BRINP1

protein-coding

BMP/retinoic acid inducible neural specific 1

Gene summary

This gene is located within a chromosomal region that shows loss of heterozygosity in some bladder cancers. It contains a 5' CpG island that may be a frequent target of hypermethylation, and it may undergo hypermethylation-based silencing in some bladder cancers. [provided by RefSeq, Jul 2008]

Previous symbols:

DBCCR1
DBC1

MANE transcript

NM_014618.3

Inheritance

—

ClinVar variants

U:2B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr9:119,153,458-119,369,435

External References & Databases

Ensembl (ENSG00000078725)

Transcript & Mutation Effects

hg38 • Region Span ~216.0 kb

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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 BRINP1 variants in ClinVar

2 Conditions Cataloged

not providedTotal: 5

not specifiedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014618.3. 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 clinvar	2
missense			2 clinvar	2 clinvar	1 clinvar	5
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	2	3	2	7

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014618.3	RefSeq	NP_055433.2	7	MANE Select
ENST00000265922.8	Ensembl	ENSP00000265922.2	7	MANE Select
ENST00000373964.2	Ensembl	ENSP00000363075.1	5	Standard
ENST00000373964.3	Ensembl	ENSP00000363075.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

AndrogenReceptor
TNFalpha

Biological Process

behavioral fear response
cell cycle arrest
short-term memory
cell death
social behavior

Molecular Function

protein binding

Cellular Component

cytoplasm
endoplasmic reticulum
dendrite
neuronal cell body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000265922
Coding exons: 7
Length: 216010
Individuals with no LoFs: 125740
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125748
p: 0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.42	383	470	0.816	0.0000304	5057
Missense (PolyPhen)		117	167.23	0.69965		1747
Synonymous	-0.791	195	181	1.07	0.0000115	1438
Loss of Function	4.61	4	32.3	0.124	0.00000163	346

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Inhibits cell proliferation by negative regulation of the G1/S transition. Mediates cell death which is not of the classical apoptotic type and regulates expression of components of the plasminogen pathway. {ECO:0000269|PubMed:11420708, ECO:0000269|PubMed:14712213, ECO:0000269|PubMed:16369496}.;

Recessive Scores

pRec: 0.136

Intolerance Scores

RVIS EVS: -0.93
RVIS percentile EVS: 9.72

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