BCAS1

Summary

BCAS1 (brain enriched myelin associated protein 1, HGNC:974) is a protein-coding gene on chromosome 20q13.2, encoding Breast carcinoma-amplified sequence 1 (O75363). Required for myelination.

This gene resides in a region at 20q13 which is amplified in a variety of tumor types and associated with more aggressive tumor phenotypes. Among the genes identified from this region, it was found to be highly expressed in three amplified breast cancer cell lines and in one breast tumor without amplification at 20q13.2. However, this gene is not in the common region of maximal amplification and its expression was not detected in the breast cancer cell line MCF7, in which this region is highly amplified. Although not consistently expressed, this gene is a candidate oncogene.

Source: NCBI Gene 8537 — RefSeq curated summary.

At a glance

• GWAS associations: 33 (top 4% of genes corpus-wide)
• Clinical variants (ClinVar): 99 total
• GTEx eGene: eQTL in 19 tissues, sQTL in 20 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 0.85 (unconstrained)
• MANE Select transcript: NM_001366298
• Notable: 99 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:974
Approved symbol	BCAS1
Name	brain enriched myelin associated protein 1
Location	20q13.2
Locus type	gene with protein product
Status	Approved
Aliases	NABC1, AIBC1, PMES-2
Ensembl gene	ENSG00000064787
Ensembl biotype	protein_coding
OMIM	602968
Entrez	8537

Gene structure

Transcript identifiers

Ensembl transcripts: 29 — 28 protein_coding, 1 protein_coding_CDS_not_defined

MANE Select: ENST00000688948

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

ENST00000688948, ENST00000371435, ENST00000395961, ENST00000422805, ENST00000448484, ENST00000685429, ENST00000685741, ENST00000686565, ENST00000688711, ENST00000689476, ENST00000690125, ENST00000879784, ENST00000879785, ENST00000879786, ENST00000879787, ENST00000960232, ENST00000960233, ENST00000960234, ENST00000960235, ENST00000960236, ENST00001008488, ENST00001008489, ENST00001019507, ENST00001108325, ENST00001108326, ENST00001108327, ENST00001112958, ENST00001131213, ENST00001133040

RefSeq mRNA: 7 — MANE Select: NM_001366298 NM_001316361, NM_001323347, NM_001366295, NM_001366296, NM_001366297, NM_001366298, NM_003657

CCDS: CCDS13444, CCDS82631, CCDS93061

Canonical transcript exons

ENST00000688948 — 13 exons

Exon	Start	End
ENSE00000662837	53953432	53953695
ENSE00000662838	53957432	53957497
ENSE00000662839	53966906	53967073
ENSE00000662840	53985287	53985499
ENSE00000662841	53995012	53995056
ENSE00001022753	53975389	53975430
ENSE00001455220	53943541	53944996
ENSE00001455230	53992512	53992646
ENSE00001624940	54028392	54028972
ENSE00001784114	53995892	53996050
ENSE00001835333	54070433	54070594
ENSE00003714232	54058647	54058723
ENSE00003754722	54058085	54058154

Expression profiles

Bgee: expression breadth ubiquitous, 243 present calls, max score 99.81.

FANTOM5 (CAGE): breadth broad, TPM avg 21.4140 / max 2143.1224, expressed in 385 samples.

Highest expression (Bgee): C1 segment of cervical spinal cord, spinal cord, inferior vagus X ganglion, corpus callosum, ventral tegmental area.

Genetic regulation across tissues (GTEx eQTL / sQTL)

BCAS1 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 19 tissues and its splicing (sQTL) in 20 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 39 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Brain Caudate basal ganglia	sqtl	1.5e-30	+1.28	20:53996239:C:T
Nerve Tibial	sqtl	2.1e-27	+0.83	20:53975487:T:C
Brain Frontal Cortex BA9	sqtl	2.7e-26	+1.36	20:53975487:T:C
Brain Hypothalamus	sqtl	5.7e-25	+1.27	20:53956285:TTC:T
Brain Spinal cord cervical c-1	sqtl	8.4e-24	+1.51	20:54002259:T:C
Brain Nucleus accumbens basal ganglia	sqtl	1.2e-23	+1.26	20:53975487:T:C
Brain Putamen basal ganglia	sqtl	5.7e-20	+1.42	20:53975487:T:C
Esophagus Mucosa	eqtl	8.3e-20	+0.25	20:54073919:T:G
Brain Hippocampus	sqtl	4.6e-18	+1.37	20:53975487:T:C
Brain Anterior cingulate cortex BA24	sqtl	1.5e-17	+1.06	20:54002259:T:C
Brain Amygdala	sqtl	2.0e-16	+1.43	20:54002259:T:C
Brain Cortex	sqtl	5.4e-14	+0.89	20:53963976:T:C
Skin Sun Exposed Lower leg	eqtl	7.4e-14	-0.45	20:54060886:G:A
Testis	sqtl	3.9e-13	+0.70	20:53960510:T:A
Brain Cerebellum	sqtl	1.2e-10	+1.07	20:53956285:TTC:T
Lung	eqtl	7.4e-10	+0.29	20:54070647:A:G
Esophagus Mucosa	sqtl	4.1e-09	-0.67	20:53956285:TTC:T
Colon Transverse	sqtl	7.5e-09	-0.72	20:53958200:C:T
Cells EBV-transformed lymphocytes	eqtl	8.7e-09	+0.40	20:53905181:A:G
Adipose Visceral Omentum	eqtl	2.7e-08	-0.31	20:54000007:G:A

FANTOM5 promoters

8 alternative TSS:

Promoter ID	TPM avg	Samples expressed
188058	16.1980	116
188063	3.0315	181
188059	1.3827	81
188056	0.3251	53
188061	0.1907	60
188062	0.1257	80
188055	0.0906	34
188057	0.0696	28

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
C1 segment of cervical spinal cord	UBERON:0006469	99.81	gold quality
spinal cord	UBERON:0002240	99.68	gold quality
inferior vagus X ganglion	UBERON:0005363	99.65	gold quality
corpus callosum	UBERON:0002336	99.43	gold quality
ventral tegmental area	UBERON:0002691	99.27	gold quality
superior vestibular nucleus	UBERON:0007227	99.27	gold quality
pons	UBERON:0000988	99.24	gold quality
middle frontal gyrus	UBERON:0002702	99.24	gold quality
medial globus pallidus	UBERON:0002477	99.23	gold quality
cranial nerve II	UBERON:0000941	99.22	gold quality
globus pallidus	UBERON:0001875	99.10	gold quality
amygdala	UBERON:0001876	99.03	gold quality
subthalamic nucleus	UBERON:0001906	98.97	gold quality
medulla oblongata	UBERON:0001896	98.94	gold quality
putamen	UBERON:0001874	98.80	gold quality
midbrain	UBERON:0001891	98.79	gold quality
substantia nigra	UBERON:0002038	98.74	gold quality
lateral globus pallidus	UBERON:0002476	98.00	gold quality
dorsal plus ventral thalamus	UBERON:0001897	97.97	gold quality
caudate nucleus	UBERON:0001873	97.80	gold quality
nucleus accumbens	UBERON:0001882	97.75	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	97.75	gold quality
olfactory bulb	UBERON:0002264	97.71	gold quality
hypothalamus	UBERON:0001898	97.48	gold quality
trigeminal ganglion	UBERON:0001675	97.35	gold quality
substantia nigra pars reticulata	UBERON:0001966	97.25	gold quality
substantia nigra pars compacta	UBERON:0001965	97.17	gold quality
cingulate cortex	UBERON:0003027	96.84	gold quality
anterior cingulate cortex	UBERON:0009835	96.81	gold quality
Ammon’s horn	UBERON:0001954	96.67	gold quality
inferior olivary complex	UBERON:0002127	96.24	gold quality
tibial nerve	UBERON:0001323	96.18	gold quality
lateral nuclear group of thalamus	UBERON:0002736	96.11	gold quality
rectum	UBERON:0001052	95.88	gold quality
dorsal root ganglion	UBERON:0000044	95.85	gold quality
right frontal lobe	UBERON:0002810	95.83	gold quality
Brodmann (1909) area 9	UBERON:0013540	95.55	gold quality
sural nerve	UBERON:0015488	95.34	gold quality
pylorus	UBERON:0001166	95.20	gold quality
telencephalon	UBERON:0001893	95.00	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	94.85	gold quality
temporal lobe	UBERON:0001871	94.66	gold quality
prefrontal cortex	UBERON:0000451	94.59	gold quality
CA1 field of hippocampus	UBERON:0003881	94.47	gold quality
palpebral conjunctiva	UBERON:0001812	94.31	gold quality
Brodmann (1909) area 10	UBERON:0013541	94.26	gold quality
mucosa of transverse colon	UBERON:0004991	94.15	gold quality
Brodmann (1909) area 46	UBERON:0006483	94.09	gold quality
frontal cortex	UBERON:0001870	93.97	gold quality
occipital lobe	UBERON:0002021	93.86	gold quality
orbitofrontal cortex	UBERON:0004167	93.71	gold quality
cerebral cortex	UBERON:0000956	93.47	gold quality
endometrium epithelium	UBERON:0004811	93.29	gold quality
neocortex	UBERON:0001950	93.27	gold quality
frontal pole	UBERON:0002795	93.10	gold quality
parietal lobe	UBERON:0001872	92.61	gold quality
nasal cavity epithelium	UBERON:0005384	92.51	gold quality
primary visual cortex	UBERON:0002436	92.35	gold quality
central nervous system	UBERON:0001017	92.26	gold quality
brain	UBERON:0000955	92.01	gold quality
forebrain	UBERON:0001890	91.81	gold quality
endothelial cell	CL:0000115	91.68	gold quality
cerebellar hemisphere	UBERON:0002245	91.62	gold quality
cerebellar cortex	UBERON:0002129	91.59	gold quality
right hemisphere of cerebellum	UBERON:0014890	91.56	gold quality
postcentral gyrus	UBERON:0002581	91.49	gold quality
cerebellum	UBERON:0002037	91.36	gold quality
amniotic fluid	UBERON:0000173	90.87	gold quality
cerebellar vermis	UBERON:0004720	90.47	gold quality
pancreatic ductal cell	CL:0002079	89.66	gold quality
superior frontal gyrus	UBERON:0002661	89.63	gold quality
colonic mucosa	UBERON:0000317	89.50	gold quality
paraflocculus	UBERON:0005351	89.27	gold quality
mucosa of sigmoid colon	UBERON:0004993	88.99	gold quality
epithelium of bronchus	UBERON:0002031	88.76	gold quality
bronchus	UBERON:0002185	88.74	gold quality
bronchial epithelial cell	CL:0002328	88.56	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	87.83	gold quality
entorhinal cortex	UBERON:0002728	87.66	gold quality
cardia of stomach	UBERON:0001162	86.63	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.03	gold quality
cervix squamous epithelium	UBERON:0006922	85.88	silver quality
mucosa of urinary bladder	UBERON:0001259	85.44	gold quality
transverse colon	UBERON:0001157	85.37	gold quality
buccal mucosa cell	CL:0002336	85.28	silver quality
trachea	UBERON:0003126	85.23	gold quality
stomach	UBERON:0000945	84.76	gold quality
body of stomach	UBERON:0001161	84.63	gold quality
mucosa of paranasal sinus	UBERON:0005030	84.01	gold quality
minor salivary gland	UBERON:0001830	83.96	gold quality
pharyngeal mucosa	UBERON:0000355	83.52	gold quality
duodenum	UBERON:0002114	83.50	gold quality
urethra	UBERON:0000057	83.45	gold quality
fundus of stomach	UBERON:0001160	83.18	gold quality
sperm	CL:0000019	82.94	gold quality
nasal cavity mucosa	UBERON:0001826	82.85	gold quality
male germ cell	CL:0000015	82.77	silver quality
Brodmann (1909) area 23	UBERON:0013554	82.39	gold quality
prostate gland	UBERON:0002367	82.27	gold quality
epithelium of nasopharynx	UBERON:0001951	82.15	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	7009.36
E-GEOD-135922	yes	1267.52
E-GEOD-125970	yes	24.66
E-GEOD-84465	yes	22.70
E-ANND-3	yes	15.35
E-MTAB-8410	yes	13.08

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 76 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Corpus callosum	tissue	1070.8
Spinal cord	tissue	1003.3
Medulla oblongata	tissue	773.8
Midbrain	tissue	610.2
Pons	tissue	563.6
Substantia nigra	tissue	536.9
Superior colliculi	tissue	495.7
Thalamus	tissue	479.9
Putamen	tissue	445.4
Periaqueductal gray	tissue	350.4
Locus coeruleus	tissue	328.8
Ventral forebrain	tissue	310.2
Hypothalamus	tissue	295.9
Nucleus accumbens	tissue	279.8
Postcentral gyrus	tissue	260.5
Hippocampal formation	tissue	252.9
Hippocampus	tissue	249.7	low
Septum	tissue	230.0
Cerebral cortex	tissue	156.8	medium
Occipital cortex	tissue	156.8
Stomach 1	tissue	150.9	high
Somatosensory cortex	tissue	144.7
Caudate putamen	tissue	143.6
Amygdala	tissue	137.6
Retrosplenial cortex	tissue	136.5
Motor cortex	tissue	132.4
Insular cortex	tissue	108.8
Retrosplenial and cingulate cortex	tissue	101.7
Basal ganglia	tissue	101.1	low
Prefrontal cortex	tissue	88.7
Olfactory bulb	tissue	79.3
Temporal cortex	tissue	77.7
Frontal cortex	tissue	73.3
Entorhinal cortex	tissue	72.2
Rectum	tissue	70.3	high
Cerebellum	tissue	65.6	high
Colon	tissue	63.9	high
Choroid plexus	tissue	36.6
Urinary bladder	tissue	33.8	high
Prostate	tissue	31.5	high
Small intestine	tissue	29.6	high
Duodenum	tissue	18.3	high
Cervix	tissue	8.3	not detected
Gallbladder	tissue	8.2	medium
Esophagus	tissue	6.9	not detected
Tonsil	tissue	6.3	low
Vagina	tissue	5.9	not detected
Appendix	tissue	5.8	high
Testis	tissue	4.0	not detected
Salivary gland	tissue	3.7	not detected
Breast	tissue	3.4	not detected
Smooth muscle	tissue	2.8	not detected
Lung	tissue	2.8	not detected
Epididymis	tissue	2.5	not detected
Fallopian tube	tissue	1.5	low
Endometrium 1	tissue	1.3	not detected
Kidney	tissue	1.3	not detected
Tongue	tissue	1.1
Adipose tissue	tissue	0.8	not detected
Lymph node	tissue	0.7	not detected

Brain sub-regions (HPA Brain Atlas): detected in 190; highest nTPM — Nucleus raphe obscurus (1286.3), Cerebellar white matter (1191.2), Nucleus cuneatus (1176.9), Nucleus gracilis (1121.4), Nucleus raphe pallidus (1078.4).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NCOA2

miRNA regulators (miRDB)

Targeting BCAS1 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 60 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-3150A-3P	99.76	64.44	1640
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-4802-3P	99.72	70.13	1273
HSA-MIR-1200	99.71	70.42	1838
HSA-MIR-4699-3P	99.71	70.15	3142
HSA-MIR-6892-3P	99.68	66.40	1178
HSA-MIR-3175	99.65	66.30	2031
HSA-MIR-183-3P	99.41	69.41	1598
HSA-MIR-4251	99.40	69.19	3363
HSA-MIR-3182	99.40	68.15	2454
HSA-MIR-2115-3P	99.31	69.68	2026
HSA-MIR-504-3P	99.30	67.18	1745
HSA-MIR-4667-3P	99.26	65.45	1608
HSA-MIR-10522-5P	99.26	68.50	2087
HSA-MIR-6504-3P	99.17	69.31	2891
HSA-MIR-10399-5P	99.17	69.87	2610

Functional genomics

gnomAD constraint: pLI 6.84e-10, LOEUF 0.855, missense Z 0.131 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000688948 — one region, missense o/e 1.03.

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Bcas1	ENSMUSG00000013523
rattus_norvegicus	Bcas1	ENSRNOG00000012906

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1924210) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 7 distinct phenotype terms.

Mouse phenotype (MP)	Records
abnormal lung morphology	1
decreased anxiety-related response	1
brain inflammation	1
abnormal axon morphology	1
decreased prepulse inhibition	1
decreased myelin sheath thickness	1
dysmyelination	1

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
BCAS1-AS1	ncRNA	124904936
CYP24A1	protein-coding	1591
MIR4756	ncRNA	100616225
PFDN4	protein-coding	5203

Protein

Protein identifiers

Breast carcinoma-amplified sequence 1 — O75363 (reviewed: O75363)

Alternative names: Amplified and overexpressed in breast cancer, Novel amplified in breast cancer 1

All UniProt accessions (10): A0A8I5KRZ2, A0A8I5KSK1, A0A8I5KUN3, A0A8I5KX57, B4DFL4, B4DHY3, G3XAF7, H0Y542, H7C1E7, O75363

UniProt curated annotations — full annotation on UniProt →

Function. Required for myelination.

Subunit / interactions. Homodimer. Interacts with DYNLL1 and DYNLL2.

Subcellular location. Cytoplasm.

Tissue specificity. Highly expressed in the brain and, more specifically, in oligodendrocytes (at protein level). Expressed in the prostate, and at lower levels in testis, intestine and colon. Overexpressed in most breast cancer cell lines and down-regulated in some colorectal tumors.

Isoforms (2)

UniProt ID	Names	Canonical?
O75363-1	1	yes
O75363-2	2, 5B

RefSeq proteins (7): NP_001303290, NP_001310276, NP_001353224, NP_001353225, NP_001353226, NP_001353227, NP_003648 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026115	NABC1	Family

UniProt features (34 total): compositionally biased region 11, modified residue 7, region of interest 5, sequence variant 5, splice variant 4, chain 1, sequence conflict 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O75363-F1	51.00	0.00

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): vesicles

Antibody reliability (HPA): IH enhanced · IF approved

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 (7)

Type	Positions
Phosphoserine	124, 192, 314, 381, 399, 552
Phosphothreonine	480

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: 119 (showing top): BROWNE_HCMV_INFECTION_30MIN_DN, BECKER_TAMOXIFEN_RESISTANCE_UP, GOZGIT_ESR1_TARGETS_DN, CHANDRAN_METASTASIS_DN, MODULE_66, GOBP_ENSHEATHMENT_OF_NEURONS, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, MODULE_48, MODULE_11, MODULE_95, CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP, MASSARWEH_TAMOXIFEN_RESISTANCE_UP, ZHENG_GLIOBLASTOMA_PLASTICITY_UP, GTATTAT_MIR3693P, MODULE_12

GO Biological Process (1): myelination (GO:0042552)

GO Cellular Component (2): cytoplasm (GO:0005737), extracellular exosome (GO:0070062)

GO top-level categories

4 GO namespaces:

Category	Terms
axon ensheathment	1
intracellular anatomical structure	1
cellular anatomical structure	1
extracellular vesicle	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 1 of 3 annotations. The rest are phylogenetic / computational / electronic (IEA).

1 experimentally-supported GO terms:

GO term	NS	Evidence
extracellular exosome	CC	high-throughput assay

Protein interactions and networks

STRING

showing 15 of 916 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BCAS1	ZNF217	O75362	824
BCAS1	QKI	Q96PU8	798
BCAS1	PLP1	P04400	750
BCAS1	ENPP6	Q6UWR7	682
BCAS1	RBPMS	Q93062	617
BCAS1	SOX10	P56693	596
BCAS1	OLIG2	Q13516	594
BCAS1	MYRF	Q9Y2G1	527
BCAS1	PDGFRA	P16234	524
BCAS1	ATN1	P54259	492
BCAS1	MBP	P02686	490
BCAS1	GPR17	Q13304	485
BCAS1	OLIG1	Q8TAK6	474
BCAS1	OPALIN	Q96PE5	448
BCAS1	CSPG4	Q6UVK1	439

IntAct

Human interaction partners of BCAS1 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

4 partners by confidence:

Partner	Interaction type	MIscore	Records
CFTR	physical association	0.370	1
GGN	association	0.350	1
DYNLL1	physical association	0.000	1
RUVBL2	physical association	0.000	1

BioGRID (20 interactions; top human partners by supporting records): ARRB2 (Affinity Capture-Western; 4 records), DYNLL1 (Affinity Capture-MS; 2 records), PRNP (Affinity Capture-MS; 2 records), CFTR (PCA), ESR2 (Affinity Capture-MS), FEN1 (Cross-Linking-MS (XL-MS)), GGN (Affinity Capture-MS), HSP90AA1 (Cross-Linking-MS (XL-MS)), PARP10 (Proximity Label-MS), PARP4 (Proximity Label-MS), PARP6 (Proximity Label-MS), RUVBL2 (Affinity Capture-MS)

Disease & clinical

Genetic variants

Variant evidence for BCAS1: 99 ClinVar records (0 pathogenic / likely pathogenic); 33 GWAS associations.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	68
Likely benign	8
Benign	6

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 28 predictions of 1,112):

Position(s)	Effect	Δscore	Sites
20:53953430–53953431	donor_loss	1.0000	4
20:53985285–53985286	donor_loss	1.0000	3
20:53985500	acceptor_gain	1.0000
20:53985501	acceptor_loss	1.0000
20:53985508	acceptor_gain	1.0000
20:53995058	acceptor_gain	1.0000
20:53995890–53995891	donor_loss	1.0000	5
20:53996051–53996052	acceptor_loss	1.0000	5
20:54058087	donor_gain	1.0000
20:54058155–54058156	acceptor_loss	1.0000	6

AlphaMissense

269 missense substitutions predicted likely pathogenic (of 4,105 scored), across 78 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
F377	8	0.853	0.951
F198	8	0.840	0.926
D567	8	0.804	0.882
D573	8	0.791	0.915
T572	6	0.872	0.941
V570	6	0.870	0.928
F290	6	0.865	0.960
M288	6	0.816	0.904
G2	6	0.798	0.931
Q571	6	0.777	0.936
M565	6	0.742	0.858
W378	6	0.668	0.819
F556	5	0.896	0.934
K558	5	0.892	0.944
K563	5	0.873	0.940
K375	5	0.858	0.902
K379	5	0.838	0.907
V575	5	0.809	0.950
K292	5	0.795	0.942
K380	5	0.759	0.822

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

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

1 prognostic cancer types:

Cancer	Prognostic	p-value
Bladder Urothelial Carcinoma (TCGA)	favorable	0.00022

Disease associations

OMIM: gene MIM:602968 | disease phenotypes:

GWAS associations

showing 30 of 33 associations:

Study	Trait	p-value
GCST006988_128	Blond vs. brown/black hair color	1e-30
GCST006075_24	Hair color	7e-27
GCST006491_19	Circulating fibroblast growth factor 23 levels	3e-24
GCST006085_63	Prostate cancer	6e-18
GCST90002404_581	Red cell distribution width	1e-17
GCST004292_27	Glomerular filtration rate (creatinine)	3e-17
GCST007916_17	Hyperuricemia	2e-16
GCST007916_18	Hyperuricemia	2e-16
GCST007918_2	Serum uric acid levels	2e-16
GCST90002403_127	Red blood cell count	3e-16
GCST007344_60	Estimated glomerular filtration rate	5e-16
GCST007919_10	Creatinine levels	9e-16
GCST003372_15	Glomerular filtration rate (creatinine)	9e-15
GCST90002392_538	Mean corpuscular volume	3e-14
GCST90002390_39	Mean corpuscular hemoglobin	2e-11
GCST004621_23	Red cell distribution width	3e-11
GCST90002397_437	Mean spheric corpuscular volume	1e-10
GCST009597_109	Multiple sclerosis	3e-10
GCST90002395_355	Mean platelet volume	3e-10
GCST005982_15	Calcium levels	1e-9
GCST90002396_465	Mean reticulocyte volume	2e-9
GCST90011900_35	Serum alkaline phosphatase levels	7e-9
GCST007324_115	Adventurousness	2e-8
GCST007833_15	Urolithiasis	3e-8
GCST006030_18	Chloride levels	4e-8
GCST007833_16	Urolithiasis	6e-8
GCST006083_8	Prostate cancer (advanced)	2e-7
GCST003790_31	Glomerular filtration rate	6e-7
GCST004001_7	Bipolar disorder or attention deficit hyperactivity disorder	8e-7
GCST002938_17	Copper levels	2e-6

EFO canonical traits (from GWAS)

10 canonical traits:

EFO ID	Trait name
EFO:0009188	Red cell distribution width
EFO:0004838	calcium measurement
EFO:0003924	hair color
EFO:0008579	risk-taking behaviour
EFO:0009104	hyperuricemia
EFO:0004761	uric acid measurement
EFO:0004527	mean corpuscular hemoglobin
EFO:0010701	mean reticulocyte volume
EFO:0004305	erythrocyte count
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects methylation	3
Benzo(a)pyrene	affects methylation, decreases expression, increases methylation	3
Calcitriol	increases expression, affects cotreatment	2
Estradiol	affects cotreatment, increases expression, decreases expression	2
Valproic Acid	decreases methylation, increases expression	2
Aflatoxin B1	increases methylation, decreases expression	2
mivebresib	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
butyraldehyde	decreases expression	1
ferrous chloride	increases expression	1
pentanal	decreases expression	1
abrine	decreases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases expression, affects cotreatment	1
incobotulinumtoxinA	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Acetaminophen	decreases expression	1
Cadmium	decreases expression	1
Silicon Dioxide	decreases expression	1
Smoke	decreases expression	1
Testosterone	affects cotreatment, increases expression	1
Tetrachlorodibenzodioxin	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	affects expression	1
Metribolone	increases expression	1
Cyclosporine	increases expression, increases methylation	1
Cadmium Chloride	increases expression	1
Okadaic Acid	increases expression	1
Copper Sulfate	decreases expression	1
Raloxifene Hydrochloride	affects cotreatment, increases expression	1
Vitamin K 3	affects expression	1

Clinical trials (associated diseases)

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