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    RNPC3 RNA binding region (RNP1, RRM) containing 3 [ Homo sapiens (human) ]

    Gene ID: 55599, updated on 9-Dec-2024

    Summary

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    Official Symbol
    RNPC3provided by HGNC
    Official Full Name
    RNA binding region (RNP1, RRM) containing 3provided by HGNC
    Primary source
    HGNC:HGNC:18666
    See related
    Ensembl:ENSG00000185946 MIM:618016; AllianceGenome:HGNC:18666
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RNP; CPHD7; IGHD5; RBM40; SNRNP65
    Summary
    Two types of spliceosomes catalyze splicing of pre-mRNAs. The major U2-type spliceosome is found in all eukaryotes and removes U2-type introns, which represent more than 99% of pre-mRNA introns. The minor U12-type spliceosome is found in some eukaryotes and removes U12-type introns, which are rare and have distinct splice consensus signals. The U12-type spliceosome consists of several small nuclear RNAs and associated proteins. This gene encodes a 65K protein that is a component of the U12-type spliceosome. This protein contains two RNA recognition motifs (RRMs), suggesting that it may contact one of the small nuclear RNAs of the minor spliceosome. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in thyroid (RPKM 16.8), endometrium (RPKM 15.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RNPC3 in Genome Data Viewer
    Location:
    1p21.1
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (103525699..103555239)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (103374641..103404182)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (104068321..104097861)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904593 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:103698107-103698264 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1412 Neighboring gene RNPC3 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1128 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1413 Neighboring gene RN7SK pseudogene 285 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:104100112-104100330 Neighboring gene amylase alpha 2B Neighboring gene actin gamma 1 pseudogene 4 Neighboring gene amylase alpha 2A

    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. Cloning and identification of a novel human RNPC3 gene that encodes a protein with two RRM domains and is expressed in the cell nucleus. Zhao E, et al. Biochem Genet, 2003 Oct. PMID 14974681
    2. A Novel RNPC3 Gene Variant Expands the Phenotype in Patients with Congenital Hypopituitarism and Neuropathy. Yavas Abali Z, et al. Horm Res Paediatr, 2024. PMID 37463572
    3. The U11/U12 snRNP 65K protein acts as a molecular bridge, binding the U12 snRNA and U11-59K protein. Benecke H, et al. EMBO J, 2005 Sep 7. PMID 16096647, Free PMC Article
    4. Pathogenic variants in RNPC3 are associated with hypopituitarism and primary ovarian insufficiency. Akin L, et al. Genet Med, 2022 Feb. PMID 34906446, Free PMC Article
    5. Establishing intellectual disability as the key feature of patients with biallelic RNPC3 variants. Yamada M, et al. Am J Med Genet A, 2021 Jun. PMID 33650182

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A Novel RNPC3 Gene Variant Expands the Phenotype in Patients with Congenital Hypopituitarism and Neuropathy.
      Title: A Novel RNPC3 Gene Variant Expands the Phenotype in Patients with Congenital Hypopituitarism and Neuropathy.
    2. Pathogenic variants in RNPC3 are associated with hypopituitarism and primary ovarian insufficiency.
      Title: Pathogenic variants in RNPC3 are associated with hypopituitarism and primary ovarian insufficiency.
    3. Establishing intellectual disability as the key feature of patients with biallelic RNPC3 variants.
      Title: Establishing intellectual disability as the key feature of patients with biallelic RNPC3 variants.
    4. Expanding the phenotype of biallelic RNPC3 variants associated with growth hormone deficiency.
      Title: Expanding the phenotype of biallelic RNPC3 variants associated with growth hormone deficiency.
    5. The authores propose that both the C-RRM folding defect and nonsense-mediated decay (NMD)-mediated decrease in the levels of the U11/U12-65K protein reduce formation of the U12-type intron recognition complex and missplicing of a subset of minor introns leading to pituitary hypoplasia and a subsequent defect in growth hormone secretion.
      Title: Mutations in the U11/U12-65K protein associated with isolated growth hormone deficiency lead to structural destabilization and impaired binding of U12 snRNA.
    6. Study shows that the C-terminal RNA recognition motif of p65 binds to the distal 3' stem-loop of U6atac. By using a binary splice site mutation suppressor assay, results demonstrate that p65 protein-binding apical stem-loop of U12 snRNA can be replaced by this U6atac distal 3' stem-loop.
      Title: U6atac snRNA stem-loop interacts with U12 p65 RNA binding protein and is functionally interchangeable with the U12 apical stem-loop III.
    7. Exome analysis of one proband revealed missense (c.1320C>A, p.P474T) and nonsense (c.1504C>T, p.R502X) mutations in the RNPC3 gene.
      Title: Defective minor spliceosome mRNA processing results in isolated familial growth hormone deficiency.
    8. U11/U12-65K contribute to di-snRNP formation and intron bridging in the minor prespliceosome
      Title: The U11/U12 snRNP 65K protein acts as a molecular bridge, binding the U12 snRNA and U11-59K protein.
    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

    Associated conditions

    Description Tests
    Isolated growth hormone deficiency, type 5
    MedGen: C4748435 OMIM: 618160 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA183, FLJ20008, FLJ25070, DKFZp667O0118

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables U12 snRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables pre-mRNA intronic binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in RNA splicing IC
    Inferred by Curator
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of U12-type spliceosomal complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U12-type spliceosomal complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    RNA-binding region-containing protein 3
    Names
    RNA-binding motif protein 40
    RNA-binding protein 40
    U11/U12 small nuclear ribonucleoprotein 65 kDa protein
    U11/U12 snRNP 65 kDa protein
    U11/U12 snRNP 65K
    U11/U12-65K

    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_017619.4 → NP_060089.1  RNA-binding region-containing protein 3

      See identical proteins and their annotated locations for NP_060089.1

      Status: REVIEWED

      Source sequence(s)
      AC095032, AY099329, BC010697, CN386195
      Consensus CDS
      CCDS781.1
      UniProtKB/Swiss-Prot
      A8K1C9, D3DT74, Q5TZ87, Q96FK7, Q96JI8, Q96LT9, Q9NSU7, Q9NXX2
      Related
      ENSP00000391432.1, ENST00000423855.7
      Conserved Domains (3) summary
      COG0724
      Location:333 → 515
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12238
      Location:28 → 100
      RRM1_RBM40_like; RNA recognition motif 1 (RRM1) found in RNA-binding protein 40 (RBM40) and similar proteins
      cd12239
      Location:419 → 501
      RRM2_RBM40_like; RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      103525699..103555239
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      103374641..103404182
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96LT9.1 GenPept UniProtKB/Swiss-Prot:Q96LT9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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