BRINP3

BMP/retinoic acid inducible neural specific 3

Basic information

Region (hg38): 1:190097657-190478404

Previous symbols: [ "FAM5C" ]

Links

ENSG00000162670 ∙ NCBI:339479 ∙ OMIM:618390 ∙ HGNC:22393 ∙ Uniprot:Q76B58 ∙ 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 BRINP3 gene.

• Inborn genetic diseases (26 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BRINP3 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						0
missense			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	0

Variants in BRINP3

This is a list of pathogenic ClinVar variants found in the BRINP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-190098058-G-T		not specified	Uncertain significance (Nov 12, 2021)
1-190098181-A-C		not specified	Uncertain significance (Sep 20, 2023)
1-190098281-T-C		not specified	Uncertain significance (Feb 12, 2024)
1-190098290-G-A		not specified	Uncertain significance (Aug 12, 2022)
1-190098328-T-C		not specified	Uncertain significance (Oct 22, 2021)
1-190098412-T-C		not specified	Likely benign (Dec 21, 2022)
1-190098421-A-T		not specified	Uncertain significance (Apr 07, 2022)
1-190098505-A-G		not specified	Uncertain significance (Feb 22, 2023)
1-190098689-A-C		not specified	Uncertain significance (Jun 22, 2023)
1-190098904-C-T		not specified	Uncertain significance (Dec 09, 2023)
1-190098929-T-G		not specified	Uncertain significance (Apr 27, 2023)
1-190099034-G-C		not specified	Uncertain significance (Feb 10, 2022)
1-190099049-G-T		not specified	Uncertain significance (Jan 24, 2023)
1-190099134-T-G		not specified	Uncertain significance (May 17, 2023)
1-190160677-G-T		not specified	Uncertain significance (May 26, 2023)
1-190160690-G-T		not specified	Uncertain significance (Aug 21, 2023)
1-190160722-A-T		not specified	Uncertain significance (Sep 29, 2023)
1-190160770-C-T		not specified	Uncertain significance (Jan 30, 2024)
1-190160772-G-C		not specified	Uncertain significance (Feb 14, 2023)
1-190160791-C-T		not specified	Uncertain significance (Apr 07, 2022)
1-190160837-A-T		not specified	Uncertain significance (Apr 25, 2023)
1-190160868-T-A		not specified	Uncertain significance (Jan 22, 2024)
1-190160890-T-C		not specified	Uncertain significance (Feb 27, 2023)
1-190226129-C-T		not specified	Uncertain significance (Jun 02, 2023)
1-190226157-T-C		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BRINP3	protein_coding	protein_coding	ENST00000367462	7	379968

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.146	0.854	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.192	424	435	0.974	0.0000256	5054
Missense in Polyphen		150	166.88	0.89887		1976
Synonymous	0.317	156	161	0.968	0.00000923	1462
Loss of Function	3.94	8	32.1	0.249	0.00000172	366

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.000305	0.000298
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000709	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits neuronal cell proliferation by negative regulation of the cell cycle transition. Promotes pituitary gonadotrope cell proliferation, migration and invasion, when overexpressed. May play a role in cell pituitary tumor development. {ECO:0000269|PubMed:17138656}.

Recessive Scores

• pRec: 0.116

Intolerance Scores

• rvis_EVS: -1.16
• rvis_percentile_EVS: 6.17

Haploinsufficiency Scores

• pHI: 0.936
• hipred: Y
• hipred_score: 0.544
• ghis: 0.639

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: Brinp3

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;mitochondrion;endoplasmic reticulum;dendrite;neuronal cell body