Seroatlas · Human Serome Atlas

LSM1

U6 snRNA-associated Sm-like protein LSm1

Also known as: CASM, LSM1_HUMAN, YJL124C

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: O15116
Gene: LSM1
Ensembl: ENSG00000175324
Chromosome: 8
Canonical length: 133 aa
Protein class: Predicted intracellular proteins
Subcellular location: Cytosol,Cytoplasmic bodies

OverviewNCBI Gene

This gene encodes a member of the LSm family of RNA-binding proteins. LSm proteins form stable heteromers that bind specifically to the 3'-terminal oligo(U) tract of U6 snRNA and may play a role in pre-mRNA splicing by mediating U4/U6 snRNP formation. Increased expression of this gene may play a role in cellular transformation and the progression of several malignancies including lung cancer, mesothelioma and breast cancer. Alternatively spliced transcript variants have been observed for this gene, and a pseudogene of this gene is located on the short arm of chromosome 9. [provided by RefSeq, Nov 2011]

Canonical amino-acid sequenceUniProt

133 residues, UniProt reviewed canonical sequence.

>O15116|LSM1
     1  MNYMPGTASL IEDIDKKHLV LLRDGRTLIG FLRSIDQFAN LVLHQTVERI HVGKKYGDIP
    61  RGIFVVRGEN VVLLGEIDLE KESDTPLQQV SIEEILEEQR VEQQTKLEAE KLKVQALKDR
   121  GLSIPRADTL DEY

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against LSM1 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.38
Highest tissue expression: 57 nTPM

Expression across tissuesHPA

Tissue

heart muscle: 57 nTPM
blood vessel: 50 nTPM
kidney: 48 nTPM
midbrain: 42 nTPM
skeletal muscle: 42 nTPM
adrenal gland: 40 nTPM

Single-cell type

esophageal apical cells: 202 nCPM
esophageal suprabasal cells: 189 nCPM
platelets: 185 nCPM
extravillous trophoblasts: 184 nCPM
megakaryocytes: 173 nCPM
oocytes: 138 nCPM

Immune cell

basophil: 162 nTPM
plasmacytoid DC: 111 nTPM
eosinophil: 105 nTPM
T-reg: 82 nTPM
non-classical monocyte: 79 nTPM
total PBMC: 79 nTPM

Brain region

thalamus: 21 nTPM
cerebellum: 20 nTPM
hypothalamus: 20 nTPM
choroid plexus: 19 nTPM
midbrain: 19 nTPM
medulla oblongata: 18 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about LSM1.

Disease | AllUniProt

Conditions LSM1 is implicated in, by any mechanism.

FICUS syndrome (FICUS) MIM:621193

Disease | GeneticClinVar

1 pathogenic / likely-pathogenic of 26 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Global developmental delay
FICUS syndrome

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 1.21
gnomAD pLI: 0.01
gnomAD missense Z: 1
DepMap mean gene effect: -0.03
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 10% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

Sm domain, eukaryotic/archaea-type
LSM domain superfamily
U6 snRNA-associated Sm-like protein Lsm1/8
Sm domain
LSM domain
Sm-like protein Lsm1

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of LSM1 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads LSM1 as an antibody target. Whether an autoantibody or antibody against LSM1 could matter depends on whether native LSM1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

LSM1 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label LSM1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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