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

Gene ID: 401474, updated on 11-Apr-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 transmembrane 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, Apr 2022]
Expression
Broad expression in thyroid (RPKM 2.1), brain (RPKM 2.1) and 22 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (118131825..118621963, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (119260296..119750442, complement)
105.20220307 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. 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
  4. 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
  5. Intronic (TTTGA)(n) insertion in SAMD12 also causes familial cortical myoclonic tremor with epilepsy. Cen Z, et al. Mov Disord, 2019 Oct. PMID 31483537

See all (23) 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
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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 variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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
  
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_2023_10

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

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