DBR1

Chr 3AR

debranching RNA lariats 1

Also known as: XGIP

NCBI Gene: 51163 ENSG00000138231 UniProt: Q9UK59 OMIM: 607024

The protein encoded by this gene is an RNA lariat debranching enzyme that hydrolyzes 2'-5' prime branched phosphodiester bonds. The encoded protein specifically targets the bonds at the branch point of excised lariat intron RNA, converting them to linear molecules that are then degraded. This protein may also be involved in retroviral replication. [provided by RefSeq, Nov 2011]

OMIM Research

OMIM ResearchGenerating clinical summary…

DNmechanismARLOEUF 1.022 OMIM phenotypes

Clinical Summary— DBR1

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

1 unique Pathogenic / Likely Pathogenic· 137 VUS of 259 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.02LOEUF

pLI 0.000

Z-score 1.50

OE 0.67 (0.45–1.02)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.79Z-score

OE missense 0.87 (0.78–0.96)

251 obs / 288.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.67 (0.45–1.02)

0≤0.351.4

Missense OE?0.87 (0.78–0.96)

0≤0.61.4

Synonymous OE?0.96

0≤1.21.6

LoF obs/exp: 16 / 23.9Missense obs/exp: 251 / 288.8Syn Z: 0.31

This gene — mechanism propensity

0.6161th %ile

GOF

0.4184th %ile

LOF

0.3647th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

259 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic1

VUS137

Likely Benign96

Benign16

Conflicting1

Pathogenic

137

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	1	0	0	0	1
Likely Pathogenic	0	0	0	0	0
VUS	8	122	5	2	137
Likely Benign	0	7	29	60	96
Benign	0	4	7	5	16
Conflicting	—				1
Total	9	133	41	67	251

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

19 pathogenic / likely-pathogenic (of 24) ClinVar copy-number / structural variants overlap DBR1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →