BCDIN3D

BCDIN3 domain containing RNA methyltransferase, the group of 7BS DNA/RNA methyltransferases

Basic information

Region (hg38): 12:49836043-49843106

Links

ENSG00000186666 ∙ NCBI:144233 ∙ OMIM:619601 ∙ HGNC:27050 ∙ Uniprot:Q7Z5W3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BCDIN3D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCDIN3D gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			20	3	1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	3	1

Variants in BCDIN3D

This is a list of pathogenic ClinVar variants found in the BCDIN3D region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-49838417-A-G		not specified	Uncertain significance (Jun 17, 2022)
12-49838477-C-T		not specified	Uncertain significance (Jan 18, 2025)
12-49838506-A-C		not specified	Uncertain significance (Oct 03, 2022)
12-49838519-A-C		not specified	Uncertain significance (Nov 11, 2024)
12-49838555-T-C		not specified	Likely benign (Sep 18, 2024)
12-49838637-C-T		not specified	Uncertain significance (Dec 26, 2024)
12-49838645-C-T		not specified	Uncertain significance (Aug 04, 2021)
12-49838652-A-G		not specified	Uncertain significance (Jul 30, 2024)
12-49838678-T-C		not specified	Likely benign (Jan 26, 2023)
12-49838696-T-C		not specified	Uncertain significance (Oct 29, 2024)
12-49838739-G-A		not specified	Uncertain significance (Sep 30, 2024)
12-49838849-A-G		not specified	Uncertain significance (Aug 28, 2024)
12-49838874-G-A		not specified	Uncertain significance (Oct 25, 2022)
12-49838931-G-A		not specified	Uncertain significance (May 08, 2024)
12-49838936-C-T		not specified	Likely benign (Sep 14, 2022)
12-49838978-A-G		not specified	Uncertain significance (Dec 03, 2024)
12-49839006-C-T		not specified	Uncertain significance (Jun 28, 2023)
12-49839014-T-C		not specified	Uncertain significance (Aug 11, 2024)
12-49842858-G-T		not specified	Uncertain significance (Jan 21, 2025)
12-49842864-C-G		not specified	Uncertain significance (May 17, 2023)
12-49842883-G-C		not specified	Uncertain significance (Nov 07, 2024)
12-49842884-A-C		not specified	Uncertain significance (Aug 30, 2021)
12-49842885-A-C		not specified	Uncertain significance (Mar 14, 2025)
12-49842906-T-C		not specified	Uncertain significance (Feb 28, 2023)
12-49843011-G-C		not specified	Uncertain significance (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCDIN3D	protein_coding	protein_coding	ENST00000333924	2	5340

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000387	0.627	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.226	159	167	0.951	0.00000841	1906
Missense in Polyphen		33	31.638	1.0431		326
Synonymous	0.404	62	66.2	0.937	0.00000321	594
Loss of Function	0.815	8	10.9	0.734	7.22e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000355	0.000355
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000171	0.000167
Middle Eastern	0.000326	0.000326
South Asian	0.0000653	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: O-methyltransferase that specifically dimethylates the 5' monophosphate of pre-miRNAs, acting as a negative regulator of miRNA processing. The 5' monophosphate of pre-miRNAs is recognized by DICER1 and is required for pre-miRNAs processing: methylation at this position reduces the processing of pre-miRNAs by DICER1. Able to mediate methylation of pre-miR-145, as well as other pre- miRNAs. {ECO:0000269|PubMed:23063121}.
• Pathway: Gene expression (Transcription);MicroRNA (miRNA) biogenesis;Gene Silencing by RNA (Consensus)

Intolerance Scores

• loftool: 0.746
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

• pHI: 0.122
• hipred: N
• hipred_score: 0.197
• ghis: 0.505

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.273

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Bcdin3d

Gene ontology

• Biological process: RNA methylation;miRNA metabolic process;negative regulation of pre-miRNA processing
• Cellular component: nucleus;cytoplasm;cytosol
• Molecular function: protein binding;O-methyltransferase activity;RNA methyltransferase activity