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    SAMSN1 SAM domain, SH3 domain and nuclear localization signals 1 [ Homo sapiens (human) ]

    Gene ID: 64092, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SAMSN1provided by HGNC
    Official Full Name
    SAM domain, SH3 domain and nuclear localization signals 1provided by HGNC
    Primary source
    HGNC:HGNC:10528
    See related
    Ensembl:ENSG00000155307 MIM:607978; AllianceGenome:HGNC:10528
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SLy2; HACS1; NASH1; SASH2; SH3D6B
    Summary
    SAMSN1 is a member of a novel gene family of putative adaptors and scaffold proteins containing SH3 and SAM (sterile alpha motif) domains (Claudio et al., 2001 [PubMed 11536050]).[supplied by OMIM, Mar 2008]
    Expression
    Biased expression in bone marrow (RPKM 36.2), appendix (RPKM 25.5) and 11 other tissues See more
    Orthologs
    all
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    Genomic context

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    See SAMSN1 in Genome Data Viewer
    Location:
    21q11.2
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (14485228..14659417, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (12840563..13014732, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (15857549..16031738, complement)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr21:15653463-15654235 Neighboring gene ATP binding cassette subfamily C member 13 (pseudogene) Neighboring gene uncharacterized LOC105369304 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18270 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18271 Neighboring gene heat shock protein family A (Hsp70) member 13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18272 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:15821444-15821607 Neighboring gene CRISPRi-validated cis-regulatory element chr21.63 Neighboring gene CRISPRi-validated cis-regulatory element chr21.64 Neighboring gene uncharacterized LOC124905053 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr21:15905912-15907111 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18274 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18275 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13214 Neighboring gene Sharpr-MPRA regulatory region 5316 Neighboring gene SAMSN1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18276 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr21:15988445-15989206 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr21:15989207-15989967 Neighboring gene uncharacterized LOC105372738 Neighboring gene CRISPRi-validated cis-regulatory element chr21.70 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13215 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18277 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18278 Neighboring gene uncharacterized LOC124905054

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. HACS1 signaling adaptor protein recognizes a motif in the paired immunoglobulin receptor B cytoplasmic domain.
      Title: HACS1 signaling adaptor protein recognizes a motif in the paired immunoglobulin receptor B cytoplasmic domain.
    2. Suppression of SAMSN1 Expression is Associated with the Malignant Phenotype of Hepatocellular Carcinoma.
      Title: Suppression of SAMSN1 Expression is Associated with the Malignant Phenotype of Hepatocellular Carcinoma.
    3. This is the first study to identify deletion of a key gene in the C57BL/KaLwRij mice that also displays reduced gene expression in patients with MM and is therefore likely to play an integral role in MM disease development.
      Title: SAMSN1 is a tumor suppressor gene in multiple myeloma.
    4. High expression of SAMSN1 is a significant risk factor for the progression free and overall survival of glioblastoma multiforme
      Title: SAMSN1 is highly expressed and associated with a poor survival in glioblastoma multiforme.
    5. the immunoinhibitory roles of SLy2 in vivo and suggest that the physiological up-regulation of SLy2 observed upon B cell activation functions to counteract excessive B cell spreading.
      Title: Immunoinhibitory adapter protein Src homology domain 3 lymphocyte protein 2 (SLy2) regulates actin dynamics and B cell spreading.
    6. In the nucleus, SLy2 interacts with the SAP30/HDAC1 complex and regulates the activity of HDAC1.
      Title: SLy2 targets the nuclear SAP30/HDAC1 complex.
    7. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    8. downregulation of SAMSN1 gene in human lung cancer.
      Title: Detailed characterization of a homozygously deleted region corresponding to a candidate tumor suppressor locus at 21q11-21 in human lung cancer.
    9. HACS1 is up-regulated by B cell activation signals and is a participant in B cell activation and differentiation.
      Title: The SH3-SAM adaptor HACS1 is up-regulated in B cell activation signaling cascades.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genetic Loci Associated with Circulating Levels of Very Long-Chain Saturated Fatty Acids.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables phosphotyrosine residue binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphotyrosine residue binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of B cell activation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of B cell activation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of adaptive immune response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of peptidyl-tyrosine phosphorylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of intracellular signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in ruffle IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    SAM domain-containing protein SAMSN-1
    Names
    SAM and SH3 domain containing 2
    SAM domain, SH3 domain and nuclear localisation signals, 1
    SAM domain, SH3 domain and nuclear localization signals protein 1
    SH3-SAM adaptor protein
    Src homology domain 3 (SH3)-containing adapter protein SH3 lymphocyte protein 2
    hematopoietic adapter-containing SH3 and sterile I+/--motif (SAM) domains 1
    hematopoietic adapter-containing SH3 and sterile alpha-motif (SAM) domains 1
    hematopoietic adaptor containing SH3 and SAM domains 1
    nuclear localization signals, SAM and SH3 domain containing 1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001256370.2 → NP_001243299.1  SAM domain-containing protein SAMSN-1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains alternate exons at the 5' end and initiates translation from an alternate start codon compared to variant 1. The resulting longer isoform (2) has a distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AA747998, AF165138, AF218085
      Consensus CDS
      CCDS58786.1
      UniProtKB/Swiss-Prot
      Q9NSI8
      Related
      ENSP00000285670.2, ENST00000285670.7
      Conserved Domains (4) summary
      cd09561
      Location:307 → 371
      SAM_SAMSN1; SAM domain of SAMSN1 subfamily
      smart00454
      Location:312 → 371
      SAM; Sterile alpha motif
      pfam12485
      Location:88 → 232
      SLY; Lymphocyte signaling adaptor protein
      cl17036
      Location:235 → 286
      SH3; Src Homology 3 domain superfamily

    2. NM_001256579.3 → NP_001243508.3  SAM domain-containing protein SAMSN-1 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AF130351, AF165138, AF198098, KF457008
      UniProtKB/Swiss-Prot
      A8MT66

    3. NM_001286523.2 → NP_001273452.1  SAM domain-containing protein SAMSN-1 isoform 3

      See identical proteins and their annotated locations for NP_001273452.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains an additional internal exon and initiates translation from an in-frame downstream start codon compared to variant 1. The resulting isoform (3) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AA747998, AF218085, HG380514
      Consensus CDS
      CCDS74774.1
      UniProtKB/TrEMBL
      S6FRS6
      Related
      ENSP00000480850.1, ENST00000619120.4
      Conserved Domains (4) summary
      cd09561
      Location:170 → 234
      SAM_SAMSN1; SAM domain of SAMSN1 subfamily
      smart00454
      Location:175 → 234
      SAM; Sterile alpha motif
      pfam12485
      Location:1 → 95
      SLY; Lymphocyte signaling adaptor protein
      cl17036
      Location:98 → 149
      SH3; Src Homology 3 domain superfamily

    4. NM_001395856.1 → NP_001382785.1  SAM domain-containing protein SAMSN-1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AF165138, AF198098, KF457008

    5. NM_001395857.1 → NP_001382786.1  SAM domain-containing protein SAMSN-1 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AF130351, AF165138, AF198098, KF457008
      Consensus CDS
      CCDS93082.1
      UniProtKB/TrEMBL
      A0A2R8Y4K8
      Related
      ENSP00000493867.1, ENST00000647101.1
      Conserved Domains (2) summary
      cd09561
      Location:535 → 599
      SAM_SAMSN1; SAM domain of SAMSN1 subfamily
      cl17036
      Location:463 → 514
      SH3; Src Homology 3 domain superfamily

    6. NM_001395858.1 → NP_001382787.1  SAM domain-containing protein SAMSN-1 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AF130351, AF165138, AF198098, KF457008
      Conserved Domains (2) summary
      cd09561
      Location:567 → 631
      SAM_SAMSN1; SAM domain of SAMSN1 subfamily
      cl17036
      Location:495 → 546
      SH3; Src Homology 3 domain superfamily

    7. NM_022136.5 → NP_071419.3  SAM domain-containing protein SAMSN-1 isoform 1

      See identical proteins and their annotated locations for NP_071419.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the predominant transcript and encodes isoform 1.
      Source sequence(s)
      AA747998, BC029112
      Consensus CDS
      CCDS42906.1
      UniProtKB/Swiss-Prot
      B3KWJ3, F8WAA1, Q8NFF7, Q9C041, Q9NSI8
      Related
      ENSP00000383411.2, ENST00000400566.6
      Conserved Domains (3) summary
      cd09561
      Location:239 → 303
      SAM_SAMSN1; SAM domain of SAMSN1 subfamily
      pfam12485
      Location:17 → 164
      SLY; Lymphocyte signaling adaptor protein
      cl17036
      Location:167 → 218
      SH3; Src Homology 3 domain superfamily

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      14485228..14659417 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011529685.1 → XP_011527987.1  SAM domain-containing protein SAMSN-1 isoform X3

      Conserved Domains (4) summary
      cd09561
      Location:189 → 253
      SAM_SAMSN1; SAM domain of SAMSN1 subfamily
      smart00454
      Location:194 → 253
      SAM; Sterile alpha motif
      pfam12485
      Location:17 → 114
      SLY; Lymphocyte signaling adaptor protein
      cl17036
      Location:117 → 168
      SH3; Src Homology 3 domain superfamily

    2. XM_047440942.1 → XP_047296898.1  SAM domain-containing protein SAMSN-1 isoform X5

    3. XM_011529684.3 → XP_011527986.1  SAM domain-containing protein SAMSN-1 isoform X2

      Conserved Domains (4) summary
      cd09561
      Location:221 → 285
      SAM_SAMSN1; SAM domain of SAMSN1 subfamily
      smart00454
      Location:226 → 285
      SAM; Sterile alpha motif
      pfam12485
      Location:2 → 146
      SLY; Lymphocyte signaling adaptor protein
      cl17036
      Location:149 → 200
      SH3; Src Homology 3 domain superfamily

    4. XM_011529686.2 → XP_011527988.1  SAM domain-containing protein SAMSN-1 isoform X4

      Conserved Domains (4) summary
      cd09561
      Location:239 → 304
      SAM_SAMSN1; SAM domain of SAMSN1 subfamily
      smart00454
      Location:244 → 304
      SAM; Sterile alpha motif
      pfam12485
      Location:17 → 164
      SLY; Lymphocyte signaling adaptor protein
      cl17036
      Location:167 → 218
      SH3; Src Homology 3 domain superfamily

    5. XM_047440941.1 → XP_047296897.1  SAM domain-containing protein SAMSN-1 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      12840563..13014732 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324756.1 → XP_054180731.1  SAM domain-containing protein SAMSN-1 isoform X3

    2. XM_054324758.1 → XP_054180733.1  SAM domain-containing protein SAMSN-1 isoform X5

    3. XM_054324755.1 → XP_054180730.1  SAM domain-containing protein SAMSN-1 isoform X2

    4. XM_054324757.1 → XP_054180732.1  SAM domain-containing protein SAMSN-1 isoform X4

    5. XM_054324759.1 → XP_054180734.1  SAM domain-containing protein SAMSN-1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NSI8.1 GenPept UniProtKB/Swiss-Prot:Q9NSI8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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