DBR1

debranching RNA lariats 1

Basic information

Region (hg38): 3:138160987-138174949

Links

ENSG00000138231 ∙ NCBI:51163 ∙ OMIM:607024 ∙ HGNC:15594 ∙ Uniprot:Q9UK59 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• encephalitis, acute, infection (viral)-induced, susceptibility to, 11 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Encephalitis, acute, infection (viral)-induced, susceptibility to, 11; Xerosis and growth failure with immune and pulmonary dysfunction syndrome	AR	Allergy/Immunology/Infectious; Cardiovascular; Endocrine	Encephalitis, acute, infection (viral)-induced, susceptibility to, can include early-onset susceptibility to viral infections, and awareness may allow preventative measures and early and aggressive management of infections; Xerosis and growth failure with immune and pulmonary dysfunction syndrome can involve immune dysfunction with increased susceptibility to infection, congenital cardiovascular anomalies, and endocrine dysfunction, and awareness may allow medical and possible surgical management	Allergy/Immunology/Infectious; Cardiovascular; Dermatologic; Endocrine; Hematologic; Neurologic	29474921; 37656279

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DBR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DBR1 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			2	35	5	42
missense			76	5	4	85
nonsense			3			3
start loss						0
frameshift			3			3
inframe indel			1	1		2
splice donor/acceptor (+/-2bp)			1			1
splice region			3	3	1	7
non coding			1	18	4	23
Total	0	0	87	59	13

Variants in DBR1

This is a list of pathogenic ClinVar variants found in the DBR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-138161853-A-G		not specified	Benign (Jan 24, 2024)
3-138161893-G-C			Uncertain significance (Aug 15, 2022)
3-138161896-G-GCAT			Likely benign (Jan 02, 2024)
3-138161898-ATCG-A			Uncertain significance (Jul 21, 2022)
3-138161901-G-A		not specified	Benign (Feb 01, 2024)
3-138161925-G-A			Likely benign (Nov 20, 2023)
3-138161943-C-A		Inborn genetic diseases	Uncertain significance (May 30, 2023)
3-138161972-C-T			Uncertain significance (Mar 12, 2022)
3-138161975-G-A			Uncertain significance (Oct 03, 2023)
3-138161987-G-C			Likely benign (Jan 13, 2024)
3-138162011-A-T			Uncertain significance (Jul 01, 2022)
3-138162012-G-A			Likely benign (Jan 03, 2024)
3-138162020-C-T		Inborn genetic diseases	Uncertain significance (May 16, 2024)
3-138162030-C-T			Benign (Jan 25, 2024)
3-138162038-T-C		Inborn genetic diseases	Likely benign (Nov 17, 2022)
3-138162043-C-G		Inborn genetic diseases	Uncertain significance (May 11, 2022)
3-138162054-C-T			Likely benign (Nov 20, 2023)
3-138162078-C-T			Likely benign (Nov 15, 2023)
3-138162079-G-A			Uncertain significance (Apr 02, 2022)
3-138162095-C-T		Inborn genetic diseases	Uncertain significance (Jun 09, 2022)
3-138162100-A-G		Inborn genetic diseases	Uncertain significance (Jun 13, 2023)
3-138162107-C-T			Uncertain significance (Apr 16, 2022)
3-138162123-A-G			Likely benign (Oct 14, 2023)
3-138162151-G-T		Inborn genetic diseases	Uncertain significance (Nov 24, 2023)
3-138162157-T-C			Uncertain significance (Jul 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DBR1	protein_coding	protein_coding	ENST00000260803	8	13938

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.18e-8	0.793	125704	0	43	125747	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.791	251	289	0.869	0.0000135	3617
Missense in Polyphen		59	84.789	0.69584		1068
Synonymous	0.312	103	107	0.962	0.00000532	996
Loss of Function	1.50	16	23.9	0.669	0.00000126	300

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000632	0.000631
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.000163	0.000163
South Asian	0.000164	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cleaves the 2'-5' phosphodiester linkage at the branch point of lariat intron pre-mRNAs after splicing and converts them into linear molecules that are subsequently degraded. It thereby facilitates ribonucleotide turnover. It may also participate in retrovirus replication via an RNA lariat intermediate in cDNA synthesis. {ECO:0000269|PubMed:10982890, ECO:0000269|PubMed:16232320}.

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.633
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.51

Haploinsufficiency Scores

• pHI: 0.265
• hipred: N
• hipred_score: 0.394
• ghis: 0.632

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.356

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dbr1
• Phenotype: immune system phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: RNA splicing, via transesterification reactions;mRNA splicing, via spliceosome;RNA phosphodiester bond hydrolysis, endonucleolytic
• Cellular component: nucleus;nucleoplasm
• Molecular function: RNA binding;RNA lariat debranching enzyme activity;metal ion binding