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    SAMD12 sterile alpha motif domain containing 12 [ Homo sapiens (human) ]

    Gene ID: 401474, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SAMD12provided by HGNC
    Official Full Name
    sterile alpha motif domain containing 12provided by HGNC
    Primary source
    HGNC:HGNC:31750
    See related
    Ensembl:ENSG00000177570 MIM:618073; AllianceGenome:HGNC:31750
    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
    FAME; MEBA; BAFME; FAME1; BAFME1; FCMTE1
    Summary
    Predicted to be involved in cell surface receptor protein tyrosine kinase signaling pathway. Predicted to be active in cytoplasmic side of plasma membrane. Implicated in familial adult myoclonic epilepsy 1. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in thyroid (RPKM 2.1), brain (RPKM 2.1) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SAMD12 in Genome Data Viewer
    Location:
    8q24.11-q24.12
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (118131825..118621963, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (119260296..119750442, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (119144064..119634202, complement)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986970 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:118824531-118825096 Neighboring gene Sharpr-MPRA regulatory region 14285 Neighboring gene EXT1 intron enhancer-blocking element 8-1-1 Neighboring gene exostosin glycosyltransferase 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:118943047-118943604 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr8:118946090-118946796 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr8:118946797-118947502 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:118969244-118969744 Neighboring gene Sharpr-MPRA regulatory region 8624 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19476 Neighboring gene small nucleolar RNA, C/D box 168 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19477 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27835 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:119030582-119031781 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:119061597-119062098 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:119062099-119062598 Neighboring gene Sharpr-MPRA regulatory region 9283 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:119086733-119087246 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:119087943-119088443 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:119087442-119087942 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27836 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr8:119115463-119116215 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19478 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19479 Neighboring gene Sharpr-MPRA regulatory region 7200 Neighboring gene uncharacterized LOC105375724 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:119451504-119452703 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19480 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:119547949-119548448 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27838 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27839 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27840 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19481 Neighboring gene SAMD12 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:119706863-119707363 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:119750142-119750655 Neighboring gene uncharacterized LOC124902007 Neighboring gene ribosomal protein S26 pseudogene 35

    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
    • 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. Clinical and genomic analysis of a large Chinese family with familial cortical myoclonic tremor with epilepsy and SAMD12 intronic repeat expansion. Zhou Y, et al. Epilepsia Open, 2021 Mar. PMID 33681653, Free PMC Article
    2. Founder effect of the TTTCA repeat insertions in SAMD12 causing BAFME1. Yeetong P, et al. Eur J Hum Genet, 2021 Feb. PMID 32973343, Free PMC Article
    3. Localization of a gene for benign adult familial myoclonic epilepsy to chromosome 8q23.3-q24.1. Mikami M, et al. Am J Hum Genet, 1999 Sep. PMID 10441581, Free PMC Article
    4. Familial adult myoclonic epilepsy type 1 SAMD12 TTTCA repeat expansion arose 17,000 years ago and is present in Sri Lankan and Indian families. Bennett MF, et al. Eur J Hum Genet, 2020 Jul. PMID 32203200, Free PMC Article
    5. LncRNA SAMD12-AS1 down-regulates P53 to promote malignant progression of glioma. Yu BX, et al. Eur Rev Med Pharmacol Sci, 2019 Oct. PMID 31646576

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Liver fibrosis-derived exosomal miR-106a-5p facilitates the malignancy by targeting SAMD12 and CADM2 in hepatocellular carcinoma.
      Title: Liver fibrosis-derived exosomal miR-106a-5p facilitates the malignancy by targeting SAMD12 and CADM2 in hepatocellular carcinoma.
    2. Founder effect of the TTTCA repeat insertions in SAMD12 causing BAFME1.
      Title: Founder effect of the TTTCA repeat insertions in SAMD12 causing BAFME1.
    3. Clinical and genomic analysis of a large Chinese family with familial cortical myoclonic tremor with epilepsy and SAMD12 intronic repeat expansion.
      Title: Clinical and genomic analysis of a large Chinese family with familial cortical myoclonic tremor with epilepsy and SAMD12 intronic repeat expansion.
    4. DNA analysis of benign adult familial myoclonic epilepsy reveals associations between the pathogenic TTTCA repeat insertion in SAMD12 and the nonpathogenic TTTTA repeat expansion in TNRC6A.
      Title: DNA analysis of benign adult familial myoclonic epilepsy reveals associations between the pathogenic TTTCA repeat insertion in SAMD12 and the nonpathogenic TTTTA repeat expansion in TNRC6A.
    5. Familial adult myoclonic epilepsy type 1 SAMD12 TTTCA repeat expansion arose 17,000 years ago and is present in Sri Lankan and Indian families.
      Title: Familial adult myoclonic epilepsy type 1 SAMD12 TTTCA repeat expansion arose 17,000 years ago and is present in Sri Lankan and Indian families.
    6. LncRNA SAMD12-AS1 down-regulates P53 to promote malignant progression of glioma.
      Title: LncRNA SAMD12-AS1 down-regulates P53 to promote malignant progression of glioma.
    7. LncRNA SAMD12-AS1 promotes cell proliferation and inhibits apoptosis by interacting with NPM1.
      Title: LncRNA SAMD12-AS1 promotes cell proliferation and inhibits apoptosis by interacting with NPM1.
    8. identified a novel expanded intronic (TTTGA)n insertion at the same site as the previously reported (TTTCA)n insertion in SAMD12
      Title: Intronic (TTTGA)(n) insertion in SAMD12 also causes familial cortical myoclonic tremor with epilepsy.
    9. We identified the pentanucleotide repeat expansion in SAMD12 as the causative mutation in Chinese FCMTE pedigrees.
      Title: Long-read sequencing identified intronic repeat expansions in SAMD12 from Chinese pedigrees affected with familial cortical myoclonic tremor with epilepsy.
    10. Abnormal expansions of TTTCA and TTTTA repeats in intron 4 of SAMD12 cause benign adult familial myoclonic epilepsy. Single-molecule, real-time sequencing of BAC clones and nanopore sequencing of genomic DNA identified two repeat configurations in SAMD12.
      Title: Expansions of intronic TTTCA and TTTTA repeats in benign adult familial myoclonic epilepsy.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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
    Epilepsy, familial adult myoclonic, 1
    MedGen: C1832841 OMIM: 601068 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide association study of brain lesion distribution in multiple sclerosis.
    EBI GWAS Catalog

    Variation

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    See Variation Viewer (GRCh37.p13)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat downregulates the expression of sterile alpha motif domain containing 12 (SAMD12) in human primary T cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ39458, MGC148139, MGC148140

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in cell surface receptor protein tyrosine kinase signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  
    is_active_in cytoplasmic side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    sterile alpha motif domain-containing protein 12
    Names
    SAM domain-containing protein 12
    benign adult familial myoclonic epilepsy 1
    familial adult myoclonic epilepsy 1
    familial cortical myoclonic tremor with epilepsy 1
    myoclonic epilepsy, benign adult familial

    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_001101676.2 → NP_001095146.1  sterile alpha motif domain-containing protein 12 isoform a

      See identical proteins and their annotated locations for NP_001095146.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) contains an alternate 3' terminal exon, resulting in a novel 3' coding region and 3' UTR. It encodes isoform a, which is shorter and has a distinct C-terminus, compared to isoform b.
      Source sequence(s)
      AP003468, AP003476, BF326714, CB241290, DA459013, DB228621, DB232393
      Consensus CDS
      CCDS47913.1
      UniProtKB/TrEMBL
      H0YEJ0
      Related
      ENSP00000435927.2, ENST00000524796.6
      Conserved Domains (1) summary
      cd09510
      Location:72 → 146
      SAM_aveugle-like; SAM domain of aveugle-like subfamily

    2. NM_001349811.2 → NP_001336740.1  sterile alpha motif domain-containing protein 12 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate in-frame splice site in the central coding region and contains an alternate 3' terminal exon, resulting in a novel 3' coding region and 3' UTR, compared to variant 2. It encodes isoform c, which is shorter and has a distinct C-terminus, compared to isoform b.
      Source sequence(s)
      AP003468, AP003476, BF326714, CB241290, DA459013, DB228621, DB232393
      Consensus CDS
      CCDS94334.1
      UniProtKB/TrEMBL
      B8ZZB7
      Related
      ENSP00000387133.5, ENST00000409003.5
      Conserved Domains (1) summary
      cl15755
      Location:72 → 136
      SAM_superfamily; SAM (Sterile alpha motif )

    3. NM_001363274.2 → NP_001350203.1  sterile alpha motif domain-containing protein 12 isoform d

      Status: VALIDATED

      Source sequence(s)
      AC023590, AP003468, DA459013, DB232393
      Conserved Domains (1) summary
      cd09510
      Location:72 → 146
      SAM_aveugle-like; SAM domain of aveugle-like subfamily

    4. NM_207506.3 → NP_997389.2  sterile alpha motif domain-containing protein 12 isoform b

      See identical proteins and their annotated locations for NP_997389.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) encodes the longest isoform (b).
      Source sequence(s)
      AC023590, AK096777, AP003468, BC121818, DA335826
      Consensus CDS
      CCDS6325.1
      UniProtKB/Swiss-Prot
      Q0P502, Q8N8I0
      Related
      ENSP00000314173.4, ENST00000314727.9
      Conserved Domains (1) summary
      cd09510
      Location:72 → 146
      SAM_aveugle-like; SAM domain of aveugle-like subfamily

    RNA

    1. NR_109794.3 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains an alternate 5' terminal exon compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AC023590, AP003468, AP003476, AP003496

    2. NR_146234.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) contains an alternate 3' exon structure compared to variant 2. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AP003468, AP003476, BU687559, DA459013, DB232393

    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_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      118131825..118621963 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047421779.1 → XP_047277735.1  sterile alpha motif domain-containing protein 12 isoform X2

    2. XM_047421780.1 → XP_047277736.1  sterile alpha motif domain-containing protein 12 isoform X3

      Related
      ENST00000649198.1

    3. XM_047421781.1 → XP_047277737.1  sterile alpha motif domain-containing protein 12 isoform X4

    4. XM_047421778.1 → XP_047277734.1  sterile alpha motif domain-containing protein 12 isoform X1

    RNA

    1. XR_007060733.1 RNA Sequence

    2. XR_007060732.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      119260296..119750442 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054360473.1 → XP_054216448.1  sterile alpha motif domain-containing protein 12 isoform X3

    2. XM_054360474.1 → XP_054216449.1  sterile alpha motif domain-containing protein 12 isoform X4

    3. XM_054360472.1 → XP_054216447.1  sterile alpha motif domain-containing protein 12 isoform X1

    RNA

    1. XR_008487848.1 RNA Sequence

    2. XR_008487847.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N8I0.2 GenPept UniProtKB/Swiss-Prot:Q8N8I0

    Gene LinkOut

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

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