Human Gene LRSAM1 (ENST00000323301.8) Description and Page Index
  Description: Homo sapiens leucine rich repeat and sterile alpha motif containing 1 (LRSAM1), transcript variant 1, mRNA. (from RefSeq NM_138361)
RefSeq Summary (NM_138361): This gene encodes a ring finger protein involved in a variety of functions, including regulation of signaling pathways and cell adhesion, mediation of self-ubiquitylation, and involvement in cargo sorting during receptor endocytosis. Mutations in this gene have been associated with Charcot-Marie-Tooth disease. Multiple transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jan 2012].
Gencode Transcript: ENST00000323301.8
Gencode Gene: ENSG00000148356.13
Transcript (Including UTRs)
   Position: hg38 chr9:127,451,513-127,503,499 Size: 51,987 Total Exon Count: 25 Strand: +
Coding Region
   Position: hg38 chr9:127,454,528-127,502,899 Size: 48,372 Coding Exon Count: 24 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesGeneReviewsMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:127,451,513-127,503,499)mRNA (may differ from genome)Protein (723 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
HGNCHPRDLynxMGIneXtProtOMIM
PubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: LRSM1_HUMAN
DESCRIPTION: RecName: Full=E3 ubiquitin-protein ligase LRSAM1; EC=6.3.2.-; AltName: Full=Leucine-rich repeat and sterile alpha motif-containing protein 1; AltName: Full=Tsg101-associated ligase; Short=hTAL;
FUNCTION: E3 ubiquitin-protein ligase that mediates monoubiquitination of TSG101 at multiple sites, leading to inactivate the ability of TSG101 to sort endocytic (EGF receptors) and exocytic (HIV-1 viral proteins) cargos.
PATHWAY: Protein modification; protein ubiquitination.
SUBUNIT: Interacts with TSG101.
SUBCELLULAR LOCATION: Cytoplasm. Note=Displays a punctuate distribution and localizes to a submembranal ring.
TISSUE SPECIFICITY: Highly expressed in adult spinal cord motoneurons as well as in fetal spinal cord and muscle tissue.
DOMAIN: The coiled coil domains interact with the SB domain of TSG101.
DOMAIN: The PTAP motifs mediate the binding to UEV domains.
DISEASE: Defects in LRSAM1 are a cause of Charcot-Marie-Tooth disease type 2P (CMT2P) [MIM:614436]. CMT2P is an axonal form of Charcot-Marie-Tooth disease, a disorder of the peripheral nervous system, characterized by progressive weakness and atrophy, initially of the peroneal muscles and later of the distal muscles of the arms. Charcot-Marie-Tooth disease is classified in two main groups on the basis of electrophysiologic properties and histopathology: primary peripheral demyelinating neuropathies (designated CMT1 when they are dominantly inherited) and primary peripheral axonal neuropathies (CMT2). Neuropathies of the CMT2 group are characterized by signs of axonal degeneration in the absence of obvious myelin alterations, normal or slightly reduced nerve conduction velocities, and progressive distal muscle weakness and atrophy. Nerve conduction velocities are normal or slightly reduced.
SIMILARITY: Contains 6 LRR (leucine-rich) repeats.
SIMILARITY: Contains 1 RING-type zinc finger.
SIMILARITY: Contains 1 SAM (sterile alpha motif) domain.

-  MalaCards Disease Associations
  MalaCards Gene Search: LRSAM1
Diseases sorted by gene-association score: charcot-marie-tooth disease, axonal, type 2p* (1667), roussy-levy syndrome* (200), charcot-marie-tooth disease* (158), charcot-marie-tooth disease type 2g (13), tooth disease (13), mixed malaria (9), blackwater fever (7), acute kidney tubular necrosis (6), anuria (5), urinary system disease (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 16.41 RPKM in Skin - Not Sun Exposed (Suprapubic)
Total median expression: 438.17 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -231.80604-0.384 Picture PostScript Text
3' UTR -272.50600-0.454 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR016179 - Insulin-like
IPR001611 - Leu-rich_rpt
IPR025875 - Leu-rich_rpt_2_copies
IPR001660 - SAM
IPR013761 - SAM/pointed
IPR011510 - SAM_2
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF12799 - Leucine Rich repeats (2 copies)
PF07647 - SAM domain (Sterile alpha motif)

ModBase Predicted Comparative 3D Structure on Q6UWE0
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004842 ubiquitin-protein transferase activity
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0046872 metal ion binding
GO:0061630 ubiquitin protein ligase activity
GO:0005225 volume-sensitive anion channel activity

Biological Process:
GO:0000209 protein polyubiquitination
GO:0006914 autophagy
GO:0007165 signal transduction
GO:0015031 protein transport
GO:0016567 protein ubiquitination
GO:0030163 protein catabolic process
GO:0045806 negative regulation of endocytosis
GO:0046755 viral budding
GO:0051865 protein autoubiquitination
GO:0070086 ubiquitin-dependent endocytosis
GO:1904417 positive regulation of xenophagy
GO:2000786 positive regulation of autophagosome assembly
GO:0098656 anion transmembrane transport

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0034702 ion channel complex


-  Descriptions from all associated GenBank mRNAs
  LF205654 - JP 2014500723-A/13157: Polycomb-Associated Non-Coding RNAs.
MA441231 - JP 2018138019-A/13157: Polycomb-Associated Non-Coding RNAs.
AK056203 - Homo sapiens cDNA FLJ31641 fis, clone NT2RI2003695, weakly similar to TRICHOHYALIN.
AK226106 - Homo sapiens mRNA for leucine rich repeat and sterile alpha motif containing 1 variant, clone: fk00416.
AY358830 - Homo sapiens clone DNA176814 leucine-rich protein (UNQ6496) mRNA, complete cds.
AK091589 - Homo sapiens cDNA FLJ34270 fis, clone FEBRA2003100.
AX747077 - Sequence 602 from Patent EP1308459.
JD271663 - Sequence 252687 from Patent EP1572962.
JD081854 - Sequence 62878 from Patent EP1572962.
BC009239 - Homo sapiens leucine rich repeat and sterile alpha motif containing 1, mRNA (cDNA clone MGC:2867 IMAGE:2988664), complete cds.
CU679267 - Synthetic construct Homo sapiens gateway clone IMAGE:100020431 5' read LRSAM1 mRNA.
AB384779 - Synthetic construct DNA, clone: pF1KB3300, Homo sapiens LRSAM1 gene for E3 ubiquitin-protein ligase LRSAM1, complete cds, without stop codon, in Flexi system.
KJ899909 - Synthetic construct Homo sapiens clone ccsbBroadEn_09303 LRSAM1 gene, encodes complete protein.
AK056305 - Homo sapiens cDNA FLJ31743 fis, clone NT2RI2007254, weakly similar to Arabidopsis thaliana ZCF61 mRNA.
AK097094 - Homo sapiens cDNA FLJ39775 fis, clone SPLEN2001476.
JD200263 - Sequence 181287 from Patent EP1572962.
JD402097 - Sequence 383121 from Patent EP1572962.
JD217195 - Sequence 198219 from Patent EP1572962.
JD477541 - Sequence 458565 from Patent EP1572962.
JD381739 - Sequence 362763 from Patent EP1572962.
JD368221 - Sequence 349245 from Patent EP1572962.
JD162191 - Sequence 143215 from Patent EP1572962.
JD495921 - Sequence 476945 from Patent EP1572962.
JD190038 - Sequence 171062 from Patent EP1572962.
JD333950 - Sequence 314974 from Patent EP1572962.
JD545933 - Sequence 526957 from Patent EP1572962.
JD175198 - Sequence 156222 from Patent EP1572962.
JD458759 - Sequence 439783 from Patent EP1572962.
AF086398 - Homo sapiens full length insert cDNA clone ZD75D05.
JD130168 - Sequence 111192 from Patent EP1572962.
JD456093 - Sequence 437117 from Patent EP1572962.
JD269091 - Sequence 250115 from Patent EP1572962.
JD188135 - Sequence 169159 from Patent EP1572962.
JD068597 - Sequence 49621 from Patent EP1572962.
JD369812 - Sequence 350836 from Patent EP1572962.
JD271634 - Sequence 252658 from Patent EP1572962.
JD484695 - Sequence 465719 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q6UWE0 (Reactome details) participates in the following event(s):

R-HSA-983157 Interaction of E3 with substrate and E2-Ub complex
R-HSA-983147 Release of E3 from polyubiquitinated substrate
R-HSA-983140 Transfer of Ub from E2 to substrate and release of E2
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-1280218 Adaptive Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: LRSM1_HUMAN, NM_138361, Q5VVV0, Q6UWE0, Q8NB40, Q96GT5, Q96MX5, Q96MZ7, TAL, uc004brc.1, uc004brc.2, uc004brc.3, uc004brc.4, UNQ6496/PRO21356
UCSC ID: uc004brc.4
RefSeq Accession: NM_138361
Protein: Q6UWE0 (aka LRSM1_HUMAN)
CCDS: CCDS6873.1, CCDS55347.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene LRSAM1:
cmt (Charcot-Marie-Tooth Hereditary Neuropathy Overview)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.