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C10orf90 chromosome 10 open reading frame 90 [ Homo sapiens (human) ]

Gene ID: 118611, updated on 3-Apr-2024

Summary

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Official Symbol
C10orf90provided by HGNC
Official Full Name
chromosome 10 open reading frame 90provided by HGNC
Primary source
HGNC:HGNC:26563
See related
Ensembl:ENSG00000154493 MIM:617735; AllianceGenome:HGNC:26563
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
FATS; bA422P15.2
Summary
Predicted to enable histone deacetylase binding activity; microtubule binding activity; and ubiquitin protein ligase activity. Predicted to be involved in several processes, including protein stabilization; regulation of cell cycle process; and response to ionizing radiation. Located in several cellular components, including cytoskeleton; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in testis (RPKM 1.4), brain (RPKM 1.2) and 2 other tissues See more
Orthologs
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Genomic context

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Location:
10q26.2
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (126424997..126670693, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (127307175..127553313, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (128113566..128359262, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ADAM metallopeptidase domain 12 Neighboring gene secretion associated Ras related GTPase 1A pseudogene 2 Neighboring gene uncharacterized LOC112267914 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:128113684-128114883 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:128128268-128129467 Neighboring gene long intergenic non-protein coding RNA 601 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:128148161-128149360 Neighboring gene uncharacterized LOC728158 Neighboring gene uncharacterized LOC105378549 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:128209578-128210777 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:128249930-128250686 Neighboring gene uncharacterized LOC124902523 Neighboring gene uncharacterized LOC105378548 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:128361288-128361510 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:128365437-128365977 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:128379081-128379804 Neighboring gene small nucleolar RNA SNORD60 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:128581076-128581576 Neighboring gene uncharacterized LOC105378550

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. [Expression of FATS in non-small cell lung cancer and its relationship with prognosis]. Zhang TM, et al. Zhonghua Zhong Liu Za Zhi, 2019 Nov 23. PMID 31770849
  2. The value of FATS expression in predicting sensitivity to radiotherapy in breast cancer. Zhang J, et al. Oncotarget, 2017 Jun 13. PMID 28402275, Free PMC Article
  3. Expression level of novel tumor suppressor gene FATS is associated with the outcome of node positive breast cancer. Zhang J, et al. Chin Med J (Engl), 2011 Sep. PMID 22040499
  4. A functional genetic variant in fragile-site gene FATS modulates the risk of breast cancer in triparous women. Song F, et al. BMC Cancer, 2015 Jul 30. PMID 26223354, Free PMC Article
  5. FATS regulates polyamine biosynthesis by promoting ODC degradation in an ERβ-dependent manner in non-small-cell lung cancer. Qiu L, et al. Cell Death Dis, 2020 Oct 9. PMID 33037185, Free PMC Article

See all (21) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The expression of FATS protein is associated with the development and is an independent prognostic factor of non-small cell lung cancer patients.
    Title: [Expression of FATS in non-small cell lung cancer and its relationship with prognosis].
  2. FATS status is a biomarker in breast cancer to identify individuals likely to benefit from radiotherapy
    Title: The value of FATS expression in predicting sensitivity to radiotherapy in breast cancer.
  3. Data identified a genetic variant in the FATS gene (905C > T, 262D/N) that is associated with susceptibility to breast cancer in a parity-dependent manner.
    Title: A functional genetic variant in fragile-site gene FATS modulates the risk of breast cancer in triparous women.
  4. FATS is an E2-independent ubiquitin ligase that stabilizes p53 and promotes its activation in response to DNA damage.
    Title: FATS is an E2-independent ubiquitin ligase that stabilizes p53 and promotes its activation in response to DNA damage.
  5. FATS is involved in the carcinogenesis and development of breast cancer and could be a potential biomarker and prognostic factor for breast cancer therapy.
    Title: Expression level of novel tumor suppressor gene FATS is associated with the outcome of node positive breast cancer.
  6. data suggest centrosomal functions for C10orf90 and KIAA1731 and new centriole-related functions for ALMS1
    Title: Centriolar association of ALMS1 and likely centrosomal functions of the ALMS motif-containing proteins C10orf90 and KIAA1731.
Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid.
EBI GWAS Catalog

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ32938

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables microtubule binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ubiquitin protein ligase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in protein polyubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein stabilization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein ubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of centriole replication IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in actin cytoskeleton IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in centriole IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in centrosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in centrosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
(E2-independent) E3 ubiquitin-conjugating enzyme FATS
Names
E2/E3 hybrid ubiquitin-protein ligase FATS
centrosomal protein C10orf90
fragile-site associated tumor suppressor homolog

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.

mRNA and Protein(s)

  1. NM_001004298.4 → NP_001004298.2  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform 2

    See identical proteins and their annotated locations for NP_001004298.2

    Status: VALIDATED

    Source sequence(s)
    AF435960, AK297577, AL705062, BC034828, CA423069, DB076049
    Consensus CDS
    CCDS31310.1
    UniProtKB/Swiss-Prot
    B9EIQ9, Q5JRP6, Q5T023, Q8NCV5, Q8WU75, Q96M02
    UniProtKB/TrEMBL
    A0A0A0MSX2
    Related
    ENSP00000284694.7, ENST00000284694.11
    Conserved Domains (1) summary
    pfam15309
    Location:568 → 697
    ALMS_motif; ALMS motif

  2. NM_001350921.2 → NP_001337850.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform 1

    Status: VALIDATED

    Source sequence(s)
    AL392108, AL583860, AL589787
    Consensus CDS
    CCDS91374.1
    UniProtKB/TrEMBL
    B4DMQ6, S4R3N7
    Related
    ENSP00000474558.3, ENST00000488181.3
    Conserved Domains (1) summary
    pfam15309
    Location:665 → 794
    ALMS_motif; ALMS motif

  3. NM_001350922.2 → NP_001337851.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform 3

    Status: VALIDATED

    Source sequence(s)
    AL392108, AL583860, AL589787
    UniProtKB/TrEMBL
    B4DMQ6
    Conserved Domains (1) summary
    pfam15309
    Location:568 → 697
    ALMS_motif; ALMS motif

  4. NM_001350923.2 → NP_001337852.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform 4

    Status: VALIDATED

    Source sequence(s)
    AL392108, AL583860, AL589787

RNA

  1. NR_146939.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL392108, AL583860, AL589787

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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    126424997..126670693 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047424560.1 → XP_047280516.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

  2. XM_047424556.1 → XP_047280512.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X1

  3. XM_047424559.1 → XP_047280515.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

  4. XM_047424558.1 → XP_047280514.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

  5. XM_047424557.1 → XP_047280513.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

  6. XM_011539217.2 → XP_011537519.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X2

    UniProtKB/TrEMBL
    A0A0A0MSX2
    Conserved Domains (2) summary
    pfam15309
    Location:596 → 723
    ALMS_motif; ALMS motif
    pfam17730
    Location:79 → 590
    Centro_C10orf90; Centrosomal C10orf90

  7. XM_047424561.1 → XP_047280517.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

  8. XM_011539223.3 → XP_011537525.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

    See identical proteins and their annotated locations for XP_011537525.1

    UniProtKB/TrEMBL
    Q5T025
    Related
    ENSP00000349318.3, ENST00000356858.7
    Conserved Domains (2) summary
    pfam15309
    Location:522 → 649
    ALMS_motif; ALMS motif
    pfam17730
    Location:5 → 516
    Centro_C10orf90; Centrosomal C10orf90

  9. XM_047424563.1 → XP_047280519.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X5

  10. XM_047424564.1 → XP_047280520.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X6

  11. XM_047424562.1 → XP_047280518.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    127307175..127553313 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054364698.1 → XP_054220673.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

  2. XM_054364692.1 → XP_054220667.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X1

  3. XM_054364696.1 → XP_054220671.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

  4. XM_054364697.1 → XP_054220672.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

  5. XM_054364695.1 → XP_054220670.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

  6. XM_054364694.1 → XP_054220669.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

  7. XM_054364693.1 → XP_054220668.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X2

  8. XM_054364699.1 → XP_054220674.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

  9. XM_054364700.1 → XP_054220675.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

  10. XM_054364702.1 → XP_054220677.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X5

  11. XM_054364703.1 → XP_054220678.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X6

  12. XM_054364701.1 → XP_054220676.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96M02.2 GenPept UniProtKB/Swiss-Prot:Q96M02

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