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

Gene ID: 55599, updated on 16-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (103525699..103555239)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (103374641..103404182)
105.20220307 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. 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
  2. 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
  3. Expanding the phenotype of biallelic RNPC3 variants associated with growth hormone deficiency. Verberne EA, et al. Am J Med Genet A, 2020 Aug. PMID 32462814, Free PMC Article
  4. Mutations in the U11/U12-65K protein associated with isolated growth hormone deficiency lead to structural destabilization and impaired binding of U12 snRNA. Norppa AJ, et al. RNA, 2018 Mar. PMID 29255062, Free PMC Article
  5. 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

See all (32) 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.
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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
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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

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_2023_10

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

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