BRINP2

Chr 1

BMP/retinoic acid inducible neural specific 2

Also known as: DBCCR1L2, FAM5B

NCBI Gene: 57795 ENSG00000198797 UniProt: Q9C0B6 OMIM: 619359

Predicted to be involved in cellular response to retinoic acid; central nervous system neuron differentiation; and negative regulation of mitotic cell cycle. Predicted to act upstream of or within locomotion and nervous system development. Predicted to be located in extracellular region. Predicted to be active in cytoplasm; dendrite; and neuronal cell body. Implicated in oral squamous cell carcinoma. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.21

Clinical Summary— BRINP2

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.

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ClinVar Variants

105 VUS of 107 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.21LOEUF

pLI 0.999

Z-score 4.74

OE 0.07 (0.03–0.21)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

0.86Z-score

OE missense 0.89 (0.82–0.96)

410 obs / 462.3 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.07 (0.03–0.21)

0≤0.351.4

Missense OE?0.89 (0.82–0.96)

0≤0.61.4

Synonymous OE?0.98

0≤1.21.6

LoF obs/exp: 2 / 30.0Missense obs/exp: 410 / 462.3Syn Z: 0.18

This gene — mechanism propensity

0.3495th %ile

GOF

0.4184th %ile

LOF

0.67top 25%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.21

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

107 submitted variants in ClinVar

ClinVar

Classification Summary

VUS105

Likely Benign1

Benign1

105

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	105	0	105
Likely Benign	1	0	1
Benign	0	1	1
Total	106	1	107

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

View in ClinVar →

22 pathogenic / likely-pathogenic (of 27) ClinVar copy-number / structural variants overlap BRINP2 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →