BAIAP2L2

Chr 22

BAR/IMD domain containing adaptor protein 2 like 2

NCBI Gene: 80115ENSG00000128298UniProt: Q6UXY1OMIM: 617536

The protein binds phosphoinositides and promotes formation of planar or curved membrane structures, localizing to RAB13-positive vesicles and intercellular contacts. Mutations cause neurodevelopmental disorder with epilepsy, cataracts, feeding difficulties, and delayed development, inherited in an autosomal recessive pattern. This gene shows very low constraint against loss-of-function variants.

OMIMResearchSummary from RefSeq, UniProt
DNmechanismLOEUF 1.10
Clinical Summary— BAIAP2L2
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
26 unique Pathogenic / Likely Pathogenic· 115 VUS of 158 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
1.10LOEUF
pLI 0.000
Z-score 1.20
OE 0.73 (0.50–1.10)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.24Z-score
OE missense 0.96 (0.87–1.06)
283 obs / 294.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.73 (0.50–1.10)
0≤0.351.4
Missense OE0.96 (0.87–1.06)
0≤0.61.4
Synonymous OE1.01
0≤1.21.6
LoF obs/exp: 17 / 23.2Missense obs/exp: 283 / 294.5Syn Z: -0.08
DN
0.7227th %ile
GOF
0.6151th %ile
LOF
0.4628th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction 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

158 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic23
Likely Pathogenic3
VUS115
Likely Benign6
Conflicting1
23
Pathogenic
3
Likely Pathogenic
115
VUS
6
Likely Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
23
0
23
Likely Pathogenic
0
0
3
0
3
VUS
0
114
1
0
115
Likely Benign
0
3
0
3
6
Benign
0
0
0
0
0
Conflicting
—1
Total0117273148

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

View in ClinVar →

Protein Context — Lollipop Plot

BAIAP2L2 · 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 5 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