DBNDD2

Summary

DBNDD2 (dysbindin domain containing 2, HGNC:15881) is a protein-coding gene on chromosome 20q13.12, encoding Dysbindin domain-containing protein 2 (Q9BQY9). May modulate the activity of casein kinase-1.

Predicted to enable ATPase binding activity. Involved in negative regulation of protein kinase activity. Predicted to be located in cytoplasm. Predicted to be active in endoplasmic reticulum and lysosome.

Source: NCBI Gene 55861 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 54 total
• MANE Select transcript: NM_001048225

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15881
Approved symbol	DBNDD2
Name	dysbindin domain containing 2
Location	20q13.12
Locus type	gene with protein product
Status	Approved
Aliases	HSMNP1
Ensembl gene	ENSG00000244274
Ensembl biotype	protein_coding
OMIM	611453
Entrez	55861

Gene structure

Transcript identifiers

Ensembl transcripts: 29 — 29 protein_coding

ENST00000357275, ENST00000360981, ENST00000372710, ENST00000372712, ENST00000372717, ENST00000372720, ENST00000372722, ENST00000372723, ENST00000443296, ENST00000867428, ENST00000867429, ENST00000867430, ENST00000867431, ENST00000867432, ENST00000867433, ENST00000867434, ENST00000867435, ENST00000867436, ENST00000867437, ENST00000867438, ENST00000867439, ENST00000867440, ENST00000867441, ENST00000965263, ENST00000965264, ENST00000965265, ENST00000965266, ENST00000965267, ENST00000965268

RefSeq mRNA: 9 — MANE Select: NM_001048225 NM_001048221, NM_001048222, NM_001048223, NM_001048224, NM_001048225, NM_001048226, NM_001197139, NM_001197140, NM_018478

CCDS: CCDS42880, CCDS42881, CCDS56193

Canonical transcript exons

ENST00000372710 — 3 exons

Exon	Start	End
ENSE00001424144	45408289	45408606
ENSE00003475742	45408801	45408938
ENSE00003921227	45409932	45410607

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 99.80.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.2965 / max 1510.3917, expressed in 1737 samples.

FANTOM5 promoters (19 alternative TSS)

Promoter ID	TPM avg	Samples expressed
184895	13.0137	1617
184907	9.9369	113
184896	4.8960	1349
184890	1.3425	582
184891	1.3023	702
184889	0.4931	306
184898	0.1447	71
209137	0.1397	67
184904	0.1384	54
184900	0.1344	64

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
C1 segment of cervical spinal cord	UBERON:0006469	99.80	gold quality
corpus callosum	UBERON:0002336	99.70	gold quality
substantia nigra	UBERON:0002038	99.57	gold quality
Ammon’s horn	UBERON:0001954	99.54	gold quality
primary visual cortex	UBERON:0002436	99.47	gold quality
putamen	UBERON:0001874	99.46	gold quality
temporal lobe	UBERON:0001871	99.33	gold quality
amygdala	UBERON:0001876	99.33	gold quality
apex of heart	UBERON:0002098	99.26	gold quality
caudate nucleus	UBERON:0001873	99.20	gold quality
heart left ventricle	UBERON:0002084	99.20	gold quality
hypothalamus	UBERON:0001898	99.14	gold quality
Brodmann (1909) area 9	UBERON:0013540	99.05	gold quality
prefrontal cortex	UBERON:0000451	99.01	gold quality
frontal cortex	UBERON:0001870	98.95	gold quality
popliteal artery	UBERON:0002250	98.93	gold quality
tibial artery	UBERON:0007610	98.93	gold quality
right frontal lobe	UBERON:0002810	98.85	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	98.84	gold quality
right coronary artery	UBERON:0001625	98.82	gold quality
nucleus accumbens	UBERON:0001882	98.81	gold quality
cerebral cortex	UBERON:0000956	98.74	gold quality
hindlimb stylopod muscle	UBERON:0004252	98.66	gold quality
right hemisphere of cerebellum	UBERON:0014890	98.66	gold quality
superior frontal gyrus	UBERON:0002661	98.63	gold quality
descending thoracic aorta	UBERON:0002345	98.59	gold quality
gastrocnemius	UBERON:0001388	98.55	gold quality
thoracic aorta	UBERON:0001515	98.54	gold quality
ascending aorta	UBERON:0001496	98.52	gold quality
cerebellum	UBERON:0002037	98.52	gold quality

Single-cell (SCXA)

Detected in 12 experiment(s), a significant marker in 12.

Experiment	Marker?	Max mean expression
E-GEOD-84465	yes	5567.44
E-HCAD-25	yes	1201.52
E-GEOD-180759	yes	470.03
E-MTAB-10287	yes	59.83
E-HCAD-10	yes	39.44
E-HCAD-1	yes	32.69
E-GEOD-135922	yes	27.21
E-HCAD-11	yes	26.52
E-MTAB-8410	yes	23.78
E-GEOD-125970	yes	16.46
E-ANND-3	yes	11.38
E-GEOD-134144	yes	11.24

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

32 targeting DBNDD2, 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-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-1260A	99.61	66.67	1098
HSA-MIR-1260B	99.61	66.67	1098
HSA-MIR-4519	99.48	66.10	859
HSA-MIR-6165	99.44	67.12	1389
HSA-MIR-6843-3P	99.26	66.42	915
HSA-MIR-6734-3P	99.15	66.27	1627
HSA-MIR-622	98.99	66.48	1050
HSA-MIR-4424	98.91	70.33	1145
HSA-MIR-2276-3P	98.76	67.75	1384
HSA-MIR-6761-5P	98.71	68.03	1504
HSA-MIR-374B-3P	98.63	68.24	1360
HSA-MIR-4722-5P	98.46	66.34	1611
HSA-MIR-1265	98.36	66.46	598
HSA-MIR-3664-3P	97.85	67.62	1452
HSA-MIR-4456	97.50	64.88	1678
HSA-MIR-1224-3P	97.24	65.92	851
HSA-MIR-3663-5P	97.01	64.84	713
HSA-MIR-6858-3P	96.37	64.41	771

Literature-anchored findings (GeneRIF, showing 2)

• CK1BP is an isoform-selective binding partner of human casein kinase-1 (PMID:16618118)
• CK1BP Reduces alpha-Synuclein Oligomerization and Aggregation Independent of Serine 129 Phosphorylation. (PMID:34831053)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch211-253b8.5	ENSDARG00000074904
mus_musculus	Dbndd2	ENSMUSG00000017734
rattus_norvegicus		ENSRNOG00000087784
drosophila_melanogaster	Dysb	FBGN0036819
caenorhabditis_elegans	dsbn-1	WBGENE00013697

Paralogs (2): DBNDD1 (ENSG00000003249), DTNBP1 (ENSG00000047579)

Protein

Protein identifiers

Dysbindin domain-containing protein 2 — Q9BQY9 (reviewed: Q9BQY9)

Alternative names: Casein kinase-1 binding protein, HSMNP1

All UniProt accessions (2): Q9BQY9, H0Y7N7

UniProt curated annotations — full annotation on UniProt →

Function. May modulate the activity of casein kinase-1. Inhibits CSNK1D autophosphorylation (in vitro).

Subunit / interactions. Monomer. Interacts with CSNK1D and CSNK1E.

Tissue specificity. Detected in brain.

Similarity. Belongs to the dysbindin family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q9BQY9-1	1	yes
Q9BQY9-2	2
Q9BQY9-3	3
Q9BQY9-4	4

RefSeq proteins (9): NP_001041686, NP_001041687, NP_001041688, NP_001041689, NP_001041690, NP_001041691, NP_001184068, NP_001184069, NP_060948 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007531	Dysbindin	Family

Pfam: PF04440

UniProt features (18 total): sequence conflict 5, splice variant 4, modified residue 4, region of interest 2, compositionally biased region 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BQY9-F1	60.09	0.03

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 (4): 217, 218, 237, 242

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 194 (showing top): WANG_CLIM2_TARGETS_UP, GOBP_REGULATION_OF_PHOSPHORYLATION, GOBP_NEGATIVE_REGULATION_OF_KINASE_ACTIVITY, GOBP_REGULATION_OF_TRANSFERASE_ACTIVITY, GOBP_NEUROGENESIS, FOXO4_01, CACCAGC_MIR138, GGGTGGRR_PAX4_03, AAAYRNCTG_UNKNOWN, CHANDRAN_METASTASIS_DN, KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP, AAACCAC_MIR140, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1, GOBP_NEGATIVE_REGULATION_OF_PHOSPHORUS_METABOLIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_MOLECULAR_FUNCTION

GO Biological Process (7): negative regulation of protein kinase activity (GO:0006469), apoptotic process (GO:0006915), regulation of signal transduction (GO:0009966), neuron projection development (GO:0031175), monoatomic ion homeostasis (GO:0050801), ERK1 and ERK2 cascade (GO:0070371), neurogenesis (GO:0022008)

GO Molecular Function (2): ATPase binding (GO:0051117), protein binding (GO:0005515)

GO Cellular Component (3): lysosome (GO:0005764), endoplasmic reticulum (GO:0005783), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
negative regulation of protein phosphorylation	1
protein kinase activity	1
negative regulation of kinase activity	1
regulation of protein kinase activity	1
programmed cell death	1
apoptotic signaling pathway	1
execution phase of apoptosis	1
signal transduction	1
regulation of cell communication	1
regulation of signaling	1
regulation of response to stimulus	1
neuron development	1
plasma membrane bounded cell projection organization	1
chemical homeostasis	1
MAPK cascade	1
nervous system development	1
cell differentiation	1
enzyme binding	1
binding	1
lytic vacuole	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

282 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DBNDD2	KITLG	P21583	670
DBNDD2	SYS1	Q8N2H4	580
DBNDD2	DBNDD1	Q9H9R9	491
DBNDD2	TMEM185B	Q9H7F4	487
DBNDD2	TMEM31	Q5JXX7	451
DBNDD2	DDX54	Q8TDD1	449
DBNDD2	DTNB	O60941	382
DBNDD2	UXT	Q9UBK9	377
DBNDD2	MANBAL	Q9NQG1	361
DBNDD2	THAP5	Q7Z6K1	357
DBNDD2	ZNF560	Q96MR9	348
DBNDD2	NOL8	Q76FK4	347
DBNDD2	TSTD1	Q8NFU3	310
DBNDD2	ZBTB34	Q8NCN2	309
DBNDD2	CCDC32	Q9BV29	308

IntAct

5 interactions, top by confidence:

A	B	Type	Score
DBNDD2	AGTR1	psi-mi:“MI:0915”(physical association)	0.370
DBNDD2	VIPR2	psi-mi:“MI:0915”(physical association)	0.370
CALCOCO2	DBNDD2	psi-mi:“MI:0915”(physical association)	0.370
DBNDD2	SFRP2	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (13): DBNDD2 (Two-hybrid), DBNDD2 (Two-hybrid), DBNDD2 (Two-hybrid), DBNDD2 (Two-hybrid), DBNDD2 (Two-hybrid), DBNDD2 (Two-hybrid), DBNDD2 (Affinity Capture-RNA), DBNDD2 (Two-hybrid), DBNDD2 (Two-hybrid), DBNDD2 (Two-hybrid), DBNDD2 (Two-hybrid), CSNK1D (Affinity Capture-Western), CSNK1E (Affinity Capture-Western)

ESM2 similar proteins: A5A752, A6NJI1, C9JUS6, C9JVW0, F8WCM5, H7C350, I3L1E1, O60393, P0DPF6, P14138, P48299, P70339, Q05AH6, Q1WG82, Q2KIS6, Q32LI1, Q3SXR2, Q3UM83, Q3UN58, Q3ZCQ2, Q5HZG9, Q5M844, Q5TGS1, Q5U2P6, Q6NUJ2, Q6P1B3, Q6PDA7, Q6UXU0, Q6UXV3, Q6ZMY3, Q6ZSR3, Q7RTU1, Q80ZG6, Q8BT88, Q8IWN7, Q8IXW0, Q8N4L8, Q8N729, Q8NEQ6, Q8TBC5

Diamond homologs: A6H7B4, Q2HJA5, Q5M831, Q5M834, Q5ZKM0, Q6DJE5, Q7ZWE6, Q91WZ8, Q96EV8, Q9BQY9, Q9CRD4, Q9CZ00, Q9H9R9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	51
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

924 predictions. Top by Δscore:

Variant	Effect	Δscore
20:45408452:A:AG	acceptor_gain	1.0000
20:45408453:C:G	acceptor_gain	1.0000
20:45408457:CA:C	acceptor_loss	1.0000
20:45408458:A:AC	acceptor_loss	1.0000
20:45408458:A:AG	acceptor_gain	1.0000
20:45408458:AG:A	acceptor_gain	1.0000
20:45408459:G:GG	acceptor_gain	1.0000
20:45408459:GG:G	acceptor_gain	1.0000
20:45408459:GGA:G	acceptor_gain	1.0000
20:45408602:GAGAC:G	donor_gain	1.0000
20:45408603:AGAC:A	donor_gain	1.0000
20:45408604:GAC:G	donor_gain	1.0000
20:45408604:GACG:G	donor_gain	1.0000
20:45408605:AC:A	donor_gain	1.0000
20:45408606:CG:C	donor_loss	1.0000
20:45408607:G:GG	donor_gain	1.0000
20:45408608:T:A	donor_loss	1.0000
20:45408799:A:AG	acceptor_gain	1.0000
20:45408800:G:GG	acceptor_gain	1.0000
20:45409930:AGG:A	acceptor_gain	1.0000
20:45409931:GGG:G	acceptor_gain	1.0000
20:45406207:GCGT:G	donor_gain	0.9900
20:45406209:GT:G	donor_gain	0.9900
20:45406211:G:GG	donor_gain	0.9900
20:45408452:ACCC:A	acceptor_gain	0.9900
20:45408457:CAGG:C	acceptor_gain	0.9900
20:45408458:AGGA:A	acceptor_gain	0.9900
20:45408459:GGAG:G	acceptor_gain	0.9900
20:45408459:GGAGC:G	acceptor_gain	0.9900
20:45408561:GA:G	donor_gain	0.9900

AlphaMissense

1700 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:45408812:A:C	S149R	0.996
20:45408814:T:A	S149R	0.996
20:45408814:T:G	S149R	0.996
20:45408531:T:C	F120L	0.991
20:45408533:C:A	F120L	0.991
20:45408533:C:G	F120L	0.991
20:45408835:T:A	N156K	0.991
20:45408835:T:G	N156K	0.991
20:45408896:T:C	F177L	0.991
20:45408898:C:A	F177L	0.991
20:45408898:C:G	F177L	0.991
20:45408826:G:A	M153I	0.990
20:45408826:G:C	M153I	0.990
20:45408826:G:T	M153I	0.990
20:45408816:T:C	I150T	0.989
20:45408816:T:A	I150N	0.988
20:45408827:G:A	E154K	0.987
20:45408840:A:T	D158V	0.987
20:45408523:G:C	R117P	0.986
20:45408825:T:G	M153R	0.986
20:45408532:T:C	F120S	0.985
20:45408816:T:G	I150S	0.985
20:45408831:T:C	V155A	0.985
20:45408822:C:T	S152F	0.984
20:45408825:T:A	M153K	0.984
20:45408828:A:G	E154G	0.984
20:45408897:T:G	F177C	0.984
20:45408534:T:C	F121L	0.983
20:45408536:C:A	F121L	0.983
20:45408536:C:G	F121L	0.983

dbSNP variants (sampled 300 via entrez): RS1000426555 (20:45410894 G>T), RS1000439674 (20:45411105 G>A,T), RS1000467575 (20:45406055 G>C), RS1000521153 (20:45405895 C>T), RS1001222018 (20:45410973 G>A), RS1001342159 (20:45405342 C>T), RS1001371240 (20:45405839 C>G), RS1002402276 (20:45410341 C>T), RS1003027577 (20:45406379 G>A,C,T), RS1003413602 (20:45407409 G>A), RS1003489365 (20:45406141 T>C), RS1003714766 (20:45406975 C>T), RS1003773843 (20:45407782 A>G), RS1004678457 (20:45406992 C>T), RS1005064550 (20:45404420 C>T)

Disease associations

OMIM: gene MIM:611453 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): breast ductal adenocarcinoma (MONDO:0005590)

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST010725_40	Malaria	1.000000e-06

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D018270	Carcinoma, Ductal, Breast	C04.557.470.200.025.232.500; C04.557.470.615.132.500; C04.588.180.390; C17.800.090.500.390

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases methylation, increases expression, affects methylation	2
Cisplatin	affects expression, decreases expression	2
beta-lapachone	increases expression	1
arsenite	affects expression	1
sodium arsenite	increases abundance, increases expression	1
butyraldehyde	increases expression	1
manganese chloride	increases abundance, increases expression	1
aflatoxin B2	increases methylation	1
pentanal	increases expression	1
azoxystrobin	decreases expression	1
deguelin	decreases expression	1
abrine	decreases expression	1
pyrachlostrobin	decreases expression	1
picoxystrobin	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Decitabine	affects expression	1
Arsenic	increases abundance, increases expression	1
Estradiol	affects cotreatment, decreases expression	1
Fluorouracil	affects response to substance	1
Lead	affects expression	1
Manganese	increases abundance, increases expression	1
Progesterone	increases expression	1
Rotenone	decreases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Triclosan	decreases expression	1
Urethane	decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	1
Cyclosporine	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT03414970	PHASE3	ACTIVE_NOT_RECRUITING	Hypofractionated Radiation Therapy After Mastectomy in Preventing Recurrence in Patients With Stage IIa-IIIa Breast Cancer
NCT00461344	PHASE2	TERMINATED	Docetaxel + Doxorubicin as Neoadjuvant Chemotherapy in Patients With Breast Cancer
NCT07499999	PHASE2	NOT_YET_RECRUITING	Randomized Double-Blind Phase II Trial of Baby Exemestane Versus Baby Tamoxifen in Post-Menopausal Women at High Risk for Breast Cancer
NCT00637364	PHASE1/PHASE2	SUSPENDED	High Intensity Focused Ultrasound Tumor Treatment for Pancreatic Cancer Pain
NCT02779855	PHASE1/PHASE2	COMPLETED	Talimogene Laherparepvec in Combination With Neoadjuvant Chemotherapy in Triple Negative Breast Cancer
NCT01753908	EARLY_PHASE1	COMPLETED	Broccoli Sprout Extract in Treating Patients With Breast Cancer
NCT01796041	EARLY_PHASE1	COMPLETED	Intraoperative Imaging of Breast Cancer With Indocyanine Green
NCT01208974	Not specified	ACTIVE_NOT_RECRUITING	Nipple-Areola Complex (NAC) Irradiation After Nipple-Sparing Mastectomy and Reconstruction
NCT01875198	Not specified	TERMINATED	Oncologic Impact of Splenectomy-omitting Radical Pancreatectomy in Well-selected Left-sided Pancreatic Cancer
NCT03543397	Not specified	UNKNOWN	MRI in Ductal Carcinoma in Situ (DCIS)
NCT03834532	Not specified	COMPLETED	Living Well After Breast Surgery