BAIAP3

Chr 16

BAI1 associated protein 3

Also known as: BAP3

NCBI Gene: 8938 ENSG00000007516 UniProt: O94812 OMIM: 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.

OMIM ResearchSummary from RefSeq, UniProt

This p53-target gene encodes a brain-specific angiogenesis inhibitor. The protein is a seven-span transmembrane protein and a member of the secretin receptor family. It interacts with the cytoplasmic region of brain-specific angiogenesis inhibitor 1. This protein also contains two C2 domains, which are often found in proteins involved in signal transduction or membrane trafficking. Its expression pattern and similarity to other proteins suggest that it may be involved in synaptic functions. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2010]

OMIM ResearchGenerating clinical summary…

GOFmechanismLOEUF 1.03

Clinical Summary— BAIAP3

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

1 unique Pathogenic / Likely Pathogenic· 179 VUS of 231 total submissions

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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 OE?0.83 (0.67–1.03)

0≤0.351.4

Missense OE?1.09 (1.03–1.15)

0≤0.61.4

Synonymous OE?1.14

0≤1.21.6

LoF obs/exp: 55 / 66.5Missense obs/exp: 827 / 760.5Syn Z: -2.01

This gene — mechanism propensity

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

231 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic1

VUS179

Likely Benign15

Benign1

Pathogenic

179

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	1	0	1
Likely Pathogenic	0	0	0	0
VUS	179	0	0	179
Likely Benign	12	0	3	15
Benign	1	0	0	1
Total	192	1	3	196

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

View in ClinVar →

44 pathogenic / likely-pathogenic (of 53) ClinVar copy-number / structural variants overlap BAIAP3 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →