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

Summary

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

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_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
[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].
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.
LRSAM1 E3 ubiquitin ligase promotes proteasomal clearance of E6-AP protein.
Title: LRSAM1 E3 ubiquitin ligase promotes proteasomal clearance of E6-AP protein.
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.
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.
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.
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.
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.
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	not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D9S904 (e-PCR), detects polymorphism
- UniSTS:59140

A008L27 (e-PCR)
- UniSTS:77177

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

EC 2.3.2.27

NP_001005374.1

EC 2.3.2.27

NP_001177652.1

EC 2.3.2.27

NP_001371071.1

EC 2.3.2.27

NP_001371072.1

EC 2.3.2.27

NP_001371073.1

EC 2.3.2.27

NP_612370.3

EC 2.3.2.27

XP_047280014.1

EC 2.3.2.27

XP_047280015.1

EC 2.3.2.27

XP_054220121.1

EC 2.3.2.27

XP_054220122.1

EC 2.3.2.27

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

NG_032008.1 RefSeqGene

Range

5001..57016

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_373

mRNA and Protein(s)

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)
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)
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)
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)
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)
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 )
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

NR_168891.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL445222

Related

ENST00000498513.6
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

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

127451486..127503501

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A6Q8PGW1
XM_047424059.1 → XP_047280015.1 E3 ubiquitin-protein ligase LRSAM1 isoform X2

Related

ENST00000676399.1