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C1orf52

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C1orf52
Identifiers
AliasesC1orf52, gm117, chromosome 1 open reading frame 52
External IDsMGI: 1913671; HomoloGene: 11968; GeneCards: C1orf52; OMA:C1orf52 - orthologs
Orthologs
SpeciesHumanMouse
Entrez

148423

66421

Ensembl

ENSG00000162642

ENSMUSG00000036873

UniProt

Q8N6N3

Q9CWU4

RefSeq (mRNA)

NM_198077

NM_025555
NM_001356284

RefSeq (protein)

NP_932343

NP_079831
NP_001343213

Location (UCSC)Chr 1: 85.25 – 85.26 MbChr 3: 145.64 – 145.65 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

Chromosome 1 open reading frame 52 is a protein in humans encoded by the C1orf52 gene. C1orf52 is localized in the nucleus and ubiquitously expressed in human tissues.[5]

Gene

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C1orf52 is located on the minus strand at 1p22.3.[6] The gene is 9,720 base pairs and has 3 exons.[7]

Gene neighborhood

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Human C1orf52 gene neighborhood. B-cell lymphoma 10 (BCL10), B-cell lymphoma antisense 1 (BCL-AS1), dimethylarginine dimethylaminohydrolase 1 (DDAH1), and synapse defective Rho GTPase homolog 2 (SYDE2) genes are located in close proximity to C1orf52 on chromosome 1.

The gene neighborhood of C1orf52 consists of B-cell lymphoma 10 (BCL10), B-cell lymphoma antisense 1 (BCL-AS1), dimethylarginine dimethylaminohydrolase 1 (DDAH1), and synapse defective Rho GTPase homolog 2 (SYDE2).[6] The BCL10 gene encodes the BCL10 scaffolding protein that controls immune and pro-inflammatory pathways by connecting antigen receptor signaling to NF-kB activation in B cells and T cells.[8] DDAH1 regulates intracellular ROS levels and apoptosis sensitivity via a SOD2-dependent pathway.[9] SYDE2 converts Rho-type GTPases into an inactive guanosine diphosphate-bound state.[10]

Transcript

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Including untranslated regions, the mRNA is 3254 nucleotides long.[11]

Transcript variants

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There is a transcript variant that includes an additional exon.[6] This alternate exon in the coding region in variant 2 results in a frameshift and early stop codon. This transcript does not form the C1orf52 protein because the product is significantly truncated and the transcript is a candidate for nonsense-mediated decay.

Exons 1 2 3 4 Protein Length (amino acids)
Transcript Variant 1 306 - 199 2750 182
Transcript Variant 2 306 127 199 2750 none

Protein

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Conceptual translation of Human C1orf52. Splice sites between exons are indicated by blue text, the domain of unknown function (DUF4660) is in grey highlight, and pink text shows disordered regions.

The C1orf52 protein consists of 182 amino acids with a molecular weight of 20 kDa and an isoelectric point of 5 pI.[7] The protein contains a domain of unknown function (DUF4660), also known as pFAM15559, that is 98 amino acids long. The domain of unknown function is flanked by two disordered regions, which make up the majority of the protein.[12] Compared to other proteins, C1orf52 is lysine and histidine deficient as well as glutamine and proline rich.[13]

No protein isoforms of C1orf52 have been reported.[14]

Human C1orf52 predicted tertiary structure labeled based on secondary structure.[15] Alpha helixes are in red and coils are in grey.[16]

Structure

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There is a high amount of disorder in the secondary and tertiary protein structure, with very few predicted alpha helixes or beta sheets.[15][17]

Regulation

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Gene

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C1orf52 is ubiquitously expressed at high levels in human tissues, with higher abundance in bone marrow, brain regions, and immune organs (thymus and thyroid), with lower expression in digestive organs.[6][18]

Protein

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The C1orf52 protein has 21 times the average abundance in humans compared to other proteins.[19] There are 3 phosphorylation sites identified through mass spectrometry.[12] Within the cell, C1orf52 is localized to the nucleus and contains a bipartite nuclear localization signal.[20]

Homology

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Paralogs

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No paralogs of C1orf52 have been identified in the human genome.[14]

Orthologs

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C1orf52 orthologs are in all common classes of vertebrates. Orthologs are also in invertebrates including sponges, marine tunicate, and lanclets. Orthologs were not found in insects, fungi, plants or protists.

Genus and Species Common Name Taxonomic Order Date of Divergence from Humans (MYA) Assession Number Sequence Length Sequence Identity to Humans Sequence Similarity to Humans
Homo Sapiens Human Primate 0 NP_932343.1 182 100% 100%
Mus musculus House Mouse Rodentia 87 NP_079831.1 180 85.2% 89.0%
Ornithorhynchus anatinus Platypus Monotreme 180 XP_028917768.1 191 61.7% 71.0%
Harpia harpyja Harpy Owl Accipitriformes 319 XP_052658103.1 183 64.6% 75.1%
Gallus gallus Chicken Galliformes 319 NP_001264489.2 183 63.0% 71.4%
Taeniopygia guttata Zebra finch Passeriformes 319 XP_030134956.3 183 62.1% 73.2%
Gopherus evgoodei Goode’s thornscrub tortoise Testudines 319 XP_038601107.1 187 64.7% 73.3%
Alligator mississippiensis Alligator Crocodilia 319 XP_014450079.3 187 62.6% 70.5%
Protobothrops mucrosquamatus Pit viper Squamata 319 XP_015668904.1 187 61.5% 69.7%
Microcaecilia unicolor Tiny Cayenne Caecilian Gymnophiona 352 XP_030062820.1 184 62.2% 72.0%
Xenopus laevis African clawed frog Anura 352 NP_001089243.1 171 60.9% 70.8%
Pleurodeles waltl Iberian ribbed newt Urodela 352 KAJ1114225.1 182 57.1% 67.9%
Protopterus annectens West African Lung Fish Ceratodontiformes 408 XP_043941971.1 181 53.5% 70.1%
Polypterus senegalus Gray bichir Polypteriformes 429 XP_039591352 188 54.3% 64.5%
Danio rerio Zebrafish Cypriniformes 429 NP_956836.1 214 45.9% 58.3%
Pristis pectinata Smalltooth Sawfish Rhinopristiformes 462 XP_051869055.1 205 44.9% 58.9%
Lampetra fluviatilis European river lamprey Petromyzontiformes 563 CAL5931002.1 242 26.7% 36.0%
Branchiostoma floridae Flordia Lanclet Amphioxiformes 581 XP_035684389.1 234 24.7% 37.7%
Styela clava Sea squirt Stolidobranchia 596 XP_039271545.1 236 25.4% 39.9%
Geodia barretti Deep Sea Sponge Tetractinellida 758 CAI8039110.1 221 27.1% 38.1%

Evolution

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Mutation rate of C1orf52 in comparison to Cytochrome C and Fibrinogen Alpha. All organisms used for C1orf52 mutation rate are on the table. Organsims shown for Cytochrome C and Fibrinogen Alpha are: Mus musculus, Gallus gallus, Alligator mississippiensis, Xenopus laevis, Danio rerio. Additional organisms shown for Cytochrome C: Pristis pectinata, Lampetra fluviatilis, Branchiostoma floridae, Styela clava.

The C1orf52 gene appears most distantly in sea sponges which diverged from humans approximately 758 million years ago.[21] C1orf52 evolves moderately quickly at a rate of 3.8 times faster than slowly evolving Cytochrome C and 0.61 times the rate of fast evolving Fibrinogen Alpha.[14]

Interacting proteins

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High throughput affinity capture-mass spectrometry supports a physical association between C1orf52 and MAD1L1 (Mitotic Arrest Deficient 1 Like 1), DENN Domain Containing 2D (DENND2D), Differentially expressed in FDCP 6 homolog (DEF6), Insulin gene enhancer protein ISL2 (ISL2), and LIM/homeobox protein 4 (LHX4).[22] [23]

Clinical Significance

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Single nucleotide polymorphisms within the second intron of human C1orf52 have been linked to metabolic syndrome, high density lipoprotein cholesterol levels, response to levetiracetam in genetic generalized epilepsy, multiple sclerosis, body mass index, and protein quantitative trait (liver).[24]

References

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  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000162642 – Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000036873 – Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ "C1orf52 protein expression summary - The Human Protein Atlas". www.proteinatlas.org. Retrieved 2024-09-21.
  6. ^ a b c d "NCBI (National Center for Biotechnology Information) Gene Entry on C1orf52".
  7. ^ a b "C1orf52 Gene - Chromosome 1 Open Reading Frame 52".
  8. ^ Luo, Yichen; Wu, Jing; Zou, Juan; Cao, Yijing; He, Yan; Ling, Hui; Zeng, Tiebing (2019-08-01). "BCL10 in cell survival after DNA damage". Clinica Chimica Acta. 495: 301–308. doi:10.1016/j.cca.2019.04.077. ISSN 0009-8981.
  9. ^ Gao, Qiming; Ni, Pinfei; Wang, Yilin; Huo, Peiyun; Zhang, Xiaojie; Wang, Sihan; Xiao, Fuyao; Li, Yixuan; Feng, Wei; Yuan, Juntao; Zhang, Teng; Li, Qiang; Fan, Boyu; Kan, Yuhao; Li, Zhirui (2024-05-01). "DDAH1 promotes neurogenesis and neural repair in cerebral ischemia". Acta Pharmaceutica Sinica B. 14 (5): 2097–2118. doi:10.1016/j.apsb.2024.02.001. ISSN 2211-3835. PMC 11119513. PMID 38799640.
  10. ^ Kouchi, Zen; Kojima, Masaki (2022-03-12). "Function of SYDE C2-RhoGAP family as signaling hubs for neuronal development deduced by computational analysis". Scientific Reports. 12 (1): 4325. Bibcode:2022NatSR..12.4325K. doi:10.1038/s41598-022-08147-7. ISSN 2045-2322. PMC 8918327. PMID 35279680.
  11. ^ "NCBI (National Center for Biotechnology Information) Nucleotide Entry on C1orf52". 5 April 2024.
  12. ^ a b "UPF0690 protein C1orf52 [Homo sapiens] - Protein - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-12.
  13. ^ "SAPS Sequence Statistics".
  14. ^ a b c "Protein BLAST: search protein databases using a protein query". blast.ncbi.nlm.nih.gov. Retrieved 2024-09-21.
  15. ^ a b "I-TASSER server for protein structure and function prediction". zhanggroup.org. Retrieved 2024-12-04.
  16. ^ "iCn3D: Web-based 3D Structure Viewer". www.ncbi.nlm.nih.gov. Retrieved 2024-12-04.
  17. ^ "AlphaFold Protein Structure Database". www.sbg.bio.ic.ac.uk. Retrieved 2024-12-12.
  18. ^ "Home - GEO - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-12.
  19. ^ "PaxDb: Protein Abundance Database". pax-db.org. Retrieved 2024-12-04.
  20. ^ "MyHits Motif Scan". psort.hgc.jp. Retrieved 2024-12-12.
  21. ^ "TimeTree :: The Timescale of Life". timetree.org. Retrieved 2024-12-03.
  22. ^ Huttlin, Edward L.; Bruckner, Raphael J.; Navarrete-Perea, Jose; Cannon, Joe R.; Baltier, Kurt; Gebreab, Fana; Gygi, Melanie P.; Thornock, Alexandra; Zarraga, Gabriela; Tam, Stanley; Szpyt, John; Gassaway, Brandon M.; Panov, Alexandra; Parzen, Hannah; Fu, Sipei (2021-05-27). "Dual proteome-scale networks reveal cell-specific remodeling of the human interactome". Cell. 184 (11): 3022–3040.e28. doi:10.1016/j.cell.2021.04.011. ISSN 1097-4172. PMC 8165030. PMID 33961781.
  23. ^ Huttlin, Edward L.; Ting, Lily; Bruckner, Raphael J.; Gebreab, Fana; Gygi, Melanie P.; Szpyt, John; Tam, Stanley; Zarraga, Gabriela; Colby, Greg; Baltier, Kurt; Dong, Rui; Guarani, Virginia; Vaites, Laura Pontano; Ordureau, Alban; Rad, Ramin (2015-07-16). "The BioPlex Network: A Systematic Exploration of the Human Interactome". Cell. 162 (2): 425–440. doi:10.1016/j.cell.2015.06.043. ISSN 1097-4172. PMC 4617211. PMID 26186194.
  24. ^ "GWAS Catalog". www.ebi.ac.uk. Retrieved 2024-12-03.
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