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    SAMD9L sterile alpha motif domain containing 9 like [ Homo sapiens (human) ]

    Gene ID: 219285, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SAMD9Lprovided by HGNC
    Official Full Name
    sterile alpha motif domain containing 9 likeprovided by HGNC
    Primary source
    HGNC:HGNC:1349
    See related
    Ensembl:ENSG00000177409 MIM:611170; AllianceGenome:HGNC:1349
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    UEF1; ATXPC; DEL7q; DRIF2; MLSM7; SCA49; C7DELq; C7orf6; M7MLS1
    Summary
    This gene encodes a cytoplasmic protein that acts as a tumor suppressor but also plays a key role in cell proliferation and the innate immune response to viral infection. The encoded protein contains an N-terminal sterile alpha motif domain. Naturally occurring mutations in this gene are associated with myeloid disorders such as juvenile myelomonocytic leukemia, acute myeloid leukemia, and myelodysplastic syndrome. Naturally occurring mutations are also associated with hepatitis-B related hepatocellular carcinoma, normophosphatemic familial tumoral calcinosis, and ataxia-pancytopenia syndrome. [provided by RefSeq, Apr 2017]
    Expression
    Broad expression in spleen (RPKM 19.4), appendix (RPKM 14.5) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SAMD9L in Genome Data Viewer
    Location:
    7q21.2
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (93130056..93148385, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (94372089..94390420, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (92759369..92777698, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 7, pseudogene Neighboring gene CRISPRi-validated cis-regulatory element chr7.3172 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:92651586-92652785 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:92657799-92658383 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:92668331-92668846 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26277 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:92669879-92670393 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr7:92673175-92673906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26278 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:92737283-92738482 Neighboring gene sterile alpha motif domain containing 9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26279 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26280 Neighboring gene HEPACAM family member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26281 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26282 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26283 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:92890341-92890842 Neighboring gene VPS50 subunit of EARP/GARPII complex

    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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    Related articles in PubMed

    1. Gain-of-function SAMD9L mutations cause a syndrome of cytopenia, immunodeficiency, MDS, and neurological symptoms. Tesi B, et al. Blood, 2017 Apr 20. PMID 28202457, Free PMC Article
    2. Identification of SAMD9L as a susceptibility locus for intravenous immunoglobulin resistance in Kawasaki disease by genome-wide association analysis. Kim JJ, et al. Pharmacogenomics J, 2020 Feb. PMID 30971808
    3. A novel germline SAMD9L mutation in a family with ataxia-pancytopenia syndrome and pediatric acute lymphoblastic leukemia. Cheah JJC, et al. Haematologica, 2019 Jul. PMID 30923096, Free PMC Article
    4. Constitutional SAMD9L mutations cause familial myelodysplastic syndrome and transient monosomy 7. Pastor VB, et al. Haematologica, 2018 Mar. PMID 29217778, Free PMC Article
    5. SAMD9L Ataxia-Pancytopenia Syndrome. Adam MP, et al. , 1993. PMID 28570036

    See all (41) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PARP14 correlates with GBM proliferation and poor prognosis by elevating expression of SAMD/SAMD9L.
      Title: PARP14 correlates with GBM proliferation and poor prognosis by elevating expression of SAMD/SAMD9L.
    2. [Pancytopenia in children caused by SAMD9/9L mutation: 5 cases report and literature review].
      Title: [Pancytopenia in children caused by SAMD9/9L mutation: 5 cases report and literature review].
    3. Functional Study of SAMD9L in Familial Gastric Cancer.
      Title: Functional Study of SAMD9L in Familial Gastric Cancer.
    4. Viral host range factors antagonize pathogenic SAMD9 and SAMD9L variants.
      Title: Viral host range factors antagonize pathogenic SAMD9 and SAMD9L variants.
    5. Clonal Elimination of the Pathogenic Allele as Diagnostic Pitfall in SAMD9L-Associated Neuropathy.
      Title: Clonal Elimination of the Pathogenic Allele as Diagnostic Pitfall in SAMD9L-Associated Neuropathy.
    6. Up-regulated SAMD9L modulated by TLR2 and HIF-1alpha as a promising biomarker in tuberculosis.
      Title: Up-regulated SAMD9L modulated by TLR2 and HIF-1α as a promising biomarker in tuberculosis.
    7. SAMD9L autoinflammatory or ataxia pancytopenia disease mutations activate cell-autonomous translational repression.
      Title: SAMD9L autoinflammatory or ataxia pancytopenia disease mutations activate cell-autonomous translational repression.
    8. Pediatric MDS and bone marrow failure-associated germline mutations in SAMD9 and SAMD9L impair multiple pathways in primary hematopoietic cells.
      Title: Pediatric MDS and bone marrow failure-associated germline mutations in SAMD9 and SAMD9L impair multiple pathways in primary hematopoietic cells.
    9. Germline predisposition in myeloid neoplasms: Unique genetic and clinical features of GATA2 deficiency and SAMD9/SAMD9L syndromes.
      Title: Germline predisposition in myeloid neoplasms: Unique genetic and clinical features of GATA2 deficiency and SAMD9/SAMD9L syndromes.
    10. Clinical evolution, genetic landscape and trajectories of clonal hematopoiesis in SAMD9/SAMD9L syndromes.
      Title: Clinical evolution, genetic landscape and trajectories of clonal hematopoiesis in SAMD9/SAMD9L syndromes.
    Submit: New GeneRIF Correction See all GeneRIFs (21)

    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

    Associated conditions

    Description Tests
    Ataxia-pancytopenia syndrome
    MedGen: C1327919 OMIM: 159550 GeneReviews: SAMD9L Ataxia-Pancytopenia Syndrome
    		Compare labs
    Monosomy 7 myelodysplasia and leukemia syndrome 1
    MedGen: C1854978 OMIM: 252270 GeneReviews: Not available
    		Compare labs
    Spinocerebellar ataxia 49
    MedGen: C5676950 OMIM: 619806 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    A systemic sclerosis and systemic lupus erythematosus pan-meta-GWAS reveals new shared susceptibility loci.
    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Potential readthrough

    Included gene: SAMD9

    Homology

    Clone Names

    • FLJ39885, KIAA2005

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in early endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    sterile alpha motif domain-containing protein 9-like
    Names
    SAM domain-containing protein 9-like
    neutrophil migration

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_053186.1 RefSeqGene

      Range
      5017..23346
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001303496.3 → NP_001290425.1  sterile alpha motif domain-containing protein 9-like

      See identical proteins and their annotated locations for NP_001290425.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 5' UTR compared to variant 1. Variants 1-9 encode the same protein.
      Source sequence(s)
      AB095926, AC000119, AY195585, BC127117
      Consensus CDS
      CCDS34681.1
      UniProtKB/Swiss-Prot
      A0JP23, A0JP24, A0PJG8, A4D1G8, D6W5Q6, Q2TV71, Q2TV75, Q2UZV8, Q8IVG5, Q8IWI4, Q8N3L9, Q8N875
      Related
      ENSP00000410062.2, ENST00000446033.2
      Conserved Domains (1) summary
      cd09528
      Location:12 → 76
      SAM_Samd9_Samd9L; SAM domain of Samd9/Samd9L subfamily

    2. NM_001303497.3 → NP_001290426.1  sterile alpha motif domain-containing protein 9-like

      See identical proteins and their annotated locations for NP_001290426.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate splice structure in the 5' UTR compared to variant 1. Variants 1-9 encode the same protein.
      Source sequence(s)
      AB095926, AC000119, AY195584, BC127117
      Consensus CDS
      CCDS34681.1
      UniProtKB/Swiss-Prot
      A0JP23, A0JP24, A0PJG8, A4D1G8, D6W5Q6, Q2TV71, Q2TV75, Q2UZV8, Q8IVG5, Q8IWI4, Q8N3L9, Q8N875
      Related
      ENSP00000408796.1, ENST00000437805.5
      Conserved Domains (1) summary
      cd09528
      Location:12 → 76
      SAM_Samd9_Samd9L; SAM domain of Samd9/Samd9L subfamily

    3. NM_001303498.3 → NP_001290427.1  sterile alpha motif domain-containing protein 9-like

      See identical proteins and their annotated locations for NP_001290427.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate exon and contains an alternate splice structure in the 5' UTR, compared to variant 1. Variants 1-9 encode the same protein.
      Source sequence(s)
      AB095926, AC000119, BC127117, DQ068177
      Consensus CDS
      CCDS34681.1
      UniProtKB/Swiss-Prot
      A0JP23, A0JP24, A0PJG8, A4D1G8, D6W5Q6, Q2TV71, Q2TV75, Q2UZV8, Q8IVG5, Q8IWI4, Q8N3L9, Q8N875
      Related
      ENSP00000391699.2, ENST00000446959.6
      Conserved Domains (1) summary
      cd09528
      Location:12 → 76
      SAM_Samd9_Samd9L; SAM domain of Samd9/Samd9L subfamily

    4. NM_001303500.3 → NP_001290429.1  sterile alpha motif domain-containing protein 9-like

      See identical proteins and their annotated locations for NP_001290429.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an alternate exon and uses an alternate splice site in the 5' UTR, compared to variant 1. Variants 1-9 encode the same protein.
      Source sequence(s)
      AB095926, AC000119, AY195582, BC127117
      Consensus CDS
      CCDS34681.1
      UniProtKB/Swiss-Prot
      A0JP23, A0JP24, A0PJG8, A4D1G8, D6W5Q6, Q2TV71, Q2TV75, Q2UZV8, Q8IVG5, Q8IWI4, Q8N3L9, Q8N875
      Related
      ENSP00000391387.2, ENST00000439952.6
      Conserved Domains (1) summary
      cd09528
      Location:12 → 76
      SAM_Samd9_Samd9L; SAM domain of Samd9/Samd9L subfamily

    5. NM_001350082.2 → NP_001337011.1  sterile alpha motif domain-containing protein 9-like

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) contains an alternate splice structure in the 5' UTR compared to variant 1. Variants 1-9 encode the same protein.
      Source sequence(s)
      AC000119
      Consensus CDS
      CCDS34681.1
      UniProtKB/Swiss-Prot
      A0JP23, A0JP24, A0PJG8, A4D1G8, D6W5Q6, Q2TV71, Q2TV75, Q2UZV8, Q8IVG5, Q8IWI4, Q8N3L9, Q8N875
      Conserved Domains (1) summary
      cd09528
      Location:12 → 76
      SAM_Samd9_Samd9L; SAM domain of Samd9/Samd9L subfamily

    6. NM_001350083.2 → NP_001337012.1  sterile alpha motif domain-containing protein 9-like

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) lacks an alternate exon in the 5' UTR, compared to variant 1. Variants 1-9 encode the same protein.
      Source sequence(s)
      AC000119
      Consensus CDS
      CCDS34681.1
      UniProtKB/Swiss-Prot
      A0JP23, A0JP24, A0PJG8, A4D1G8, D6W5Q6, Q2TV71, Q2TV75, Q2UZV8, Q8IVG5, Q8IWI4, Q8N3L9, Q8N875
      Related
      ENSP00000514494.1, ENST00000699641.1
      Conserved Domains (1) summary
      cd09528
      Location:12 → 76
      SAM_Samd9_Samd9L; SAM domain of Samd9/Samd9L subfamily

    7. NM_001350084.2 → NP_001337013.1  sterile alpha motif domain-containing protein 9-like

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) contains an alternate splice structure in the 5' UTR compared to variant 1. Variants 1-9 encode the same protein.
      Source sequence(s)
      AC000119
      Consensus CDS
      CCDS34681.1
      UniProtKB/Swiss-Prot
      A0JP23, A0JP24, A0PJG8, A4D1G8, D6W5Q6, Q2TV71, Q2TV75, Q2UZV8, Q8IVG5, Q8IWI4, Q8N3L9, Q8N875
      Related
      ENSP00000405760.1, ENST00000411955.5
      Conserved Domains (1) summary
      cd09528
      Location:12 → 76
      SAM_Samd9_Samd9L; SAM domain of Samd9/Samd9L subfamily

    8. NM_001350085.2 → NP_001337014.1  sterile alpha motif domain-containing protein 9-like

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) uses an alternate splice site in the 5' UTR, compared to variant 1. Variants 1-9 encode the same protein.
      Source sequence(s)
      AC000119
      Consensus CDS
      CCDS34681.1
      UniProtKB/Swiss-Prot
      A0JP23, A0JP24, A0PJG8, A4D1G8, D6W5Q6, Q2TV71, Q2TV75, Q2UZV8, Q8IVG5, Q8IWI4, Q8N3L9, Q8N875
      Conserved Domains (1) summary
      cd09528
      Location:12 → 76
      SAM_Samd9_Samd9L; SAM domain of Samd9/Samd9L subfamily

    9. NM_152703.5 → NP_689916.2  sterile alpha motif domain-containing protein 9-like

      See identical proteins and their annotated locations for NP_689916.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1-9 encode the same protein.
      Source sequence(s)
      AB095926, AC000119, AY195586, BC127117
      Consensus CDS
      CCDS34681.1
      UniProtKB/Swiss-Prot
      A0JP23, A0JP24, A0PJG8, A4D1G8, D6W5Q6, Q2TV71, Q2TV75, Q2UZV8, Q8IVG5, Q8IWI4, Q8N3L9, Q8N875
      Related
      ENSP00000326247.4, ENST00000318238.9
      Conserved Domains (1) summary
      cd09528
      Location:12 → 76
      SAM_Samd9_Samd9L; SAM domain of Samd9/Samd9L subfamily

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      93130056..93148385 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      94372089..94390420 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IVG5.2 GenPept UniProtKB/Swiss-Prot:Q8IVG5

    Gene LinkOut

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

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