BAALC

Summary

BAALC (BAALC binder of MAP3K1 and KLF4, HGNC:14333) is a protein-coding gene on chromosome 8q22.3, encoding Brain and acute leukemia cytoplasmic protein (Q8WXS3). May play a synaptic role at the postsynaptic lipid rafts possibly through interaction with CAMK2A.

This gene was identified by gene expression studies in patients with acute myeloid leukemia (AML). The gene is conserved among mammals and is not found in lower organisms. Tissues that express this gene develop from the neuroectoderm. Multiple alternatively spliced transcript variants that encode different proteins have been described for this gene; however, some of the transcript variants are found only in AML cell lines.

Source: NCBI Gene 79870 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 26 total
• GTEx eGene: eQTL in 30 tissues, sQTL in 5 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.44 (unconstrained)
• MANE Select transcript: NM_024812

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14333
Approved symbol	BAALC
Name	BAALC binder of MAP3K1 and KLF4
Location	8q22.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000164929
Ensembl biotype	protein_coding
OMIM	606602
Entrez	79870

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 11 protein_coding, 4 protein_coding_CDS_not_defined

MANE Select: ENST00000309982

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 3, TSL 3: 2, TSL 4: 1, TSL 5: 3

ENST00000309982, ENST00000297574, ENST00000306391, ENST00000330955, ENST00000438105, ENST00000517863, ENST00000519507, ENST00000521926, ENST00000523754, ENST00000964302, ENST00001009308, ENST00001118827, ENST00001123095, ENST00001123096, ENST00001137096

RefSeq mRNA: 3 — MANE Select: NM_024812 NM_001024372, NM_001364874, NM_024812

CCDS: CCDS47906, CCDS6297, CCDS94326

Canonical transcript exons

ENST00000309982 — 3 exons

Exon	Start	End
ENSE00001523107	103140725	103141057
ENSE00002114046	103227989	103230305
ENSE00003691623	103212919	103213085

Expression profiles

Bgee: expression breadth ubiquitous, 213 present calls, max score 98.89.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.2535 / max 797.6099, expressed in 1027 samples.

Highest expression (Bgee): putamen, frontal lobe, superior vestibular nucleus, anterior cingulate cortex, caudate nucleus.

Genetic regulation across tissues (GTEx eQTL / sQTL)

BAALC is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 30 tissues and its splicing (sQTL) in 5 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 35 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Cells Cultured fibroblasts	eqtl	1.3e-34	+0.37	8:103125090:C:T
Whole Blood	eqtl	2.5e-12	+0.36	8:103138921:C:T
Brain Frontal Cortex BA9	eqtl	1.9e-11	-0.47	8:103138581:C:T
Brain Nucleus accumbens basal ganglia	eqtl	8.4e-11	+0.27	8:103151694:T:C
Brain Caudate basal ganglia	eqtl	1.1e-10	+0.20	8:103125913:G:T
Brain Cerebellum	eqtl	5.6e-09	-0.21	8:103178849:T:C
Brain Cortex	eqtl	6.1e-08	+0.26	8:103151694:T:C
Brain Cerebellar Hemisphere	eqtl	1.2e-06	+0.22	8:103143624:C:T
Brain Putamen basal ganglia	eqtl	1.4e-06	+0.15	8:103125913:G:T
Brain Anterior cingulate cortex BA24	eqtl	2.7e-06	+0.28	8:103151694:T:C
Stomach	eqtl	6.9e-06	-0.31	8:103113261:G:A
Pituitary	eqtl	7.9e-06	+0.25	8:103168772:G:A
Brain Hippocampus	eqtl	1.4e-05	-0.20	8:103178849:T:C
Colon Sigmoid	eqtl	3.3e-05	+0.22	8:103125090:C:T
Muscle Skeletal	eqtl	7.4e-05	-0.18	8:103139153:A:C
Brain Hypothalamus	eqtl	3.6e-04	-0.28	8:103179754:G:A
Esophagus Muscularis	eqtl	4.1e-04	+0.23	8:103100991:C:T
Spleen	eqtl	4.5e-04	+0.26	8:103144375:A:G
Artery Aorta	eqtl	5.2e-04	+0.31	8:103117196:C:A
Pituitary	sqtl	8.1e-04	-0.38	8:103219839:A:C

FANTOM5 promoters

5 alternative TSS:

Promoter ID	TPM avg	Samples expressed
90103	25.6563	995
90104	2.1014	485
205280	0.2027	123
90105	0.1949	106
90102	0.0983	57

Top tissues by expression

showing 100 of 288 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
putamen	UBERON:0001874	98.89	gold quality
right frontal lobe	UBERON:0002810	98.80	gold quality
superior vestibular nucleus	UBERON:0007227	98.74	gold quality
anterior cingulate cortex	UBERON:0009835	98.73	gold quality
caudate nucleus	UBERON:0001873	98.71	gold quality
cingulate cortex	UBERON:0003027	98.69	gold quality
amygdala	UBERON:0001876	98.67	gold quality
hypothalamus	UBERON:0001898	98.58	gold quality
cranial nerve II	UBERON:0000941	98.57	gold quality
substantia nigra	UBERON:0002038	98.49	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	98.49	gold quality
prefrontal cortex	UBERON:0000451	98.47	gold quality
Brodmann (1909) area 9	UBERON:0013540	98.47	gold quality
midbrain	UBERON:0001891	98.45	gold quality
lateral globus pallidus	UBERON:0002476	98.35	gold quality
nucleus accumbens	UBERON:0001882	98.28	gold quality
frontal cortex	UBERON:0001870	98.23	gold quality
medulla oblongata	UBERON:0001896	98.23	gold quality
ventral tegmental area	UBERON:0002691	98.20	gold quality
Ammon’s horn	UBERON:0001954	97.98	gold quality
spinal cord	UBERON:0002240	97.97	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	97.91	gold quality
telencephalon	UBERON:0001893	97.87	gold quality
neocortex	UBERON:0001950	97.83	gold quality
subthalamic nucleus	UBERON:0001906	97.73	gold quality
pons	UBERON:0000988	97.69	gold quality
corpus callosum	UBERON:0002336	97.63	gold quality
substantia nigra pars reticulata	UBERON:0001966	97.60	gold quality
substantia nigra pars compacta	UBERON:0001965	97.58	gold quality
cerebral cortex	UBERON:0000956	97.57	gold quality
dorsal plus ventral thalamus	UBERON:0001897	97.53	gold quality
endothelial cell	CL:0000115	97.48	gold quality
temporal lobe	UBERON:0001871	97.44	gold quality
parietal lobe	UBERON:0001872	97.41	gold quality
postcentral gyrus	UBERON:0002581	97.41	gold quality
CA1 field of hippocampus	UBERON:0003881	97.41	gold quality
superior frontal gyrus	UBERON:0002661	97.27	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	97.19	gold quality
forebrain	UBERON:0001890	97.14	gold quality
brain	UBERON:0000955	96.72	gold quality
Brodmann (1909) area 46	UBERON:0006483	96.65	gold quality
inferior vagus X ganglion	UBERON:0005363	96.44	gold quality
orbitofrontal cortex	UBERON:0004167	96.26	gold quality
globus pallidus	UBERON:0001875	96.08	gold quality
occipital lobe	UBERON:0002021	96.02	gold quality
inferior olivary complex	UBERON:0002127	95.97	gold quality
lateral nuclear group of thalamus	UBERON:0002736	95.89	gold quality
medial globus pallidus	UBERON:0002477	95.52	gold quality
entorhinal cortex	UBERON:0002728	95.50	gold quality
primary visual cortex	UBERON:0002436	95.46	gold quality
cerebellar vermis	UBERON:0004720	95.08	gold quality
right hemisphere of cerebellum	UBERON:0014890	94.34	gold quality
cerebellar cortex	UBERON:0002129	93.74	gold quality
cerebellar hemisphere	UBERON:0002245	93.70	gold quality
cerebellum	UBERON:0002037	93.60	gold quality
Brodmann (1909) area 23	UBERON:0013554	93.43	gold quality
middle temporal gyrus	UBERON:0002771	93.22	gold quality
cortical plate	UBERON:0005343	92.18	gold quality
adenohypophysis	UBERON:0002196	89.32	gold quality
ganglionic eminence	UBERON:0004023	88.86	gold quality
pituitary gland	UBERON:0000007	88.66	gold quality
left adrenal gland cortex	UBERON:0035825	86.83	gold quality
left adrenal gland	UBERON:0001234	86.74	gold quality
adrenal cortex	UBERON:0001235	85.84	gold quality
right adrenal gland	UBERON:0001233	85.46	gold quality
adrenal gland	UBERON:0002369	84.82	gold quality
adult organism	UBERON:0007023	84.79	gold quality
right adrenal gland cortex	UBERON:0035827	84.31	gold quality
spleen	UBERON:0002106	82.21	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.20	gold quality
omental fat pad	UBERON:0010414	80.79	gold quality
peritoneum	UBERON:0002358	80.75	gold quality
adipose tissue of abdominal region	UBERON:0007808	79.89	gold quality
ventricular zone	UBERON:0003053	79.71	gold quality
upper lobe of left lung	UBERON:0008952	78.65	gold quality
islet of Langerhans	UBERON:0000006	78.31	gold quality
colonic epithelium	UBERON:0000397	77.56	gold quality
choroid plexus epithelium	UBERON:0003911	77.49	gold quality
upper lobe of lung	UBERON:0008948	77.26	gold quality
olfactory bulb	UBERON:0002264	76.93	silver quality
right lung	UBERON:0002167	76.50	gold quality
adipose tissue	UBERON:0001013	76.41	gold quality
stromal cell of endometrium	CL:0002255	76.25	gold quality
subcutaneous adipose tissue	UBERON:0002190	75.70	gold quality
connective tissue	UBERON:0002384	75.55	gold quality
left lobe of thyroid gland	UBERON:0001120	75.05	gold quality
right lobe of thyroid gland	UBERON:0001119	74.97	gold quality
hindlimb stylopod muscle	UBERON:0004252	74.55	gold quality
calcaneal tendon	UBERON:0003701	74.49	gold quality
secondary oocyte	CL:0000655	74.47	gold quality
thyroid gland	UBERON:0002046	74.06	gold quality
mucosa of stomach	UBERON:0001199	73.51	gold quality
embryo	UBERON:0000922	73.39	gold quality
muscle layer of sigmoid colon	UBERON:0035805	73.05	gold quality
right ovary	UBERON:0002118	72.80	gold quality
apex of heart	UBERON:0002098	72.43	gold quality
anatomical system	UBERON:0000467	72.18	gold quality
multicellular organism	UBERON:0000468	72.18	gold quality
material anatomical entity	UBERON:0000465	72.16	gold quality
dorsal root ganglion	UBERON:0000044	71.87	silver quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-9067	yes	334.32
E-MTAB-8271	yes	16.37
E-ANND-3	yes	3.98
E-CURD-11	no	6.22

HPA expression

RNA tissue specificity: Tissue enriched

showing 60 of 76 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Frontal cortex	tissue	274.0
Locus coeruleus	tissue	247.0
Hippocampus	tissue	227.0	medium
Postcentral gyrus	tissue	220.8
Nucleus accumbens	tissue	150.5
Caudate putamen	tissue	144.5
Cerebral cortex	tissue	109.1	medium
Motor cortex	tissue	109.1
Spinal cord	tissue	105.2
Prefrontal cortex	tissue	103.9
Amygdala	tissue	101.4
Hippocampal formation	tissue	101.3
Thalamus	tissue	100.8
Pons	tissue	100.1
Somatosensory cortex	tissue	95.7
Medulla oblongata	tissue	95.2
Temporal cortex	tissue	92.7
Midbrain	tissue	92.2
Entorhinal cortex	tissue	91.8
Occipital cortex	tissue	91.7
Retrosplenial cortex	tissue	90.6
Periaqueductal gray	tissue	90.5
Retrosplenial and cingulate cortex	tissue	90.1
Insular cortex	tissue	88.2
Substantia nigra	tissue	87.8
Hypothalamus	tissue	82.9
Septum	tissue	76.2
Superior colliculi	tissue	74.0
Ventral forebrain	tissue	67.8
Putamen	tissue	66.8
Cerebellum	tissue	62.8	high
Basal ganglia	tissue	60.5	medium
Corpus callosum	tissue	57.4
Olfactory bulb	tissue	46.1
Choroid plexus	tissue	32.5
Pituitary gland	tissue	23.7
Retina	tissue	18.0
Adrenal gland	tissue	11.4	low
Spleen	tissue	9.5	low
Adipose tissue	tissue	8.0	not detected
Placenta	tissue	5.0	not detected
Lung	tissue	4.1	low
Fallopian tube	tissue	3.6	low
Bone marrow	tissue	3.2	low
Urinary bladder	tissue	2.3	not detected
Heart muscle	tissue	2.1	not detected
Liver	tissue	2.1	not detected
Appendix	tissue	2.0	not detected
Ovary	tissue	1.8	not detected
Skeletal muscle	tissue	1.8	not detected
Smooth muscle	tissue	1.7	not detected
Breast	tissue	1.6	not detected
Endometrium 1	tissue	1.6	not detected
Rectum	tissue	1.5	not detected
Colon	tissue	1.5	not detected
Gallbladder	tissue	1.5	not detected
Thyroid gland	tissue	1.4	not detected
Small intestine	tissue	1.4	not detected
Cervix	tissue	1.3	not detected
Skin 1	tissue	1.3	not detected

Brain sub-regions (HPA Brain Atlas): detected in 189; highest nTPM — Posterior thalamic nucleus (449.4), Medial geniculate body (353.3), Lateral thalamic nuclei (321.1), Ventral posteromedial thalamic nucleus (313.6), Medial dorsal thalamic nucleus (310.2).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): RUNX1

miRNA regulators (miRDB)

Targeting BAALC by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 108 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-4713-3P	100.00	65.92	505
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-6793-5P	99.97	65.95	758
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-323A-3P	99.79	70.30	1739
HSA-MIR-3617-5P	99.75	69.41	1968
HSA-MIR-641	99.75	69.35	1975

Functional genomics

gnomAD constraint: pLI 0.00323, LOEUF 1.44, missense Z -0.748 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000309982 — one region, missense o/e 1.04.

Literature-anchored findings (GeneRIF, showing 40)

• The BAALC gene, located on chromosome 8q22.3, encodes a protein with no homology to any known proteins or functional domains. (PMID:15604894)
• High transcript levels occur in leukemic blasts from some patients with acute myeloid leukemia. (PMID:15749074)
• Low expression of both ERG and BAALC identifies T-ALL patients with a distinctly favorable long-term outcome. (PMID:17646667)
• high BAALC expression is an independent adverse prognostic factor and is associated with a specific gene-expression profile (PMID:18378853)
• Up-regulation of BAALC gene may be an important alteration in AML-M2 patients with t(8;21) translocation. (PMID:18671757)
• Presence of both EVI1 and/or BAALC in chronic myeloid patients was found to modulate the disease pattern (PMID:18752846)
• Overexpression of BAALC and ERG either separate or concomitant predict adverse clinical outcome and may define important risk factor in cytogenetically normal acute myeloid leukemia (PMID:19555438)
• BAALC is a relevant prognostic marker in intermediate-risk acute myeloid leukemia patients, with high versus low BAALC expressors showing lower complete remission rate after salvage therapy. (PMID:19943049)
• High BAALC expression is associated with chemoresistance in adult B-precursor acute lymphoblastic leukemia. (PMID:20065290)
• CEBPA mutation status and BAALC expression are important prognostic factors in acute myeloid leukemia patients with normal cytogenetics. (PMID:20306678)
• 1-5-6-8 BAALC isoform expression may be associated with an adverse prognosis in pediatric acute myeloid leukemia with normal karyotype. (PMID:20495894)
• In contrast to BAALC, which likely represents only a surrogate marker of treatment failure in acute leukemia, IGFBP7 regulates the proliferation of leukemic cells and might be involved in chemotherapy resistance (PMID:20535151)
• High BAALC expression levels are associated with acute myeloid leukemia. (PMID:20841507)
• Low ERG and BAALC expression (E/B(low)) and NOTCH1/FBXW7 (N/F) mutations have been proposed as powerful prognostic markers in large cohorts of adult T-ALL. (PMID:21835957)
• Presence of FLT3-ITD and high BAALC expression are independent prognostic markers in childhood acute myeloid leukemia. (PMID:21967978)
• These findings indicate that BAALC gene is “paused” and that in leukemia cells its transcription can be activated or repressed by mechanisms acting on epigenetic marks. (PMID:22197554)
• A high MEBE (MN1,ERG, BAALC, EVI1) expression score is an unfavorable prognostic marker in Myelodysplastic syndrome and is associated with an increased risk for progression to Acute myeloid leukemia. (PMID:22488406)
• identify a heritable genomic feature predisposing to overexpression of an oncogene (BAALC), thereby possibly leading to enhanced AML leukemogenesis (PMID:22493267)
• high expression of miR-3151 is an independent prognosticator for poor outcome in cytogenetically normal-AML and affects different outcome end points than its host gene, BAALC (PMID:22529287)
• data show that higher levels of VEGF-A(CSF) are closely related to CNS leukemia (CNSL), and VEGF-A(CSF) may be a better predictor than the other risk factors elucidating the pathogenesis and development of CNSL (PMID:23287429)
• Higher BAALC expression and FLT3-ITD mutation, both individually and in combination, were associated with worse survival outcomes in CN-AML, and this was also applicable in NPM1-mutated CN-AML, known as a favorable-risk group. (PMID:23647058)
• higher post-HSCT BAALC and WT1 expressions in patients with CBF-AML may be good markers of minimal residual disease for the prediction of survival and relapse after HSCT. (PMID:23672350)
• BAALC overexpression retains its negative prognostic role across all cytogenetic risk groups in acute myeloid leukemia patients. (PMID:23760853)
• Investigated the prognostic impact of brain and acute leukemia, cytoplasmic (BAALC) expression in acute myeloid leukemia with normal karyotype. (PMID:23865362)
• miR-3151 introns within BAALC have roles in driving leukemogenesis by deregulating the TP53 pathway (PMID:24736457)
• Thus low MDR1/low BAALC expression identifies a subgroup of intermediate cytogenetic risk AML patients with a remarkably good long-term outcome achieved by chemotherapy alone. (PMID:24855032)
• study indicates that overexpression of BAALC serves as an independent prognostic biomarker in acute myeloid leukemia (PMID:25428390)
• Evaluating WT1 and BAALC gene expression at diagnosis may improve standard risk stratification and possibly refine the therapeutic approach for Myelodysplastic Syndromes patients. (PMID:26012361)
• demonstrated that BAALC blocks ERK-mediated monocytic differentiation of acute myeloid leukemia cells by trapping Kruppel-like factor 4 (KLF4) in the cytoplasm and inhibiting its function in the nucleus (PMID:26050649)
• combined determination of both miR-3151 and BAALC improved this prognostic stratification, with patients with low levels of both parameters showing a better outcome compared with those patients harboring increased levels of one or both markers (PMID:26430723)
• BAALC and ERG genes are specific significant molecular markers in acute myeloid leukemia disease progression, response to treatment and survival. (PMID:26625814)
• Study provide evidence for an association of rs62527607 [GT] SNP of BAALC gene with multidrug resistance in childhood ALL. (PMID:27372260)
• BAALC expression-based minimal residual disease detection during therapy may be considered a strategy to identify patients at high risk of relapse. (PMID:27662611)
• despite of their well-known adverse role in prognosis of AML, neither BAALC nor ERG expression levels at diagnosis had effect on survival of AML patients who underwent allo-HSCT. (PMID:29696374)
• Downregulation of miR-326 and overexpression of BALLC in drug-resistant acute lymphoblastic leukemia cell line and patients compared with the parental cell line and drug-sensitive patients was found. The expression profiles of miR-326 and BAALC were inversely correlated. Bioinformatics data showed a possible regulatory role for miR-326 on BAALC mRNA. (PMID:32129446)
• Long non-coding RNA LRRC75A-AS1 facilitates triple negative breast cancer cell proliferation and invasion via functioning as a ceRNA to modulate BAALC. (PMID:32811810)
• Allogeneic stem cell transplantation mitigates the adverse prognostic impact of high diagnostic BAALC and MN1 expression in AML. (PMID:32862286)
• Prognostic significance of combined BAALC and MN1 gene expression level in acute myeloid leukemia with normal karyotype. (PMID:33242229)
• Physical interaction between BAALC and DBN1 induces chemoresistance in leukemia. (PMID:33453340)
• iPSC modeling of stage-specific leukemogenesis reveals BAALC as a key oncogene in severe congenital neutropenia. (PMID:33894142)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	baalca	ENSDARG00000077775
danio_rerio	baalcb	ENSDARG00000089549
mus_musculus	Baalc	ENSMUSG00000022296
rattus_norvegicus	Baalc	ENSRNOG00000004697

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Sus scrofa	Q8WNE9	82.1%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
BAALC-AS1	ncRNA	100499183
BAALC-AS2	ncRNA	157556
LINC01181	ncRNA	379034
FZD6	protein-coding	8323
MIR3151	ncRNA	100422992
SNORD173	snoRNA	109623480
CTHRC1	protein-coding	115908

Protein

Protein identifiers

Brain and acute leukemia cytoplasmic protein — Q8WXS3 (reviewed: Q8WXS3)

All UniProt accessions (1): Q8WXS3

UniProt curated annotations — full annotation on UniProt →

Function. May play a synaptic role at the postsynaptic lipid rafts possibly through interaction with CAMK2A.

Subunit / interactions. Interacts with CAMK2A.

Subcellular location. Cytoplasm. Synapse. Synaptosome. Membrane raft. Postsynaptic density.

Tissue specificity. Predominantly expressed in neuroectoderm-derived tissues. Expressed in the brain and spinal cord, and at low levels, in the adrenal gland. In the bone marrow, confined to the CD34+ progenitor cells. Not found in peripheral blood mononuclear cells, nor lymph nodes. Tends to be expressed at high levels in acute myeloid leukemia and glioblastoma cells.

Post-translational modifications. Palmitoylation and myristoylation target the protein to the lipid rafts.

Isoforms (6)

UniProt ID	Names	Canonical?
Q8WXS3-2	1, 1-6-8	yes
Q8WXS3-1	2, 1-5-6-8
Q8WXS3-3	3, 1-5-6-7-8
Q8WXS3-4	4, 1-2
Q8WXS3-5	5, 1-4-5-6-8
Q8WXS3-6	6, 1-8

RefSeq proteins (3): NP_001019543, NP_001351803, NP_079088* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009728	BAALC	Family

Pfam: PF06989

UniProt features (18 total): splice variant 8, compositionally biased region 3, region of interest 2, lipid moiety-binding region 2, initiator methionine 1, chain 1, sequence variant 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WXS3-F1	60.47	0.00

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): cytosol; nucleoplasm

Antibody reliability (HPA): IH approved · IF supported

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2)

Type	Positions
N-myristoyl glycine	2
S-palmitoyl cysteine	3

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 131 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, VERHAAK_AML_WITH_NPM1_MUTATED_DN, GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN, TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_ERYTHROCYTE_UP, MARTINEZ_RB1_TARGETS_UP, NIKOLSKY_BREAST_CANCER_8Q12_Q22_AMPLICON, chr8q22, HOEBEKE_LYMPHOID_STEM_CELL_UP, GOCC_NEURON_PROJECTION, DOUGLAS_BMI1_TARGETS_UP, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, ATGTCAC_MIR489, BOQUEST_STEM_CELL_DN, MODULE_47, MULLIGHAN_MLL_SIGNATURE_2_DN

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (6): cytoplasm (GO:0005737), cytosol (GO:0005829), postsynaptic density (GO:0014069), neuron projection (GO:0043005), membrane raft (GO:0045121), synapse (GO:0045202)

GO top-level categories

9 GO namespaces:

Category	Terms
cellular anatomical structure	2
binding	1
intracellular anatomical structure	1
cytoplasm	1
asymmetric synapse	1
postsynaptic specialization	1
plasma membrane bounded cell projection	1
membrane microdomain	1
cell junction	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 2 of 7 annotations. The rest are phylogenetic / computational / electronic (IEA).

2 experimentally-supported GO terms:

GO term	NS	Evidence
cytoplasm	CC	direct assay
cytosol	CC	direct assay

Protein interactions and networks

IntAct

Human interaction partners of BAALC in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

4 partners by confidence:

Partner	Interaction type	MIscore	Records
AGTR1	physical association	0.370	1
ATXN1	physical association	0.370	1
CHEK2	physical association	0.370	1
MDFI	physical association	0.370	1

BioGRID (23 interactions; top human partners by supporting records): KLF4 (Two-hybrid; 5 records), MAP3K1 (Two-hybrid; 4 records), AGTR1 (Two-hybrid), AP1G1 (Two-hybrid), ATP1B3 (Two-hybrid), ATXN1 (Two-hybrid), CHD1L (Two-hybrid), CHEK2 (Two-hybrid), CINP (Two-hybrid), MDFI (Two-hybrid), NAA10 (Two-hybrid), NAA11 (Two-hybrid), OSBPL1A (Two-hybrid), RNF2 (Two-hybrid), SETD3 (Affinity Capture-MS)

SIGNOR signaling

1 signaling interactions:

A	Effect	B	Mechanism
RUNX1	“up-regulates quantity by expression”	BAALC	“transcriptional regulation”

Disease & clinical

Genetic variants

Variant evidence for BAALC: 26 ClinVar records (0 pathogenic / likely pathogenic); 3 GWAS associations.

ClinVar

26 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	21
Likely benign	2
Benign	0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 21 predictions of 448):

Position(s)	Effect	Δscore	Sites
8:103141059	donor_loss	1.0000
8:103141058–103141059	donor_loss	0.9900	3
8:103198088	acceptor_gain	0.9900
8:103227980	acceptor_gain	0.9900
8:103227987–103227988	acceptor_loss	0.9900	4
8:103227987	acceptor_loss	0.9800	2
8:103183351	acceptor_gain	0.9700
8:103212855	acceptor_gain	0.9700
8:103213086–103213087	donor_loss	0.9700	6
8:103213085	donor_loss	0.9600

AlphaMissense

180 missense substitutions predicted likely pathogenic (of 942 scored), across 33 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
S6	8	0.874	0.987
D9	8	0.826	0.932
D32	8	0.757	0.923
W27	7	0.984	0.997
W19	7	0.972	0.995
C3	7	0.964	0.988
E24	7	0.964	0.986
E12	7	0.915	0.954
S18	7	0.907	0.992
E17	7	0.847	0.962
P13	6	0.958	0.978
T23	6	0.957	0.990
G2	6	0.956	0.992
G5	6	0.953	0.983
G4	6	0.945	0.987
L28	6	0.930	0.993
T26	6	0.917	0.983
T20	6	0.907	0.984
R14	6	0.870	0.968
T29	6	0.745	0.959

HPA cancer prognostics

RNA cancer specificity: Cancer enriched (Glioblastoma Multiforme)

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

2 prognostic cancer types:

Cancer	Prognostic	p-value
Stomach Adenocarcinoma (TCGA)	unfavorable	0.00011
Pancreatic Adenocarcinoma (validation)	unfavorable	0.000544

Disease associations

OMIM: gene MIM:606602 | disease phenotypes:

GWAS associations

3 associations:

Study	Trait	p-value
GCST006035_4	Breast cancer and/or colorectal cancer	3e-7
GCST009615_8	Triglyceride levels x loop diuretics use interaction	4e-6
GCST003815_81	Late-onset Alzheimer’s disease	5e-6

EFO canonical traits (from GWAS)

2 canonical traits:

EFO ID	Trait name
EFO:1001870	late-onset Alzheimers disease
EFO:0004530	triglyceride measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

31 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases methylation, increases expression	5
trichostatin A	affects cotreatment, decreases expression	3
entinostat	decreases expression, affects cotreatment	2
Arsenic Trioxide	decreases expression	2
Tretinoin	increases expression	2
TL8-506	increases expression, affects cotreatment	1
methylmercuric chloride	decreases expression	1
uranyl acetate	affects expression	1
bisphenol A	decreases methylation, affects cotreatment	1
ferrous chloride	increases expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression, decreases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	decreases methylation	1
Temozolomide	decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
Carbamazepine	affects expression	1
Doxorubicin	decreases expression	1
Endosulfan	decreases expression	1
Estradiol	affects cotreatment, decreases expression	1
Lead	affects expression	1
Lipopolysaccharides	increases expression, decreases reaction	1
Poly I-C	affects cotreatment, increases expression	1
Progesterone	affects cotreatment, decreases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Uranium	affects expression	1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

1 trials:

NCT	Phase	Status	Title
NCT01907555	Not specified	COMPLETED	Clinical, Molecular and Physiopathological Study of Cohen Syndrome and Cohen-like Syndromes