BAALC

Chr 8

BAALC binder of MAP3K1 and KLF4

NCBI Gene: 79870ENSG00000164929UniProt: Q8WXS3

BAALC encodes a protein that may function at postsynaptic lipid rafts through interaction with calcium/calmodulin-dependent protein kinase II alpha. Mutations cause autosomal recessive developmental and epileptic encephalopathy with onset in infancy, characterized by severe intellectual disability, seizures, and brain malformations. The gene shows low constraint to loss-of-function variation.

Summary from RefSeq, UniProt
Research Assistant →
0
Active trials
3
Pubs (1 yr)
39
P/LP submissions
0%
P/LP missense
1.55
LOEUF
Multiple*
Mechanism· predicted
Clinical Summary— BAALC
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
39 unique Pathogenic / Likely Pathogenic· 26 VUS of 71 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
1.55LOEUF
pLI 0.004
Z-score 0.66
OE 0.70 (0.34–1.55)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.26Z-score
OE missense 1.09 (0.90–1.31)
78 obs / 71.9 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.70 (0.34–1.55)
0≤0.351.4
Missense OE1.09 (0.90–1.31)
0≤0.61.4
Synonymous OE0.86
0≤1.21.6
LoF obs/exp: 4 / 5.7Missense obs/exp: 78 / 71.9Syn Z: 0.58
DN
0.6552th %ile
GOF
0.75top 25%
LOF
0.3550th %ile

This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

GOFprediction above median
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

71 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic38
Likely Pathogenic1
VUS26
Likely Benign2
38
Pathogenic
1
Likely Pathogenic
26
VUS
2
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
38
0
38
Likely Pathogenic
0
0
1
0
1
VUS
0
20
6
0
26
Likely Benign
0
2
0
0
2
Benign
0
0
0
0
0
Total02245067

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

View in ClinVar →

Protein Context — Lollipop Plot

BAALC · protein map & ClinVar variants

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

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
Overexpression of BAALC: clinical significance in Chinese de novo acute myeloid leukemia.
Zhou JD et al.·Med Oncol
2015
BAALC gene expression tells a serious patient outcome tale in NPM1-wild type/FLT3-ITD negative cytogenetically normal-acute myeloid leukemia in adults.
Verma D et al.·Blood Cells Mol Dis
2022
Prognostic genes related to mitochondrial dynamics and mitophagy in diffuse large B-cell lymphoma are identified and validated using an integrated analysis of bulk and single-cell RNA sequencing.
Chen Q et al.·Front Immunol
2025
Performance evaluation and clinical impact of the Oncomine Myeloid Research Assay for gene expression analysis in myeloid haematologic malignancies.
Jeon MJ et al.·J Clin Pathol
2023
RUNX1 variant as a genetic predisposition factor for acute myeloid leukemia.
Javadlar M et al.·Exp Mol Pathol
2020
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