BAIAP3

BAI1 associated protein 3, the group of UNC13 homologs|C2 domain containing

Basic information

Region (hg38): 16:1333638-1349439

Links

ENSG00000007516 ∙ NCBI:8938 ∙ OMIM:604009 ∙ HGNC:948 ∙ Uniprot:O94812 ∙ 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 BAIAP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BAIAP3 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			162	9	5	176
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	162	9	6

Variants in BAIAP3

This is a list of pathogenic ClinVar variants found in the BAIAP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1334672-G-A		not specified	Likely benign (Apr 26, 2023)
16-1334675-G-T		not specified	Uncertain significance (Feb 15, 2023)
16-1334714-T-C			Benign (Jul 01, 2024)
16-1334734-G-A		not specified	Uncertain significance (Jul 12, 2022)
16-1334740-G-A		not specified	Uncertain significance (Jun 25, 2024)
16-1334745-C-G		not specified	Uncertain significance (Jul 05, 2023)
16-1338544-C-T		not specified	Uncertain significance (Nov 13, 2024)
16-1338547-G-A		not specified	Likely benign (Jan 07, 2025)
16-1338554-C-T		not specified	Uncertain significance (Jul 31, 2024)
16-1338575-G-A		not specified	Uncertain significance (Apr 22, 2022)
16-1338575-G-C		not specified	Uncertain significance (Mar 28, 2024)
16-1338580-G-A		not specified	Uncertain significance (Jul 20, 2021)
16-1338614-G-A		not specified	Uncertain significance (Mar 01, 2025)
16-1338627-G-T		not specified	Uncertain significance (May 30, 2023)
16-1338667-G-T		not specified	Uncertain significance (Dec 13, 2024)
16-1338671-C-T			Benign (Oct 01, 2022)
16-1338906-C-G		not specified	Uncertain significance (Oct 26, 2021)
16-1338909-G-A		not specified	Uncertain significance (Nov 10, 2024)
16-1338918-G-A		not specified	Uncertain significance (Dec 28, 2023)
16-1338958-G-A		not specified	Uncertain significance (Jun 06, 2023)
16-1338976-T-C		not specified	Uncertain significance (Jun 17, 2024)
16-1338982-G-C		not specified	Uncertain significance (Mar 01, 2025)
16-1339164-G-C		not specified	Uncertain significance (Jun 29, 2023)
16-1339173-C-T		not specified	Uncertain significance (Oct 12, 2021)
16-1339174-G-A		not specified	Uncertain significance (Aug 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BAIAP3	protein_coding	protein_coding	ENST00000324385	34	15838

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.38e-32	0.00301	125554	0	187	125741	0.000744

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.857	827	761	1.09	0.0000504	7574
Missense in Polyphen		295	289.68	1.0184		2855
Synonymous	-2.01	390	343	1.14	0.0000249	2426
Loss of Function	1.31	55	66.5	0.827	0.00000312	717

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00251	0.00246
Ashkenazi Jewish	0.00241	0.00238
East Asian	0.000658	0.000653
Finnish	0.000187	0.000185
European (Non-Finnish)	0.000653	0.000624
Middle Eastern	0.000658	0.000653
South Asian	0.000533	0.000523
Other	0.00117	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions in endosome to Golgi retrograde transport. In response to calcium influx, may interact with SNARE fusion receptors and membrane phospholipids to mediate endosome fusion with the trans-Golgi network. By promoting the recycling of secretory vesicle transmembrane proteins, it indirectly controls dense-core secretory vesicle biogenesis, maturation and their ability to mediate the constitutive and regulated secretion of neurotransmitters and hormones. May regulate behavior and food intake by controlling calcium-stimulated exocytosis of neurotransmitters including NPY and serotonin and hormones like insulin (PubMed:28626000). Proposed to play a role in hypothalamic neuronal firing by modulating gamma-aminobutyric acid (GABA)ergic inhibitory neurotransmission (By similarity). {ECO:0000250|UniProtKB:Q80TT2, ECO:0000269|PubMed:28626000}.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0999

Intolerance Scores

• loftool: 0.880
• rvis_EVS: -2.15
• rvis_percentile_EVS: 1.47

Haploinsufficiency Scores

• pHI: 0.296
• hipred: N
• hipred_score: 0.275
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.718

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Baiap3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: positive regulation of neurotransmitter secretion;exocytosis;G protein-coupled receptor signaling pathway;regulation of synaptic transmission, GABAergic;positive regulation of insulin secretion involved in cellular response to glucose stimulus;retrograde transport, endosome to Golgi;regulation of dense core granule exocytosis;dense core granule maturation
• Cellular component: cytosol;plasma membrane;dense core granule;early endosome membrane;late endosome membrane;trans-Golgi network membrane;recycling endosome membrane;presynapse
• Molecular function: SNARE binding;calcium ion binding;protein binding;phospholipid binding;syntaxin binding