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

Summary

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

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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	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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-75240 (e-PCR)
- UniSTS:5418

RH66389 (e-PCR)
- UniSTS:86318

RH80323 (e-PCR)
- UniSTS:91267

RH102107 (e-PCR)
- UniSTS:96441

SHGC-34189 (e-PCR)
- UniSTS:25067

D11S3316 (e-PCR)
- UniSTS:152558

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)

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