Seroatlas · Human Serome Atlas

LSM4

U6 snRNA-associated Sm-like protein LSm4

Also known as: LSM4_HUMAN, YER112W

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

Protein identityUniProt · HPA

UniProt accession: Q9Y4Z0
Gene: LSM4
Ensembl: ENSG00000130520
Chromosome: 19
Canonical length: 139 aa
Protein class: Predicted intracellular proteins
Subcellular location: Vesicles

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. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]

Canonical amino-acid sequenceUniProt

139 residues, UniProt reviewed canonical sequence.

>Q9Y4Z0|LSM4
     1  MLPLSLLKTA QNHPMLVELK NGETYNGHLV SCDNWMNINL REVICTSRDG DKFWRMPECY
    61  IRGSTIKYLR IPDEIIDMVK EEVVAKGRGR GGLQQQKQQK GRGMGGAGRG VFGGRGRGGI
   121  PGTGRGQPEK KPGRQAGKQ

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against LSM4 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): 0.49
Highest tissue expression: 138 nTPM

Expression across tissuesHPA

Tissue

skeletal muscle: 138 nTPM
cerebral cortex: 127 nTPM
choroid plexus: 126 nTPM
adrenal gland: 125 nTPM
testis: 122 nTPM
kidney: 122 nTPM

Single-cell type

late spermatids: 1,065 nCPM
extravillous trophoblasts: 556 nCPM
migrating cytotrophoblasts: 455 nCPM
differentiating spermatogonia: 425 nCPM
esophageal basal cells: 390 nCPM
hofbauer cells: 365 nCPM

Immune cell

plasmacytoid DC: 360 nTPM
total PBMC: 284 nTPM
intermediate monocyte: 259 nTPM
myeloid DC: 253 nTPM
classical monocyte: 224 nTPM
NK-cell: 221 nTPM

Brain region

choroid plexus: 91 nTPM
thalamus: 78 nTPM
pons: 78 nTPM
hypothalamus: 77 nTPM
midbrain: 73 nTPM
cerebral cortex: 71 nTPM

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): 0.99
gnomAD pLI: 0.02
gnomAD missense Z: 1.6
DepMap mean gene effect: -1.79
DepMap dependency class: pan

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 6% 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
Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3
Sm domain
LSM domain
Sm-like protein Lsm4

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of LSM4 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 LSM4 as an antibody target. Whether an autoantibody or antibody against LSM4 could matter depends on whether native LSM4 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

LSM4 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 LSM4 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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