BAIAP3

Chr 16

BAI1 associated protein 3

Also known as: BAP3

NCBI Gene: 8938ENSG00000007516UniProt: O94812OMIM: 604009

BAIAP3 encodes a protein that functions in endosome to Golgi retrograde transport and controls dense-core secretory vesicle biogenesis, regulating the secretion of neurotransmitters and hormones including NPY, serotonin, and insulin. Mutations cause autosomal recessive neurodevelopmental disorders affecting behavior and food intake through impaired neurotransmitter release. The gene shows minimal constraint against loss-of-function variants, consistent with recessive inheritance patterns.

OMIMResearchSummary from RefSeq, UniProt
GOFmechanismLOEUF 1.03
Clinical Summary— BAIAP3
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
49 unique Pathogenic / Likely Pathogenic· 272 VUS of 384 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.03LOEUF
pLI 0.000
Z-score 1.31
OE 0.83 (0.67–1.03)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.86Z-score
OE missense 1.09 (1.03–1.15)
827 obs / 760.5 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.83 (0.67–1.03)
0≤0.351.4
Missense OE1.09 (1.03–1.15)
0≤0.61.4
Synonymous OE1.14
0≤1.21.6
LoF obs/exp: 55 / 66.5Missense obs/exp: 827 / 760.5Syn Z: -2.01
DN
0.5378th %ile
GOF
0.6834th %ile
LOF
0.3744th %ile

The highest-scoring mechanism for this gene is gain-of-function.

GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

384 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic48
Likely Pathogenic1
VUS272
Likely Benign21
Benign7
48
Pathogenic
1
Likely Pathogenic
272
VUS
21
Likely Benign
7
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
48
0
48
Likely Pathogenic
0
0
1
0
1
VUS
1
260
11
0
272
Likely Benign
0
17
0
4
21
Benign
0
5
1
1
7
Total1282615349

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

BAIAP3 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 4 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients