BRINP2

BMP/retinoic acid inducible neural specific 2

Basic information

Region (hg38): 1:177170958-177282422

Previous symbols: [ "FAM5B" ]

Links

ENSG00000198797 ∙ NCBI:57795 ∙ OMIM:619359 ∙ HGNC:13746 ∙ Uniprot:Q9C0B6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BRINP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BRINP2 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					1	1
missense			41			41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	0	1

Variants in BRINP2

This is a list of pathogenic ClinVar variants found in the BRINP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-177230024-G-A		not specified	Uncertain significance (Sep 30, 2021)
1-177230040-T-G		not specified	Uncertain significance (Aug 08, 2022)
1-177230069-T-A		not specified	Uncertain significance (Aug 17, 2022)
1-177230130-G-A		not specified	Uncertain significance (Sep 27, 2021)
1-177255967-C-G		not specified	Uncertain significance (Nov 23, 2021)
1-177255983-T-G		not specified	Uncertain significance (Jun 29, 2023)
1-177256049-G-T		not specified	Uncertain significance (Feb 23, 2023)
1-177256056-A-G		not specified	Uncertain significance (Mar 18, 2024)
1-177256068-A-G		not specified	Uncertain significance (Feb 13, 2023)
1-177257211-A-G		not specified	Uncertain significance (Oct 30, 2023)
1-177257256-G-C		not specified	Uncertain significance (Mar 28, 2022)
1-177257256-G-T		not specified	Uncertain significance (Feb 05, 2024)
1-177257322-A-G		not specified	Uncertain significance (Jun 23, 2023)
1-177257344-G-A		not specified	Uncertain significance (Jan 05, 2022)
1-177273552-C-T		not specified	Uncertain significance (Jul 25, 2024)
1-177273581-G-T		not specified	Uncertain significance (Oct 30, 2024)
1-177276219-A-C		not specified	Uncertain significance (Mar 02, 2023)
1-177276228-G-A		not specified	Uncertain significance (Oct 25, 2024)
1-177276234-G-A		not specified	Uncertain significance (Jun 29, 2023)
1-177276259-C-T			Benign (Dec 14, 2017)
1-177276306-G-T		not specified	Uncertain significance (Jul 08, 2022)
1-177276398-T-A		not specified	Uncertain significance (Dec 16, 2022)
1-177276417-G-A		not specified	Uncertain significance (Feb 22, 2023)
1-177278574-G-A		not specified	Uncertain significance (Dec 16, 2023)
1-177278625-T-G		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BRINP2	protein_coding	protein_coding	ENST00000361539	7	110926

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000636	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.864	410	462	0.887	0.0000278	5124
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.00000901	0.00000879
Middle Eastern	0.000164	0.000163
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.260
• hipred: Y
• hipred_score: 0.793
• ghis: 0.625

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Brinp2

Gene ontology

• 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