BCDIN3D BCDIN3 domain containing RNA methyltransferase [Homo sapiens (human)] - Gene

Summary

Official Symbol: BCDIN3Dprovided by HGNC
Official Full Name: BCDIN3 domain containing RNA methyltransferaseprovided by HGNC
Primary source: HGNC:HGNC:27050
See related: Ensembl:ENSG00000186666 MIM:619601; AllianceGenome:HGNC:27050
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
Summary: This gene encodes an RNA methyltransferase which belongs to the rossmann fold methyltransferase family, and serves as a 5'-methylphosphate capping enzyme that is specific for cytoplasmic histidyl tRNA. The encoded protein contains an S-adenosylmethionine binding domain and uses the methyl group donor, S-adenosylmethionine. This gene is overexpressed in breast cancer cells, and is related to the tumorigenic phenotype and poor prognosis of breast cancer. The encoded protein is thought to promote the cellular invasion of breast cancer cells, by downregulating the expression of tumor suppressor miRNAs through the dimethylation of the 5-monophosphate of the corresponding precursor miRNAs. [provided by RefSeq, Apr 2017]
Expression: Ubiquitous expression in prostate (RPKM 3.3), lymph node (RPKM 3.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12q13.12

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (49836043..49843106, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (49799057..49806118, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (50229826..50236889, complement)

Chromosome 12 - NC_000012.12 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 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?

MiR-195-3p inhibits cell proliferation in cervical cancer by targeting BCDIN3D.
Title: MiR-195-3p inhibits cell proliferation in cervical cancer by targeting BCDIN3D.
BCDIN3D RNA methyltransferase stimulates Aldolase C expression and glycolysis through let-7 microRNA in breast cancer cells.
Title: BCDIN3D RNA methyltransferase stimulates Aldolase C expression and glycolysis through let-7 microRNA in breast cancer cells.
CDIN3D is a tRNAHis-specific 5'-monomethylphosphate capping enzyme that discriminates tRNAHis from other tRNA species, and the structural information presented in this study also provides the molecular basis for the development of drugs against breast cancers.
Title: Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.
Results indicate that tRNAHis interaction with BCDIN3D plays non-canonical roles, one of which is to regulate the generation of tRNAHis 3' fragments.
Title: BCDIN3D regulates tRNAHis 3' fragment processing.
BCDIN3D might serve as an important prognostic factor for triple-negative breast cancer
Title: Elevated expression of RNA methyltransferase BCDIN3D predicts poor prognosis in breast cancer.
BCDIN3D acts as a cytoplasmic tRNAHis-specific 5-methylphosphate capping enzyme.
Title: Human BCDIN3D monomethylates cytoplasmic histidine transfer RNA.
Human BCDIN3D monomethylates the 5'-monophosphate of cytoplasmic tRNAHis in vitro. In BCDN3D-knockout cells, established byCRISPR/Cas9 editing, the methyl moiety at the 5'-monophosphate of cytoplasmic tRNAHis is lost, and the exogenous expression of BCDIN3D in the knockout cells restores the modification in cytoplasmic tRNAHis.
Title: Human BCDIN3D monomethylates cytoplasmic histidine transfer RNA.
BCDIN3D depletion leads to lower pre-miR-145 and concomitantly increased mature miR-145 levels in breast cancer cells, which suppresses their tumorigenic phenotypes.
Title: Human RNA methyltransferase BCDIN3D regulates microRNA processing.
Observational study of gene-disease association. (HuGE Navigator)
Title: Analyses of shared genetic factors between asthma and obesity in children.
Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
Title: Implication of genetic variants near NEGR1, SEC16B, TMEM18, ETV5/DGKG, GNPDA2, LIN7C/BDNF, MTCH2, BCDIN3D/FAIM2, SH2B1, FTO, MC4R, and KCTD15 with obesity and type 2 diabetes in 7705 Chinese.

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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

EBI GWAS Catalog

Description
Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. EBI GWAS Catalog EBI GWAS CatalogPubMed
NRXN3 is a novel locus for waist circumference: a genome-wide association study from the CHARGE Consortium. EBI GWAS Catalog EBI GWAS CatalogPubMed
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

PMC156606P1 (e-PCR)
- UniSTS:271408

PMC156606P2 (e-PCR)
- UniSTS:271409

PMC156606P3 (e-PCR)
- UniSTS:271410

D8S2278 (e-PCR)
- UniSTS:473906

PMC156606P4 (e-PCR)
- UniSTS:271411

D8S2279 (e-PCR)
- UniSTS:473907

sY3084 (e-PCR)
- UniSTS:515126

L18426 (e-PCR)
- UniSTS:34648

SHGC-17415 (e-PCR)
- UniSTS:25459

RH79782 (e-PCR)
- UniSTS:88215

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables O-methyltransferase activity	EXP Inferred from Experiment more info	PubMed
enables O-methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables pre-miRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables small RNA 2'-O-methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables tRNA methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA methylation	IDA Inferred from Direct Assay more info	PubMed
involved_in miRNA metabolic process	TAS Traceable Author Statement more info
involved_in negative regulation of pre-miRNA processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of pre-miRNA processing	IDA Inferred from Direct Assay more info	PubMed
involved_in pre-miRNA processing	IDA Inferred from Direct Assay more info	PubMed
involved_in tRNA methylation	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: RNA 5'-monophosphate methyltransferase

Names: BCDIN3 domain containing RNA methyltransfease; BCDIN3 domain-containing protein; pre-miRNA 5'-monophosphate methyltransferase; probable methyltransferase BCDIN3D

NP_859059.1

EC 2.1.1.-

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.