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.

• not_specified (36 variants)
• not_provided (1 variants)
• Oromandibular-limb_hypogenesis_spectrum (1 variants)

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. These statistics are base on transcript: NM_000181708.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			33	3	1	37
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	33	3	1

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