BAIAP2L2

Chr 22

BAR/IMD domain containing adaptor protein 2 like 2

NCBI Gene: 80115 ENSG00000128298 UniProt: Q6UXY1 OMIM: 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.

OMIM ResearchSummary from RefSeq, UniProt

The protein encoded by this gene binds phosphoinositides and promotes the formation of planar or curved membrane structures. The encoded protein is found in RAB13-positive vesicles and at intercellular contacts with the plasma membrane. [provided by RefSeq, Dec 2012]

OMIM ResearchGenerating clinical summary…

DNmechanismLOEUF 1.10

Clinical Summary— BAIAP2L2

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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· 114 VUS of 131 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 OE?0.73 (0.50–1.10)

0≤0.351.4

Missense OE?0.96 (0.87–1.06)

0≤0.61.4

Synonymous OE?1.01

0≤1.21.6

LoF obs/exp: 17 / 23.2Missense obs/exp: 283 / 294.5Syn Z: -0.08

This gene — mechanism propensity

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

131 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic1

VUS114

Likely Benign6

Pathogenic

114

VUS

Likely 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	114	0	0	114
Likely Benign	3	0	3	6
Benign	0	0	0	0
Total	117	1	3	121

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

View in ClinVar →

25 pathogenic / likely-pathogenic (of 27) ClinVar copy-number / structural variants overlap BAIAP2L2 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →