Gene

  • Protein details for TM9SF3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Transmembrane 9 superfamily member 3
    Protein Accession:
    Secondary Accessions:
    • Q5TB57
    • Q6UWE7
    • Q9NWL8
    • Q9P0G9
    • Q9UHW8

    Protein attributes for TM9SF3 Gene

    589 amino acids
    Molecular mass:
    67888 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAF67014.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=AAQ89178.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=BAA91362.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for TM9SF3 Gene

Post-translational modifications for TM9SF3 Gene

  • Glycosylation at Asn174 and Asn419
  • Ubiquitination at Lys59 and Lys210
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • TM9S3_HUMAN (1842)

Other Protein References for TM9SF3 Gene

No data available for DME Specific Peptides for TM9SF3 Gene

Domains & Families for TM9SF3 Gene

Gene Families for TM9SF3 Gene

Protein Domains for TM9SF3 Gene

  • Nonaspanin (TM9SF)

Suggested Antigen Peptide Sequences for TM9SF3 Gene

GenScript: Design optimal peptide antigens:
  • TM9SF3 protein (Q8WUB5_HUMAN)
  • cDNA FLJ14882 fis, clone PLACE1003537, weakly similar to ENDOSOMAL P24A PROTEIN (Q96JZ5_HUMAN)
  • SM-11044-binding protein (TM9S3_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the nonaspanin (TM9SF) (TC 9.A.2) family.
  • Belongs to the nonaspanin (TM9SF) (TC 9.A.2) family.
genes like me logo Genes that share domains with TM9SF3: view

Function for TM9SF3 Gene

Phenotypes From GWAS Catalog for TM9SF3 Gene

genes like me logo Genes that share phenotypes with TM9SF3: view

Animal Model Products

  • Taconic Biosciences Mouse Models for TM9SF3

CRISPR Products

miRNA for TM9SF3 Gene

miRTarBase miRNAs that target TM9SF3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TM9SF3

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TM9SF3 Gene

Localization for TM9SF3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TM9SF3 Gene

Membrane. Multi-pass membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TM9SF3 gene
Compartment Confidence
plasma membrane 3
golgi apparatus 2
extracellular 1
cytoskeleton 1
nucleus 1
endoplasmic reticulum 1
endosome 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TM9SF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA,IBA 21873635
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with TM9SF3: view

Pathways & Interactions for TM9SF3 Gene

PathCards logo

SuperPathways for TM9SF3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for TM9SF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0072657 protein localization to membrane IBA 21873635
genes like me logo Genes that share ontologies with TM9SF3: view

No data available for Pathways by source and SIGNOR curated interactions for TM9SF3 Gene

Drugs & Compounds for TM9SF3 Gene

No Compound Related Data Available

Transcripts for TM9SF3 Gene

mRNA/cDNA for TM9SF3 Gene

18 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TM9SF3

Alternative Splicing Database (ASD) splice patterns (SP) for TM9SF3 Gene

No ASD Table

Relevant External Links for TM9SF3 Gene

GeneLoc Exon Structure for

Expression for TM9SF3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TM9SF3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TM9SF3 Gene

This gene is overexpressed in Nasal epithelium (41.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TM9SF3 Gene

Protein tissue co-expression partners for TM9SF3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TM9SF3

SOURCE GeneReport for Unigene cluster for TM9SF3 Gene:


Evidence on tissue expression from TISSUES for TM9SF3 Gene

  • Liver(4.5)
  • Muscle(4.4)
  • Adrenal gland(4.3)
  • Nervous system(4.2)
  • Intestine(3.7)
  • Lung(3.2)
  • Kidney(2.5)
  • Skin(2.3)
  • Blood(2.3)
  • Heart(2.1)
  • Stomach(2.1)
  • Eye(2)
genes like me logo Genes that share expression patterns with TM9SF3: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TM9SF3 Gene

Orthologs for TM9SF3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TM9SF3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia TM9SF3 30 31
  • 99.82 (n)
(Bos Taurus)
Mammalia TM9SF3 30 31
  • 95.91 (n)
(Canis familiaris)
Mammalia TM9SF3 30 31
  • 95.8 (n)
(Ornithorhynchus anatinus)
Mammalia TM9SF3 31
  • 95 (a)
(Monodelphis domestica)
Mammalia TM9SF3 31
  • 95 (a)
(Rattus norvegicus)
Mammalia Tm9sf3 30
  • 92.67 (n)
(Mus musculus)
Mammalia Tm9sf3 30 17 31
  • 92.22 (n)
(Gallus gallus)
Aves TM9SF3 30 31
  • 86.43 (n)
(Anolis carolinensis)
Reptilia TM9SF3 31
  • 96 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia tm9sf3 30
  • 83.45 (n)
Str.6006 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.12856 30
(Danio rerio)
Actinopterygii tm9sf3 30 31
  • 80.4 (n)
Dr.26978 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004882 30
  • 67.93 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG10590 30 31
  • 65.84 (n)
(Caenorhabditis elegans)
Secernentea Y41D4A.4 30 31
  • 63.59 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes EMP70 31
  • 25 (a)
TMN2 31
  • 24 (a)
Thale Cress
(Arabidopsis thaliana)
eudicotyledons TMN1 30
  • 60.57 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.3627 30
(Glycine max)
eudicotyledons Gma.5446 30
(Oryza sativa)
Liliopsida Os12g0175700 30
  • 60.18 (n)
(Hordeum vulgare)
Liliopsida Hv.4691 30
(Zea mays)
Liliopsida Zm.4030 30
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.9350 31
  • 76 (a)
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.4192 30
Species where no ortholog for TM9SF3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for TM9SF3 Gene

Gene Tree for TM9SF3 (if available)
Gene Tree for TM9SF3 (if available)
Evolutionary constrained regions (ECRs) for TM9SF3: view image

Paralogs for TM9SF3 Gene

Paralogs for TM9SF3 Gene

(4) SIMAP similar genes for TM9SF3 Gene using alignment to 4 proteins:

  • L8EB11_HUMAN
  • Q5TB53_HUMAN
genes like me logo Genes that share paralogs with TM9SF3: view

Variants for TM9SF3 Gene

Additional dbSNP identifiers (rs#s) for TM9SF3 Gene

Structural Variations from Database of Genomic Variants (DGV) for TM9SF3 Gene

Variant ID Type Subtype PubMed ID
esv1534879 CNV insertion 17803354
esv3337079 CNV insertion 20981092
esv3577627 CNV gain 25503493
esv3579086 CNV loss 25503493
nsv1110852 OTHER inversion 24896259
nsv481191 CNV novel sequence insertion 20440878
nsv509363 CNV insertion 20534489
nsv825530 CNV loss 20364138
nsv948151 CNV duplication 23825009

Variation tolerance for TM9SF3 Gene

Residual Variation Intolerance Score: 15.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.71; 15.17% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TM9SF3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TM9SF3 Gene

Disorders for TM9SF3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for TM9SF3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
tumoral calcinosis, hyperphosphatemic, familial, 1
  • hftc1
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for TM9SF3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with TM9SF3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TM9SF3 Gene

Publications for TM9SF3 Gene

  1. The iodocyanopindolol and SM-11044 binding protein belongs to the TM9SF multispanning membrane protein superfamily. (PMID: 11595169) Sugasawa T … Nahmias C (Gene 2001) 2 3 23
  2. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PMID: 16385451) Grupe A … Goate A (American journal of human genetics 2006) 3 41
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 3 4
  5. LMBR1L regulates lymphopoiesis through Wnt/β-catenin signaling. (PMID: 31073040) Choi JH … Beutler B (Science (New York, N.Y.) 2019) 3

Products for TM9SF3 Gene

Sources for TM9SF3 Gene