BRINP2

protein-coding

BMP/retinoic acid inducible neural specific 2

Gene summary

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]

Previous symbols:

FAM5B

MANE transcript

NM_021165.4

Inheritance

—

ClinVar variants

U:108B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr1:177,170,958-177,282,422

External References & Databases

Ensembl (ENSG00000198797)

Transcript & Mutation Effects

hg38 • Region Span ~111.5 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BRINP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 107

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021165.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			107 clinvar	1 clinvar		108
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	108	1	1	110

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021165.4	RefSeq	NP_066988.1	7	MANE Select
ENST00000361539.5	Ensembl	ENSP00000354481.4	7	MANE Select
ENST00000907914.1	Ensembl	ENSP00000577973.1	7	Standard
ENST00000907914.2	Ensembl	ENSP00000577973.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell cycle arrest
positive regulation of neuron differentiation
negative regulation of mitotic cell cycle
cellular response to retinoic acid

Cellular Component

extracellular region
endoplasmic reticulum
dendrite
neuronal cell body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361539
Coding exons: 7
Length: 110926
Individuals with no LoFs: 125743
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125748
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.864	410	462	0.887	0.0000278	5124
Missense (PolyPhen)		119	174.97	0.68012		1976
Synonymous	0.181	184	187	0.983	0.0000103	1593
Loss of Function	4.74	2	30.0	0.0666	0.00000156	328

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000090	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Inhibits neuronal cell proliferation by negative regulation of the cell cycle transition. {ECO:0000250}.;

Intolerance Scores

RVIS EVS: -1.15
RVIS percentile EVS: 6.27

Essentials

Essential (CRISPR): N
Essential (gene trap): N

Gene Damage Prediction

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