Details for: FAM53A

Gene ID: 152877

Gene Type:  Protein-coding  - A gene that serves as a template for producing a messenger RNA (mRNA) molecule, which is then translated into a functional protein.

Symbol: FAM53A

Ensembl ID: ENSG00000174137

Description: family with sequence similarity 53 member A

Selected Context(s): 

Cell Significance Landscape

Contexts:

Associated with

Significant Cells

Cell Significance Index (CSI) scores for the chosen context(s)

  • ependymal cell CL0000065
    CSI 2.93
    rCSI 5.94%
    PRS 98.4

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.
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Other Information

This section provides additional information about the gene, including a description generated by an AI language model and details about associated proteins.

## Summary [FAM53A](/details-gene/152877) is a protein-coding gene located on chromosome 4p16.3. As a member of the poorly characterized Family with sequence similarity 53, its function is not well-established, although available annotations suggest a role in intracellular trafficking. Specifically, functional data implicates [FAM53A](/details-gene/152877) in the process of [Protein import into nucleus](/details-gene/152877) ([GO:0006606](https://www.ebi.ac.uk/QuickGO/term/GO:0006606)) and localizes it to the [Nucleus](/details-gene/152877) ([GO:0005634](https://www.ebi.ac.uk/QuickGO/term/GO:0005634)). **Overall**, expression analysis indicates that the gene's activity is most significant in [ependymal cells](/details-cell/CL0000065), a specialized type of glial cell in the central nervous system. ## Cellular Roles and Expression Landscape The expression profile of [FAM53A](/details-gene/152877) points towards a specialized role within the central nervous system. The gene exhibits its highest cellular significance in [ependymal cells](/details-cell/CL0000065) (CSI: 2.93), which are the epithelial-like cells lining the ventricular system of the brain and the central canal of the spinal cord. These cells are critical for the production, circulation, and homeostasis of cerebrospinal fluid (CSF), and they form a key barrier between the CSF and brain parenchyma. The high significance of [FAM53A](/details-gene/152877) in this specific cell type suggests it may be integral to the unique biological functions of the ependymal layer. The lack of significant expression in other cell types within the available data further implies a highly restricted and specialized function, although a broader analysis is required to fully define its expression landscape. ## Pathways and Molecular Function The annotated molecular function of [FAM53A](/details-gene/152877) is consistent with a role in regulating nuclear activity. Gene Ontology annotations place it within the biological process of [Protein import into nucleus](/details-gene/152877) ([GO:0006606](https://www.ebi.ac.uk/QuickGO/term/GO:0006606)), with the protein product localizing to the [Nucleus](/details-gene/152877) ([GO:0005634](https://www.ebi.ac.uk/QuickGO/term/GO:0005634)). This function is fundamental for controlling gene expression, as the import of transcription factors and other regulatory proteins into the nucleus is a critical control point. In the context of its high expression in [ependymal cells](/details-cell/CL0000065), [FAM53A](/details-gene/152877) may facilitate the transport of specific proteins required to maintain the specialized transcriptional program underlying ependymal cell identity, ciliary function, and CSF secretion. While its existence has been confirmed in large-scale cDNA and genome sequencing projects ([Link](https://doi.org/10.1038/ng1285), [Link](https://doi.org/10.1038/nature03466)), the specific substrates it helps import into the nucleus remain to be identified. ## Research Directions Given the specific expression of [FAM53A](/details-gene/152877) in [ependymal cells](/details-cell/CL0000065) and its putative role in nuclear import, several research avenues emerge to elucidate its physiological importance. **Proposed Hypotheses:** 1. [FAM53A](/details-gene/152877) is essential for the proper development and function of the ependymal cell layer. Its disruption may impair the nuclear import of transcription factors critical for ciliogenesis or the expression of ion channels involved in CSF production, potentially leading to conditions such as hydrocephalus. 2. Considering that ependymal cells can serve as a quiescent neural stem cell population, [FAM53A](/details-gene/152877) might regulate the nuclear trafficking of proteins that control the balance between quiescence and activation in response to brain injury, thereby influencing neuro-reparative processes. **Suggested Experimental Approach:** To test the hypothesis that [FAM53A](/details-gene/152877) is critical for ependymal cell function, a conditional knockout mouse model could be generated. By crossing a floxed-[FAM53A](/details-gene/152877) mouse with a line expressing Cre recombinase under an ependymal-specific promoter (e.g., *Foxj1*-Cre), the gene can be selectively deleted in this cell lineage. The resulting phenotype could be assessed through magnetic resonance imaging (MRI) to detect ventricular enlargement (a sign of hydrocephalus), immunofluorescence to analyze ependymal layer integrity and cilia morphology, and tracer studies to measure CSF flow dynamics. Furthermore, single-cell RNA sequencing of the ventricular zone could reveal the specific downstream transcriptional programs that are dysregulated upon [FAM53A](/details-gene/152877) loss. **Therapeutic Potential:** The therapeutic potential of [FAM53A](/details-gene/152877) is currently speculative and dependent on its as-yet-unknown role in disease. Its intracellular localization makes it a challenging direct target for conventional biologics or small molecules. However, if its dysfunction is linked to neurological disorders like hydrocephalus or brain tumors such as ependymomas, it could serve as a valuable diagnostic or prognostic biomarker. Its highly specific expression pattern suggests that therapeutic strategies aimed at modulating its activity, perhaps through targeted gene therapy or antisense oligonucleotides, could achieve high specificity with minimal off-target effects in other tissues.

Genular Protein ID: 1528804506

Symbol: FA53A_HUMAN

Name: N/A

UniProtKB Accession Codes:

Q6NSI3 Q6ZUL5

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 1 CTD 1 ChiTaRS 1 DMDM 1 DNASU 1 DisGeNET 1 EMBL 2 Ensembl 3 ExpressionAtlas 1 GO 2 GeneCards 1 GeneTree 1 GenomeRNAi 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 InterPro 1 KEGG 1 MANE-Select 1 MassIVE 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PRO 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 1 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 1 RNAct 1 RefSeq 5 STRING 1 SignaLink 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 14702039

Title: Complete sequencing and characterization of 21,243 full-length human cDNAs.

PubMed ID: 14702039

DOI: 10.1038/ng1285

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

PubMed ID: 23186163

Title: Toward a comprehensive characterization of a human cancer cell phosphoproteome.

PubMed ID: 23186163

DOI: 10.1021/pr300630k

Sequence Information:

  • Length: 398
  • Mass: 42585
  • Checksum: 045E6F7C1969CD00
  • Sequence:
    • MVTLITEKLQ SQSLDDLTCK AEAGPLQYSA ETLNKSGRLF PLELNDQSPW KVFSGGPPVR 
SQAATGPDFS FLPGLSAAAH TMGLQWQPQS PRPGAGLGAA STVDPSESTG SSTAPPTKRH 
CRSLSEPEEL VRCRSPWRPG SSKVWTPVSK RRCDSGGSAT RQGSPGAVLP RSAVWSTGPT 
SPATPRPSSA SGGFVDSSEG SAGSGPLWCS AESCLPSTRR RPSLSQERLA GAGTPLPWAS 
SSPTSTPALG GRRGLLRCRS QPCVLSGKRS RRKRRREEDA RWTRPSLDFL KMTQTLKNSK 
SLCSLNYEDD DEDDTPVKTV LSSPCDSRGL PGITMPGCSQ RGLRTSPVHP NLWASRESVT 
SDGSRRSSGD PRDGDSVGEE GVFPRARWEL DLEQIENN

Genular Protein ID: 1703445065

Symbol: C9JYQ7_HUMAN

Name: N/A

UniProtKB Accession Codes:

C9JYQ7

Database IDs:

ARBA 1 Antibodypedia 1 Bgee 1 BioGRID-ORCS 1 CTD 1 ChiTaRS 1 DNASU 1 DisGeNET 1 EMBL 4 Ensembl 2 GeneTree 1 HGNC 1 InterPro 1 NCBI Taxonomy 1 OrthoDB 1 PANTHER 2 PeptideAtlas 1 Pfam 1 Proteomes 2 ProteomicsDB 2 RefSeq 2 SAM 1 UCSC 1 VEuPathDB 1

Citations:

PubMed ID: 11237011

Title: Initial sequencing and analysis of the human genome.

PubMed ID: 11237011

DOI: 10.1038/35057062

PubMed ID: 11181995

Title: The sequence of the human genome.

PubMed ID: 11181995

DOI: 10.1126/science.1058040

PubMed ID: 15496913

Title: Finishing the euchromatic sequence of the human genome.

PubMed ID: 15496913

DOI: 10.1038/nature03001

PubMed ID: 15815621

Title: Generation and annotation of the DNA sequences of human chromosomes 2 and 4.

PubMed ID: 15815621

DOI: 10.1038/nature03466

PubMed ID: 23186163

Title: Toward a comprehensive characterization of a human cancer cell phosphoproteome.

PubMed ID: 23186163

Sequence Information:

  • Length: 360
  • Mass: 38671
  • Checksum: 019974E0CDF0CDEB
  • Sequence:
    • MVTLITEKLQ SQSLDDLTCK AEAGPLQYSA ETLNKSGRLF PLELNDQSPW KVFSGGPPVR 
SQAATGPDFS FLPGLSAAAH TMGLQWQPQS PRPGAGLGAA STVDPSESTG SSTAPPTKRH 
CRSLSEPEEL VRCRSPWRPG SSKVWTPVSK RRCDSGGSAT RQGSPGAVLP RSAVWSTGPT 
SPATPRPSSA SGGFVDSSEG SAGSGPLWCS AESCLPSTRR RPSLSQERLA GAGTPLPWAS 
SSPTSTPALG GRRGLLRCRS QPCVLSGKRS RRKRRREEDA RWTRPSLDFL KMTQPHSCAR 
ECESRVRGLG VSLQHLSGPS SQSRGSTLNE NKTPWFEMEG NLAPEDFKKF KKPLLPQLRR