This gene encodes a sterile alpha motif domain-containing protein. The encoded protein localizes to the cytoplasm and may play a role in regulating cell proliferation and apoptosis. Mutations in this gene are the cause of normophosphatemic familial tumoral calcinosis. Alternate splicing results in multiple transcript variants that encode the same protein.[provided by RefSeq, Ju... See more...

Aliases for SAMD9 Gene

Aliases for SAMD9 Gene

  • Sterile Alpha Motif Domain Containing 9 2 3 5
  • Sterile Alpha Motif Domain-Containing Protein 9 3 4
  • SAM Domain-Containing Protein 9 3 4
  • KIAA2004 2 4
  • C7orf5 3 4
  • DRIF1 3 4
  • OEF1 3 4
  • Expressed In Aggressive Fibromatosis 3
  • Chromosome 7 Open Reading Frame 5 2
  • FLJ20073 2
  • M7MLS2 3
  • MIRAGE 3
  • SAMD9 5
  • NFTC 3
  • OEF2 3

External Ids for SAMD9 Gene

Previous HGNC Symbols for SAMD9 Gene

  • C7orf5

Previous GeneCards Identifiers for SAMD9 Gene

  • GC07M092373
  • GC07M092566
  • GC07M092728
  • GC07M087337

Summaries for SAMD9 Gene

Entrez Gene Summary for SAMD9 Gene

  • This gene encodes a sterile alpha motif domain-containing protein. The encoded protein localizes to the cytoplasm and may play a role in regulating cell proliferation and apoptosis. Mutations in this gene are the cause of normophosphatemic familial tumoral calcinosis. Alternate splicing results in multiple transcript variants that encode the same protein.[provided by RefSeq, Jul 2010]

GeneCards Summary for SAMD9 Gene

SAMD9 (Sterile Alpha Motif Domain Containing 9) is a Protein Coding gene. Diseases associated with SAMD9 include Mirage Syndrome and Tumoral Calcinosis, Normophosphatemic, Familial. An important paralog of this gene is SAMD9L.

UniProtKB/Swiss-Prot Summary for SAMD9 Gene

  • May play a role in the inflammatory response to tissue injury and the control of extra-osseous calcification, acting as a downstream target of TNF-alpha signaling. Involved in the regulation of EGR1, in coordination with RGL2. May be involved in endosome fusion.

Gene Wiki entry for SAMD9 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SAMD9 Gene

Genomics for SAMD9 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SAMD9 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH07J093115 Promoter/Enhancer 1.7 EPDnew FANTOM5 Ensembl ENCODE 258.9 +0.7 658 4.6 ZIC2 YY1 BCL11A IRF2 EP300 ELF1 RFX5 STAT3 TBP EBF1 SAMD9 HSALNG0059565 SAMD9L VPS50 piR-48553-292 CDK6
GH07J092807 Enhancer 1.4 FANTOM5 ENCODE dbSUPER 4.2 +308.6 308582 4.1 BCLAF1 SP1 ZNF600 IKZF1 NCOR1 MYC JUND ZNF592 POLR2A CEBPA HSALNG0059555 CDK6 CDK6-AS1 CYP51A1 SAMD9 RBM48 FAM133B PEX1 lnc-FAM133B-4
GH07J092829 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 1.9 +283.7 283724 9.8 BCLAF1 ZNF207 MYC JUND ATF2 KLF9 POLR2A CEBPA ZSCAN16 ZIC2 CDK6 CDK6-AS1 lnc-FAM133B-5 ENSG00000243107 KRIT1 GATAD1 PEX1 AKAP9 FAM133B MTERF1
GH07J092638 Promoter/Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 2.9 +474.6 474550 10.3 BCLAF1 SP1 JUND BCL11A CEBPB TRIM22 EP300 IRF4 EBF1 CBFB ENSG00000287932 HSALNG0059553 LOC112268009 CDK6 CDK6-AS1 FAM133B GATAD1 KRIT1 ANKIB1 SAMD9
GH07J093165 Enhancer 0.7 FANTOM5 ENCODE 5.6 -47.6 -47648 1.2 CEBPB ARID3A SPI1 MTA2 DPF2 RELB CEBPG HEPACAM2 SAMD9 piR-46256-049 SAMD9L
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SAMD9 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SAMD9

Top Transcription factor binding sites by QIAGEN in the SAMD9 gene promoter:
  • AML1a
  • HSF1 (long)
  • HSF1short
  • NF-AT
  • NF-AT1
  • NF-AT2
  • NF-AT3
  • NF-AT4
  • Pax-4a
  • Pax-6

Genomic Locations for SAMD9 Gene

Latest Assembly
chr7:93,099,513-93,118,023
(GRCh38/hg38)
Size:
18,511 bases
Orientation:
Minus strand

Previous Assembly
chr7:92,728,831-92,747,292
(GRCh37/hg19 by Entrez Gene)
Size:
18,462 bases
Orientation:
Minus strand

chr7:92,728,829-92,747,336
(GRCh37/hg19 by Ensembl)
Size:
18,508 bases
Orientation:
Minus strand

Genomic View for SAMD9 Gene

Genes around SAMD9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SAMD9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SAMD9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SAMD9 Gene

Proteins for SAMD9 Gene

  • Protein details for SAMD9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5K651-SAMD9_HUMAN
    Recommended name:
    Sterile alpha motif domain-containing protein 9
    Protein Accession:
    Q5K651
    Secondary Accessions:
    • A2RU68
    • Q5K649
    • Q6P080
    • Q75N21
    • Q8IVG6
    • Q9NXS8

    Protein attributes for SAMD9 Gene

    Size:
    1589 amino acids
    Molecular mass:
    184281 Da
    Quaternary structure:
    • Interacts with RGL2 (PubMed:21160498). Interacts with EEA1 (PubMed:24029230).
    SequenceCaution:
    • Sequence=AAH65769.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=AAQ04689.3; Type=Miscellaneous discrepancy; Note=Unlikely isoform. Aberrant splice sites.; Evidence={ECO:0000305}; Sequence=BAA90932.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAC23101.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

neXtProt entry for SAMD9 Gene

Post-translational modifications for SAMD9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SAMD9 Gene

No data available for DME Specific Peptides for SAMD9 Gene

Domains & Families for SAMD9 Gene

Gene Families for SAMD9 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for SAMD9 Gene

InterPro:
Blocks:
  • Sterile alpha motif SAM
  • Sterile alpha motif homology 2

Suggested Antigen Peptide Sequences for SAMD9 Gene

GenScript: Design optimal peptide antigens:
  • Sterile alpha motif domain-containing protein 9 (SAMD9_HUMAN)
genes like me logo Genes that share domains with SAMD9: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SAMD9 Gene

Function for SAMD9 Gene

Molecular function for SAMD9 Gene

UniProtKB/Swiss-Prot Function:
May play a role in the inflammatory response to tissue injury and the control of extra-osseous calcification, acting as a downstream target of TNF-alpha signaling. Involved in the regulation of EGR1, in coordination with RGL2. May be involved in endosome fusion.
UniProtKB/Swiss-Prot Induction:
Up-regulated by TNF-alpha through p38 MAPKs and NF-kappa-B. Up-regulated by osmotic shock. Induced by IFNG.

Phenotypes From GWAS Catalog for SAMD9 Gene

Gene Ontology (GO) - Molecular Function for SAMD9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 24029230
genes like me logo Genes that share ontologies with SAMD9: view
genes like me logo Genes that share phenotypes with SAMD9: view

Human Phenotype Ontology for SAMD9 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

miRNA for SAMD9 Gene

miRTarBase miRNAs that target SAMD9

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SAMD9

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for SAMD9 Gene

Localization for SAMD9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SAMD9 Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
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 SAMD9 gene
Compartment Confidence
cytosol 5
endosome 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SAMD9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA,IDA 16960814
GO:0005829 cytosol IDA --
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with SAMD9: view

Pathways & Interactions for SAMD9 Gene

PathCards logo

SuperPathways for SAMD9 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SAMD9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0034058 endosomal vesicle fusion IDA 24029230
genes like me logo Genes that share ontologies with SAMD9: view

No data available for Pathways by source and SIGNOR curated interactions for SAMD9 Gene

Drugs & Compounds for SAMD9 Gene

No Compound Related Data Available

Transcripts for SAMD9 Gene

mRNA/cDNA for SAMD9 Gene

2 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SAMD9

Alternative Splicing Database (ASD) splice patterns (SP) for SAMD9 Gene

No ASD Table

Relevant External Links for SAMD9 Gene

GeneLoc Exon Structure for
SAMD9

Expression for SAMD9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SAMD9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SAMD9 Gene

This gene is overexpressed in Esophagus - Mucosa (x8.6) and Whole Blood (x4.6).

Protein differential expression in normal tissues from HIPED for SAMD9 Gene

This gene is overexpressed in Cervix (28.3) and Lymph node (10.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SAMD9 Gene



Protein tissue co-expression partners for SAMD9 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SAMD9

SOURCE GeneReport for Unigene cluster for SAMD9 Gene:

Hs.65641

mRNA Expression by UniProt/SwissProt for SAMD9 Gene:

Q5K651-SAMD9_HUMAN
Tissue specificity: Widely expressed. Very low levels are detected in skeletal muscle. Not detected in brain. Down-regulated in aggressive fibromatosis, as well as in breast and colon cancers. Up-regulated in fibroblasts from patients with normophosphatemic tumoral calcinosis (NFTC).

Evidence on tissue expression from TISSUES for SAMD9 Gene

  • Intestine(4.3)
  • Nervous system(4.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SAMD9 Gene

Germ Layers:
  • ectoderm
Systems:
  • digestive
  • integumentary
  • nervous
Regions:
Head and neck:
  • eye
  • head
  • mouth
General:
  • skin
genes like me logo Genes that share expression patterns with SAMD9: view

Primer products for research

Orthologs for SAMD9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SAMD9 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SAMD9 29 30
  • 99.56 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SAMD9 29 30
  • 86.38 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia RGD1563091 29
  • 82.13 (n)
Oppossum
(Monodelphis domestica)
Mammalia SAMD9 30
  • 80 (a)
OneToOne
Chicken
(Gallus gallus)
Aves -- 30
  • 49 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 54 (a)
OneToMany
Zebrafish
(Danio rerio)
Actinopterygii LOC101886156 29
  • 53.37 (n)
si:ch211-141h20.6 30
  • 38 (a)
ManyToMany
si:ch1073-209h18.1 30
  • 36 (a)
ManyToMany
CU633740.1 30
  • 36 (a)
ManyToMany
si:ch211-113e8.9 30
  • 35 (a)
ManyToMany
CU929417.2 30
  • 34 (a)
ManyToMany
BX537350.1 30
  • 27 (a)
ManyToMany
Species where no ortholog for SAMD9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • Dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • 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)
  • Mouse (Mus musculus)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for SAMD9 Gene

ENSEMBL:
Gene Tree for SAMD9 (if available)
TreeFam:
Gene Tree for SAMD9 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SAMD9: view image
Alliance of Genome Resources:
Additional Orthologs for SAMD9

Paralogs for SAMD9 Gene

Paralogs for SAMD9 Gene

(1) SIMAP similar genes for SAMD9 Gene using alignment to 2 proteins:

  • SAMD9_HUMAN
  • C9JKF1_HUMAN
genes like me logo Genes that share paralogs with SAMD9: view

Variants for SAMD9 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SAMD9 Gene

SNP ID Clinical significance and condition Chr 07 pos Variation AA Info Type
1002048 Uncertain Significance: not provided 93,105,046(-) T/A
NM_017654.4(SAMD9):c.1052A>T (p.Asp351Val)
MISSENSE
1005053 Uncertain Significance: not provided 93,105,782(-) G/A
NM_017654.4(SAMD9):c.316C>T (p.Arg106Cys)
MISSENSE
1005429 Uncertain Significance: not provided 93,105,764(-) G/C
NM_017654.4(SAMD9):c.334C>G (p.Gln112Glu)
MISSENSE
1008069 Uncertain Significance: not provided 93,101,374(-) C/A
NM_017654.4(SAMD9):c.4724G>T (p.Gly1575Val)
MISSENSE
1013554 Uncertain Significance: not provided 93,102,397(-) C/T
NM_017654.4(SAMD9):c.3701G>A (p.Gly1234Glu)
MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SAMD9 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SAMD9 Gene

Variant ID Type Subtype PubMed ID
nsv5845 CNV deletion 18451855

Variation tolerance for SAMD9 Gene

Residual Variation Intolerance Score: 46.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.92; 79.66% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SAMD9 Gene

Human Gene Mutation Database (HGMD)
SAMD9
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SAMD9
Leiden Open Variation Database (LOVD)
SAMD9

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SAMD9 Gene

Disorders for SAMD9 Gene

MalaCards: The human disease database

(16) MalaCards diseases for SAMD9 Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

UniProtKB/Swiss-Prot

SAMD9_HUMAN
  • Tumoral calcinosis, normophosphatemic, familial (NFTC) [MIM:610455]: An uncommon, life-threatening disorder characterized by progressive deposition of calcified masses in cutaneous and subcutaneous tissues. Serum phosphate levels are normal. Clinical features include painful calcified ulcerative lesions and massive calcium deposition in the mid- and lower dermis, severe skin and bone infections, erythematous papular skin eruption in infancy, conjunctivitis, and gingivitis. NFTC shows a striking resemblance to acquired dystrophic calcinosis, in which tissue calcification occurs as a consequence of tissue injury/inflammation. {ECO:0000269 PubMed:16960814, ECO:0000269 PubMed:18094730}. Note=The disease is caused by variants affecting the gene represented in this entry.
  • MIRAGE syndrome (MIRAGE) [MIM:617053]: A form of syndromic adrenal hypoplasia characterized by myelodysplasia, infection, restriction of growth, adrenal hypoplasia, genital phenotypes, and enteropathy. {ECO:0000269 PubMed:27182967}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for SAMD9

genes like me logo Genes that share disorders with SAMD9: view

No data available for Genatlas for SAMD9 Gene

Publications for SAMD9 Gene

  1. SAMD9 mutations cause a novel multisystem disorder, MIRAGE syndrome, and are associated with loss of chromosome 7. (PMID: 27182967) Narumi S … Hasegawa T (Nature genetics 2016) 2 3 4 72
  2. Normophosphatemic familial tumoral calcinosis is caused by deleterious mutations in SAMD9, encoding a TNF-alpha responsive protein. (PMID: 18094730) Chefetz I … Sprecher E (The Journal of investigative dermatology 2008) 3 4 72
  3. A deleterious mutation in SAMD9 causes normophosphatemic familial tumoral calcinosis. (PMID: 16960814) Topaz O … Sprecher E (American journal of human genetics 2006) 3 4 72
  4. Germline loss-of-function SAMD9 and SAMD9L alterations in adult myelodysplastic syndromes. (PMID: 30322869) Nagata Y … Maciejewski JP (Blood 2018) 3 72
  5. Germline SAMD9 mutation in siblings with monosomy 7 and myelodysplastic syndrome. (PMID: 28487541) Schwartz JR … Klco JM (Leukemia 2017) 3 72

Products for SAMD9 Gene

Sources for SAMD9 Gene