BCAP29

Summary

BCAP29 (B cell receptor associated protein 29, HGNC:24131) is a protein-coding gene on chromosome 7q22.3, encoding B-cell receptor-associated protein 29 (Q9UHQ4). May play a role in anterograde transport of membrane proteins from the endoplasmic reticulum to the Golgi.

Involved in osteoblast differentiation. Located in membrane.

Source: NCBI Gene 55973 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 14 total
• MANE Select transcript: NM_018844

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24131
Approved symbol	BCAP29
Name	B cell receptor associated protein 29
Location	7q22.3
Locus type	gene with protein product
Status	Approved
Aliases	BAP29, DKFZp686M2086
Ensembl gene	ENSG00000075790
Ensembl biotype	protein_coding
OMIM	619612
Entrez	55973

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 19 protein_coding, 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000005259, ENST00000379117, ENST00000421217, ENST00000436699, ENST00000442065, ENST00000445771, ENST00000457837, ENST00000465919, ENST00000466094, ENST00000473124, ENST00000479917, ENST00000482371, ENST00000486326, ENST00000490060, ENST00000491150, ENST00000494086, ENST00000863056, ENST00000863057, ENST00000863058, ENST00000863059, ENST00000863060, ENST00000863061, ENST00000957685, ENST00000957686, ENST00000957687

RefSeq mRNA: 9 — MANE Select: NM_018844 NM_001008405, NM_001363482, NM_001363483, NM_001371353, NM_001371354, NM_001371355, NM_001371356, NM_001371357, NM_018844

CCDS: CCDS34730, CCDS34731

Canonical transcript exons

ENST00000005259 — 8 exons

Exon	Start	End
ENSE00001707386	107618328	107620478
ENSE00001924831	107580246	107580301
ENSE00003503141	107595867	107596002
ENSE00003598828	107593955	107594105
ENSE00003784441	107583882	107583982
ENSE00003788065	107613332	107613432
ENSE00003791337	107600397	107600505
ENSE00003899231	107580759	107580864

Expression profiles

Bgee: expression breadth ubiquitous, 167 present calls, max score 98.30.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 42.8660 / max 443.1959, expressed in 1821 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
80450	42.2752	1821
80449	0.4317	224
80452	0.1361	31
80451	0.0230	5

Top tissues by expression

267 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	98.30	gold quality
smooth muscle tissue	UBERON:0001135	96.53	gold quality
right lobe of thyroid gland	UBERON:0001119	95.24	gold quality
ascending aorta	UBERON:0001496	95.17	gold quality
thoracic aorta	UBERON:0001515	95.14	gold quality
left lobe of thyroid gland	UBERON:0001120	95.02	gold quality
islet of Langerhans	UBERON:0000006	94.98	gold quality
descending thoracic aorta	UBERON:0002345	94.81	gold quality
rectum	UBERON:0001052	94.80	gold quality
left testis	UBERON:0004533	94.70	gold quality
right testis	UBERON:0004534	94.70	gold quality
right coronary artery	UBERON:0001625	94.29	gold quality
left coronary artery	UBERON:0001626	94.26	gold quality
aorta	UBERON:0000947	93.97	gold quality
cortical plate	UBERON:0005343	93.67	gold quality
adrenal tissue	UBERON:0018303	93.65	gold quality
tibial artery	UBERON:0007610	93.48	gold quality
popliteal artery	UBERON:0002250	93.47	gold quality
thyroid gland	UBERON:0002046	93.37	gold quality
right atrium auricular region	UBERON:0006631	93.18	gold quality
artery	UBERON:0001637	93.15	gold quality
endocervix	UBERON:0000458	93.06	gold quality
body of uterus	UBERON:0009853	92.92	gold quality
ectocervix	UBERON:0012249	92.76	gold quality
colonic epithelium	UBERON:0000397	92.74	gold quality
gall bladder	UBERON:0002110	92.73	gold quality
coronary artery	UBERON:0001621	92.40	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	92.26	gold quality
monocyte	CL:0000576	91.92	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	91.92	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-119	yes	18.31
E-ANND-3	yes	10.78
E-MTAB-4850	no	551.56
E-GEOD-36552	no	54.13

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

203 targeting BCAP29, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-4803	99.98	71.99	3117
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-548AN	99.97	70.91	2817

Literature-anchored findings (GeneRIF, showing 2)

• Bap29varP acts as an essential chaperone, influencing the processing and trafficking of Pgp to the cell surface. (PMID:18097552)
• we believe that in contrast to traditional gene fusions, DUS4L-BCAP29 cannot be used as a cancer biomarker. Instead, it is a fusion transcript that exists in normal physiology and that its pro-growth effect is not unique to cancer cells. (PMID:28415823)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	bcap29	ENSDARG00000016231
mus_musculus	Bcap29	ENSMUSG00000020650
rattus_norvegicus	Bcap29	ENSRNOG00000007884
drosophila_melanogaster	CG13887	FBGN0035165
caenorhabditis_elegans		WBGENE00021883

Paralogs (1): BCAP31 (ENSG00000185825)

Protein

Protein identifiers

B-cell receptor-associated protein 29 — Q9UHQ4 (reviewed: Q9UHQ4)

All UniProt accessions (11): Q9UHQ4, B7Z2L0, C9IYK6, C9JGJ9, C9JP06, C9JTE9, E9PAJ1, F8WB99, F8WDG1, H0Y7N8, H7C5E2

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in anterograde transport of membrane proteins from the endoplasmic reticulum to the Golgi. May be involved in CASP8-mediated apoptosis.

Subunit / interactions. Homodimer. Heterodimer with BCAP31. Binds CASP8 (isoform 9) as a complex containing BCAP31, BCAP29, BCL2 and/or BCL2L1. Interacts with VAMP3, VAMP1 and membrane IgD immunoglobulins. May interact with ACTG1 and non-muscle myosin II.

Subcellular location. Endoplasmic reticulum membrane.

Similarity. Belongs to the BCAP29/BCAP31 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9UHQ4-1	1	yes
Q9UHQ4-2	2

RefSeq proteins (9): NP_001008405, NP_001350411, NP_001350412, NP_001358282, NP_001358283, NP_001358284, NP_001358285, NP_001358286, NP_061332* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008417	BAP29/BAP31	Family
IPR040463	BAP29/BAP31_N	Domain
IPR041672	Bap31/Bap29_C	Domain

Pfam: PF05529, PF18035

UniProt features (17 total): topological domain 4, sequence conflict 3, transmembrane region 3, chain 1, short sequence motif 1, compositionally biased region 1, splice variant 1, helix 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
4W7Z	X-RAY DIFFRACTION	2.2
4W7Y	X-RAY DIFFRACTION	2.5
4W80	X-RAY DIFFRACTION	3.2

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UHQ4-F1	85.51	0.48

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 208 (showing top): HORIUCHI_WTAP_TARGETS_DN, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_OSTEOBLAST_DIFFERENTIATION, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_PROTEIN_LOCALIZATION_TO_ENDOPLASMIC_RETICULUM, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, WANG_LMO4_TARGETS_DN, GOBP_OSSIFICATION, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, JIANG_AGING_CEREBRAL_CORTEX_UP, ZHANG_BREAST_CANCER_PROGENITORS_UP, MODULE_48

GO Biological Process (7): osteoblast differentiation (GO:0001649), intracellular protein transport (GO:0006886), endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), apoptotic process (GO:0006915), protein localization to endoplasmic reticulum exit site (GO:0070973), protein transport (GO:0015031), vesicle-mediated transport (GO:0016192)

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

GO Cellular Component (3): endoplasmic reticulum membrane (GO:0005789), membrane (GO:0016020), endoplasmic reticulum (GO:0005783)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular protein localization	2
intracellular transport	2
cytoplasm	2
transport	2
ossification	1
cell differentiation	1
protein transport	1
intercellular transport	1
Golgi vesicle transport	1
programmed cell death	1
apoptotic signaling pathway	1
execution phase of apoptosis	1
protein localization to endoplasmic reticulum	1
establishment of protein localization	1
cellular process	1
binding	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
cellular anatomical structure	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

840 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BCAP29	DUS4L	O95620	721
BCAP29	GPR22	Q99680	644
BCAP29	COG5	Q9UP83	633
BCAP29	BCAP31	P51572	552
BCAP29	NDFIP2	Q9NV92	523
BCAP29	PDXDC1	Q6P996	512
BCAP29	TAPBP	O15533	488
BCAP29	PDIA3	P30101	486
BCAP29	NDFIP1	Q9BT67	483
BCAP29	CALR	P27797	472
BCAP29	ABCB11	O95342	469
BCAP29	ABCB1	P08183	442
BCAP29	PRKAR2B	P31323	420
BCAP29	C1QL4	Q86Z23	407
BCAP29	SEC61A1	P38378	355

IntAct

37 interactions, top by confidence:

A	B	Type	Score
BCAP31	BCAP29	psi-mi:“MI:0915”(physical association)	0.670
BCAP29	BCAP31	psi-mi:“MI:0914”(association)	0.670
BCAP29	CALCOCO2	psi-mi:“MI:0915”(physical association)	0.560
SCN3B	ABCC5	psi-mi:“MI:0914”(association)	0.530
PBXIP1	GOLIM4	psi-mi:“MI:0914”(association)	0.530
ZNF197	BCAP29	psi-mi:“MI:0915”(physical association)	0.400
SERPINA5	BCAP29	psi-mi:“MI:0915”(physical association)	0.400
ARHGEF17	BCAP29	psi-mi:“MI:0915”(physical association)	0.400
BCAP29	DRD2	psi-mi:“MI:0915”(physical association)	0.370
BCAP29	PA	psi-mi:“MI:0915”(physical association)	0.370
CREB3	BCAP29	psi-mi:“MI:0915”(physical association)	0.370
	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
ARHGAP15	PGRMC1	psi-mi:“MI:0914”(association)	0.350
BCAP31	ATL3	psi-mi:“MI:0914”(association)	0.350
COPE	ESYT2	psi-mi:“MI:0914”(association)	0.350
PGRMC1	NBAS	psi-mi:“MI:0914”(association)	0.350
TTYH1	TMEM223	psi-mi:“MI:0914”(association)	0.350
SAAL1	QSOX1	psi-mi:“MI:0914”(association)	0.350
ASPH	POTEF	psi-mi:“MI:0914”(association)	0.350
BCAP31	LIPA	psi-mi:“MI:0914”(association)	0.350
FEZ1	KCNN4	psi-mi:“MI:0914”(association)	0.350
PACC1	IPO5	psi-mi:“MI:0914”(association)	0.350
SAAL1	TMEM223	psi-mi:“MI:0914”(association)	0.350
MFSD5	ILVBL	psi-mi:“MI:0914”(association)	0.350
SLC19A2	TMEM223	psi-mi:“MI:0914”(association)	0.350
SLC27A2	RIMOC1	psi-mi:“MI:0914”(association)	0.350
SLC27A5	MEIOC	psi-mi:“MI:0914”(association)	0.350
SLC30A5	NBAS	psi-mi:“MI:0914”(association)	0.350

BioGRID (77): ATP5O (Co-fractionation), BCAP29 (Co-fractionation), BCAP29 (Co-fractionation), BCAP29 (Co-fractionation), BCAP29 (Co-fractionation), NACA2 (Co-fractionation), P4HB (Co-fractionation), RPN1 (Co-fractionation), BCAP29 (Two-hybrid), BCAP29 (Affinity Capture-MS), BCAP29 (Affinity Capture-MS), CALCOCO2 (Affinity Capture-MS), BCAP29 (Affinity Capture-RNA), BCAP29 (Affinity Capture-MS), BCAP31 (Affinity Capture-Western)

ESM2 similar proteins: A1DB12, A5JYQ9, B3NIN0, B4IAB8, B4PET6, B4QJ33, B6JWP7, F4JIN3, G5EEK9, G5EGP4, O14290, O74432, O94673, O94689, P35180, P35723, P37296, P46964, P51572, Q02328, Q02774, Q04210, Q07451, Q0WT48, Q18695, Q19555, Q28GF5, Q32KL9, Q4V7N7, Q54E04, Q54K74, Q5B905, Q5R8H3, Q5R9U7, Q61334, Q61335, Q61ZW5, Q641M3, Q6C6U9, Q6FIQ1

Diamond homologs: P51572, Q32KL9, Q5R8H3, Q5R9U7, Q61334, Q61335, Q9UHQ4, Q54K74, Q07451, O14290

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	2
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

1587 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:107580785:T:A	W5R	0.987
7:107580785:T:C	W5R	0.987
7:107594067:A:C	R102S	0.986
7:107594067:A:T	R102S	0.986
7:107593957:G:C	A66P	0.984
7:107594101:T:A	W114R	0.984
7:107594101:T:C	W114R	0.984
7:107594084:G:A	G108E	0.983
7:107594072:T:C	L104P	0.981
7:107594053:T:C	F98L	0.979
7:107594055:T:A	F98L	0.979
7:107594055:T:G	F98L	0.979
7:107583943:T:C	F52L	0.976
7:107583945:C:A	F52L	0.976
7:107583945:C:G	F52L	0.976
7:107580839:T:C	C23R	0.975
7:107583971:T:A	V61D	0.975
7:107580787:G:C	W5C	0.971
7:107580787:G:T	W5C	0.971
7:107594066:G:C	R102T	0.971
7:107594083:G:A	G108R	0.971
7:107594083:G:C	G108R	0.971
7:107583883:T:A	W32R	0.969
7:107583883:T:C	W32R	0.969
7:107594066:G:T	R102I	0.967
7:107580821:G:A	G17R	0.964
7:107580821:G:C	G17R	0.964
7:107594070:T:A	N103K	0.962
7:107594070:T:G	N103K	0.962
7:107594093:T:C	L111P	0.962

dbSNP variants (sampled 300 via entrez): RS1000136549 (7:107583401 T>C), RS1000219322 (7:107591897 T>C), RS1000241756 (7:107611299 G>A), RS1000297434 (7:107583157 G>A), RS1000380425 (7:107597351 T>C), RS1000440130 (7:107604614 C>A,T), RS1000463060 (7:107618245 G>C), RS1000554981 (7:107592965 T>G), RS1000555638 (7:107599934 C>G,T), RS1000611368 (7:107599720 A>G), RS1000649148 (7:107597577 T>G), RS1000661160 (7:107599744 C>A,G), RS1000798016 (7:107593614 G>A), RS1000858358 (7:107622864 C>A,G,T), RS1000883381 (7:107605668 G>A)

Disease associations

OMIM: gene MIM:619612 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): primary amenorrhea (MONDO:1060208)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST005194_212	Coronary artery disease	4.000000e-08
GCST005195_20	Coronary artery disease	5.000000e-08
GCST005196_148	Coronary artery disease	6.000000e-06
GCST005956_26	Waist-to-hip ratio adjusted for BMI	2.000000e-08
GCST005962_48	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	2.000000e-06
GCST010479_5	Coronary artery disease	5.000000e-08

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, decreases methylation	5
Air Pollutants	affects expression, increases abundance, decreases expression	2
Particulate Matter	decreases expression, increases abundance	2
FR900359	decreases phosphorylation	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
cinnamaldehyde	increases expression	1
beta-lapachone	increases expression, decreases expression	1
beta-methylcholine	affects expression	1
pinosylvin	decreases expression	1
monomethylarsonous acid	decreases expression	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
jinfukang	decreases expression	1
gardiquimod	increases expression, decreases reaction	1
Sunitinib	decreases expression	1
Zoledronic Acid	affects cotreatment, increases expression	1
Fluvastatin	affects cotreatment, increases expression	1
Vehicle Emissions	decreases expression, increases abundance	1
Benzo(a)pyrene	affects methylation	1
Calcitriol	increases expression, affects cotreatment	1
Doxorubicin	decreases expression	1
Hydrogen Peroxide	affects expression	1
Methyl Methanesulfonate	decreases expression	1
Ozone	affects expression, increases abundance	1
Silicon Dioxide	increases expression	1
Dihydrotestosterone	increases expression	1
Sulindac	increases expression	1
Testosterone	affects cotreatment, increases expression	1
Tretinoin	increases expression	1

Clinical trials (associated diseases)

1 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT07164248	Not specified	COMPLETED	Evaluation of Bone Mineral Density Indications and Outcomes in Female Adolescents: Implications for Early Detection of Osteopenia/Osteoporosis and Gynecologic Practice