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LRSAM1 leucine rich repeat and sterile alpha motif containing 1 [ Homo sapiens (human) ]

Gene ID: 90678, updated on 7-Apr-2024

Summary

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Official Symbol
LRSAM1provided by HGNC
Official Full Name
leucine rich repeat and sterile alpha motif containing 1provided by HGNC
Primary source
HGNC:HGNC:25135
See related
Ensembl:ENSG00000148356 MIM:610933; AllianceGenome:HGNC:25135
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
TAL; CMT2P; RIFLE
Summary
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]
Expression
Ubiquitous expression in skin (RPKM 9.6), bone marrow (RPKM 7.7) and 24 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
9q33.3-q34.11
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (127451486..127503501)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (139658436..139710463)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (130213765..130265780)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:130185748-130186690 Neighboring gene zinc finger protein 79 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29040 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:130211857-130212400 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130212943-130213486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29041 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29042 Neighboring gene small nucleolar RNA, H/ACA box 65 Neighboring gene ribosomal protein L12 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130226032-130226532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130226533-130227033 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130251390-130251970 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130251971-130252551 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130256483-130257002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130262849-130263350 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130266531-130267404 Neighboring gene niban apoptosis regulator 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130285667-130286168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130286169-130286668 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130287309-130287861 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130293634-130294194 Neighboring gene uncharacterized LOC105376281 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130314335-130314834 Neighboring gene Sharpr-MPRA regulatory region 14561 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130323322-130324026 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130324732-130325436 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130325437-130326140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:130328804-130329344 Neighboring gene FAM129B intron CAGE-defined low expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20304 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130331508-130332048 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:130332049-130332588 Neighboring gene Sharpr-MPRA regulatory region 10550 Neighboring gene uncharacterized LOC124902276

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. LRSAM1 E3 Ubiquitin Ligase Promotes Choriocarcinoma Progression and Metastasis via p53/p21 Signaling Impediment. Li Q, et al. Biomed Res Int, 2022. PMID 36093406, Free PMC Article
  2. Location matters - Genotype-phenotype correlation in LRSAM1 mutations associated with rare Charcot-Marie-Tooth neuropathy CMT2P. Reilich P, et al. Neuromuscul Disord, 2021 Feb. PMID 33414056
  3. LRSAM1 E3 ubiquitin ligase promotes proteasomal clearance of E6-AP protein. Mishra R, et al. Cell Signal, 2021 Jan. PMID 33207262
  4. Ubiquitin ligase LRSAM1 suppresses neurodegenerative diseases linked aberrant proteins induced cell death. Mishra R, et al. Int J Biochem Cell Biol, 2020 Mar. PMID 31982566
  5. LRSAM1 variants and founder effect in French families with ataxic form of Charcot-Marie-Tooth type 2. Peretti A, et al. Eur J Hum Genet, 2019 Sep. PMID 30996334, Free PMC Article

See all (69) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A novel mutation in the LRSAM1 gene in a family with early onset autosomal dominant Charcot-Marie-Tooth type 2P.
    Title: A novel mutation in the LRSAM1 gene in a family with early onset autosomal dominant Charcot-Marie-Tooth type 2P.
  2. [Novel MFN2, BSCL2 and LRSAM1 variants in a cohort of Chinese patients with Charcot-Marie-Tooth disease].
    Title: [Novel MFN2, BSCL2 and LRSAM1 variants in a cohort of Chinese patients with Charcot-Marie-Tooth disease].
  3. C698R mutation in Lrsam1 gene impairs nerve regeneration in a CMT2P mouse model.
    Title: C698R mutation in Lrsam1 gene impairs nerve regeneration in a CMT2P mouse model.
  4. LRSAM1 E3 ubiquitin ligase promotes proteasomal clearance of E6-AP protein.
    Title: LRSAM1 E3 ubiquitin ligase promotes proteasomal clearance of E6-AP protein.
  5. Location matters - Genotype-phenotype correlation in LRSAM1 mutations associated with rare Charcot-Marie-Tooth neuropathy CMT2P.
    Title: Location matters - Genotype-phenotype correlation in LRSAM1 mutations associated with rare Charcot-Marie-Tooth neuropathy CMT2P.
  6. Ubiquitin ligase LRSAM1 suppresses neurodegenerative diseases linked aberrant proteins induced cell death.
    Title: Ubiquitin ligase LRSAM1 suppresses neurodegenerative diseases linked aberrant proteins induced cell death.
  7. Identification of novel pathogenic copy number variations in Charcot-Marie-Tooth disease.
    Title: Identification of novel pathogenic copy number variations in Charcot-Marie-Tooth disease.
  8. Our results confirm the localization of variants in its catalytic C-terminal RING domain and broaden the phenotypic spectrum of LRSAM1-related neuropathies, including painful and predominantly sensory ataxic forms.
    Title: LRSAM1 variants and founder effect in French families with ataxic form of Charcot-Marie-Tooth type 2.
  9. We report a novel LRSAM1 mutation c.2021-2024del (p.E674VfsX11) in 4 members of a Chinese autosomal dominant Charcot-Marie-Tooth disease type 2 family
    Title: A novel mutation of LRSAM1 in a Chinese family with Charcot-Marie-Tooth disease.
  10. The article systematically represents the molecular functions, nature and detailed characterization of LRSAM1 E3 ubiquitin ligase, which are linked to molecular mechanisms of neurodegeneration. (Review)
    Title: LRSAM1 E3 ubiquitin ligase: molecular neurobiological perspectives linked with brain diseases.
Submit: New GeneRIF Correction See all GeneRIFs (25)

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
Charcot-Marie-Tooth disease axonal type 2P
MedGen: C3280797 OMIM: 614436 GeneReviews: Not available
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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
Pr55(Gag) gag TAL, a Tsg101-associated ligase, binds and ubiquitinates Tsg101; TAL-mediated binding and ubiquitination of Tsg101 cooperatively regulate release of HIV-1 Gag PubMed

Go to the HIV-1, Human Interaction Database

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

Clone Names

  • FLJ31641

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin protein ligase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in autophagy IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of endocytosis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of autophagosome assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of xenophagy IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein autoubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein polyubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in ubiquitin-dependent endocytosis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in viral budding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
E3 ubiquitin-protein ligase LRSAM1
Names
RING finger leucine repeat rich
RING-type E3 ubiquitin transferase LRSAM1
Tsg101-associated ligase
NP_001005373.1
NP_001005374.1
NP_001177652.1
NP_001371071.1
NP_001371072.1
NP_001371073.1
NP_612370.3
XP_047280014.1
XP_047280015.1
XP_054220121.1
XP_054220122.1

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.

Genomic

  1. NG_032008.1 RefSeqGene

    Range
    5001..57016
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_373

mRNA and Protein(s)

  1. NM_001005373.4 → NP_001005373.1  E3 ubiquitin-protein ligase LRSAM1 isoform 1

    See identical proteins and their annotated locations for NP_001005373.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same isoform (1).
    Source sequence(s)
    AL445222
    Consensus CDS
    CCDS6873.1
    UniProtKB/Swiss-Prot
    Q5VVV0, Q6UWE0, Q8NB40, Q96GT5, Q96MX5, Q96MZ7
    UniProtKB/TrEMBL
    A0A6Q8PGF7
    Related
    ENSP00000300417.6, ENST00000300417.11
    Conserved Domains (5) summary
    cd09523
    Location:567 → 631
    SAM_TAL; SAM domain of TAL subfamily
    COG4886
    Location:65 → 181
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:33 → 54
    LRR_RI; leucine-rich repeat [structural motif]
    cd16515
    Location:674 → 713
    RING-HC_LRSAM1; RING finger, HC subclass, found in leucine-rich repeat and sterile alpha motif-containing protein 1 (LRSAM1) and similar proteins
    pfam17380
    Location:257 → 474
    DUF5401; Family of unknown function (DUF5401)

  2. NM_001005374.4 → NP_001005374.1  E3 ubiquitin-protein ligase LRSAM1 isoform 1

    See identical proteins and their annotated locations for NP_001005374.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same isoform (1).
    Source sequence(s)
    AY358830, BC009239
    Consensus CDS
    CCDS6873.1
    UniProtKB/Swiss-Prot
    Q5VVV0, Q6UWE0, Q8NB40, Q96GT5, Q96MX5, Q96MZ7
    UniProtKB/TrEMBL
    A0A6Q8PGF7
    Related
    ENSP00000362419.1, ENST00000373322.1
    Conserved Domains (5) summary
    cd09523
    Location:567 → 631
    SAM_TAL; SAM domain of TAL subfamily
    COG4886
    Location:65 → 181
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:33 → 54
    LRR_RI; leucine-rich repeat [structural motif]
    cd16515
    Location:674 → 713
    RING-HC_LRSAM1; RING finger, HC subclass, found in leucine-rich repeat and sterile alpha motif-containing protein 1 (LRSAM1) and similar proteins
    pfam17380
    Location:257 → 474
    DUF5401; Family of unknown function (DUF5401)

  3. NM_001190723.3 → NP_001177652.1  E3 ubiquitin-protein ligase LRSAM1 isoform 2

    See identical proteins and their annotated locations for NP_001177652.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AK056203, BC009239, DA165729
    Consensus CDS
    CCDS55347.1
    UniProtKB/TrEMBL
    A0A6Q8PFT9
    Related
    ENSP00000362421.4, ENST00000373324.8
    Conserved Domains (8) summary
    cd09523
    Location:540 → 604
    SAM_TAL; SAM domain of TAL subfamily
    smart00454
    Location:544 → 604
    SAM; Sterile alpha motif
    cd00116
    Location:67 → 162
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:33 → 54
    LRR_RI; leucine-rich repeat [structural motif]
    pfam10267
    Location:308 → 416
    Tmemb_cc2; Predicted transmembrane and coiled-coil 2 protein
    pfam12799
    Location:127 → 166
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:127 → 181
    LRR_8; Leucine rich repeat
    pfam13920
    Location:647 → 689
    zf-C3HC4_3; Zinc finger, C3HC4 type (RING finger)

  4. NM_001384142.1 → NP_001371071.1  E3 ubiquitin-protein ligase LRSAM1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL445222
    Consensus CDS
    CCDS6873.1
    UniProtKB/Swiss-Prot
    Q5VVV0, Q6UWE0, Q8NB40, Q96GT5, Q96MX5, Q96MZ7
    UniProtKB/TrEMBL
    A0A6Q8PGF7
    Conserved Domains (5) summary
    cd09523
    Location:567 → 631
    SAM_TAL; SAM domain of TAL subfamily
    COG4886
    Location:65 → 181
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:33 → 54
    LRR_RI; leucine-rich repeat [structural motif]
    cd16515
    Location:674 → 713
    RING-HC_LRSAM1; RING finger, HC subclass, found in leucine-rich repeat and sterile alpha motif-containing protein 1 (LRSAM1) and similar proteins
    pfam17380
    Location:257 → 474
    DUF5401; Family of unknown function (DUF5401)

  5. NM_001384143.1 → NP_001371072.1  E3 ubiquitin-protein ligase LRSAM1 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL445222
    Consensus CDS
    CCDS94485.1
    UniProtKB/TrEMBL
    A0A6Q8PFT9, A0A6Q8PGW1
    Related
    ENSP00000501598.1, ENST00000675572.1
    Conserved Domains (5) summary
    cd09523
    Location:536 → 598
    SAM_TAL; SAM domain of TAL subfamily
    COG4886
    Location:65 → 181
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:33 → 54
    LRR_RI; leucine-rich repeat [structural motif]
    cd16515
    Location:641 → 680
    RING-HC_LRSAM1; RING finger, HC subclass, found in leucine-rich repeat and sterile alpha motif-containing protein 1 (LRSAM1) and similar proteins
    pfam17380
    Location:257 → 474
    DUF5401; Family of unknown function (DUF5401)

  6. NM_001384144.1 → NP_001371073.1  E3 ubiquitin-protein ligase LRSAM1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL445222
    Conserved Domains (4) summary
    PRK12704
    Location:27 → 113
    PRK12704; phosphodiesterase; Provisional
    cd16515
    Location:411 → 450
    RING-HC_LRSAM1; RING finger, HC subclass, found in leucine-rich repeat and sterile alpha motif-containing protein 1 (LRSAM1) and similar proteins
    pfam17380
    Location:3 → 211
    DUF5401; Family of unknown function (DUF5401)
    cl15755
    Location:304 → 368
    SAM_superfamily; SAM (Sterile alpha motif )

  7. NM_138361.5 → NP_612370.3  E3 ubiquitin-protein ligase LRSAM1 isoform 1

    See identical proteins and their annotated locations for NP_612370.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1, 2 and 3 encode the same isoform (1).
    Source sequence(s)
    AI364608, AK091589, BC009239, DA726792
    Consensus CDS
    CCDS6873.1
    UniProtKB/Swiss-Prot
    Q5VVV0, Q6UWE0, Q8NB40, Q96GT5, Q96MX5, Q96MZ7
    UniProtKB/TrEMBL
    A0A6Q8PGF7
    Related
    ENSP00000322937.4, ENST00000323301.8
    Conserved Domains (5) summary
    cd09523
    Location:567 → 631
    SAM_TAL; SAM domain of TAL subfamily
    COG4886
    Location:65 → 181
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:33 → 54
    LRR_RI; leucine-rich repeat [structural motif]
    cd16515
    Location:674 → 713
    RING-HC_LRSAM1; RING finger, HC subclass, found in leucine-rich repeat and sterile alpha motif-containing protein 1 (LRSAM1) and similar proteins
    pfam17380
    Location:257 → 474
    DUF5401; Family of unknown function (DUF5401)

RNA

  1. NR_168891.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL445222
    Related
    ENST00000498513.6

  2. NR_168892.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL445222
    Related
    ENST00000675641.1

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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    127451486..127503501
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047424058.1 → XP_047280014.1  E3 ubiquitin-protein ligase LRSAM1 isoform X1

    UniProtKB/TrEMBL
    A0A6Q8PGW1

  2. XM_047424059.1 → XP_047280015.1  E3 ubiquitin-protein ligase LRSAM1 isoform X2

    Related
    ENST00000676399.1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    139658436..139710463
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054364146.1 → XP_054220121.1  E3 ubiquitin-protein ligase LRSAM1 isoform X1

  2. XM_054364147.1 → XP_054220122.1  E3 ubiquitin-protein ligase LRSAM1 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6UWE0.1 GenPept UniProtKB/Swiss-Prot:Q6UWE0

Gene LinkOut

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

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