DBNDD1

Summary

DBNDD1 (dysbindin domain containing 1, HGNC:28455) is a protein-coding gene on chromosome 16q24.3, encoding Dysbindin domain-containing protein 1 (Q9H9R9).

Predicted to be involved in regulation of signal transduction. Predicted to be located in cytoplasm.

Source: NCBI Gene 79007 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 39 total
• MANE Select transcript: NM_001042610

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28455
Approved symbol	DBNDD1
Name	dysbindin domain containing 1
Location	16q24.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC3101, FLJ12582
Ensembl gene	ENSG00000003249
Ensembl biotype	protein_coding
OMIM	620388
Entrez	79007

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 7 protein_coding, 1 nonsense_mediated_decay, 1 TEC

ENST00000002501, ENST00000304733, ENST00000392973, ENST00000568330, ENST00000568662, ENST00000568838, ENST00000623401, ENST00000930202, ENST00000930203

RefSeq mRNA: 5 — MANE Select: NM_001042610 NM_001042610, NM_001288708, NM_001288709, NM_001371581, NM_024043

CCDS: CCDS10991, CCDS42223, CCDS73931

Canonical transcript exons

ENST00000002501 — 4 exons

Exon	Start	End
ENSE00001188340	90019311	90019456
ENSE00003580754	90008784	90008924
ENSE00003633821	90009284	90009430
ENSE00003897420	90004871	90006492

Expression profiles

Bgee: expression breadth ubiquitous, 188 present calls, max score 95.94.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.3126 / max 182.9177, expressed in 1291 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
158668	8.4738	1111
158670	2.0724	700
158669	0.6264	368
158667	0.1148	69
158666	0.0251	7

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right frontal lobe	UBERON:0002810	95.94	gold quality
anterior cingulate cortex	UBERON:0009835	94.68	gold quality
cingulate cortex	UBERON:0003027	94.51	gold quality
prefrontal cortex	UBERON:0000451	93.17	gold quality
cortical plate	UBERON:0005343	92.73	gold quality
Brodmann (1909) area 9	UBERON:0013540	92.12	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	91.93	gold quality
hindlimb stylopod muscle	UBERON:0004252	91.85	gold quality
right hemisphere of cerebellum	UBERON:0014890	91.85	gold quality
amygdala	UBERON:0001876	91.01	gold quality
neocortex	UBERON:0001950	91.00	gold quality
frontal cortex	UBERON:0001870	90.76	gold quality
lower esophagus mucosa	UBERON:0035834	90.65	gold quality
cerebellar hemisphere	UBERON:0002245	90.24	gold quality
cerebellar cortex	UBERON:0002129	90.14	gold quality
gastrocnemius	UBERON:0001388	89.85	gold quality
caudate nucleus	UBERON:0001873	88.40	gold quality
cerebral cortex	UBERON:0000956	88.32	gold quality
muscle of leg	UBERON:0001383	88.09	gold quality
cerebellum	UBERON:0002037	88.00	gold quality
ganglionic eminence	UBERON:0004023	87.96	gold quality
telencephalon	UBERON:0001893	87.05	gold quality
putamen	UBERON:0001874	86.76	gold quality
nucleus accumbens	UBERON:0001882	86.76	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	86.26	gold quality
esophagus mucosa	UBERON:0002469	86.11	gold quality
forebrain	UBERON:0001890	85.68	gold quality
brain	UBERON:0000955	85.30	gold quality
hypothalamus	UBERON:0001898	85.05	gold quality
temporal lobe	UBERON:0001871	84.57	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.48

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

40 targeting DBNDD1, 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-4283	100.00	66.42	2097
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-636	99.80	69.58	1500
HSA-MIR-378G	99.71	64.90	1106
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-4753-5P	99.54	68.51	1356
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-4761-5P	99.51	66.69	804
HSA-MIR-4519	99.48	66.10	859
HSA-MIR-2392	99.43	67.50	708
HSA-MIR-5695	99.41	67.48	1047
HSA-MIR-3978	99.24	68.39	2201
HSA-MIR-7974	99.24	65.48	1137
HSA-MIR-361-3P	99.19	66.45	1381
HSA-MIR-3199	99.17	65.19	696
HSA-MIR-8052	99.17	65.01	719
HSA-MIR-1286	99.09	66.23	1046
HSA-MIR-3619-5P	99.00	68.87	2308
HSA-MIR-2355-5P	98.83	65.51	1589
HSA-MIR-214-3P	98.71	68.12	2128
HSA-MIR-761	98.71	68.07	2051
HSA-MIR-4646-3P	98.65	66.98	693
HSA-MIR-4299	98.28	66.96	850
HSA-MIR-4303	98.01	68.13	2304

Literature-anchored findings (GeneRIF, showing 3)

• Our results therefore support involvement of the dysbindin gene in cognitive function (PMID:19077176)
• TRIM32 is a widely expressed ubiquitin ligase and binds and ubiquitinates dysbindin. (PMID:19349376)
• Backbone and side chain resonance assignment of the intrinsically disordered human DBNDD1 protein. (PMID:35474152)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	dbndd1	ENSDARG00000090108
mus_musculus	Dbndd1	ENSMUSG00000031970
rattus_norvegicus	Dbndd1	ENSRNOG00000026974
drosophila_melanogaster	Dysb	FBGN0036819
caenorhabditis_elegans	dsbn-1	WBGENE00013697

Paralogs (2): DTNBP1 (ENSG00000047579), DBNDD2 (ENSG00000244274)

Protein

Protein identifiers

Dysbindin domain-containing protein 1 — Q9H9R9 (reviewed: Q9H9R9)

All UniProt accessions (4): Q9H9R9, D3DX86, H3BLZ2, H3BS76

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the dysbindin family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9H9R9-1	1	yes
Q9H9R9-2	2
Q9H9R9-3	3

RefSeq proteins (5): NP_001036075, NP_001275637, NP_001275638, NP_001358510, NP_076948 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007531	Dysbindin	Family

Pfam: PF04440

UniProt features (9 total): region of interest 2, modified residue 2, splice variant 2, chain 1, compositionally biased region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H9R9-F1	61.46	0.04

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): 95, 119

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 82 (showing top): GCANCTGNY_MYOD_Q6, CAGCTG_AP4_Q5, MODULE_503, NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON, MODULE_195, MODULE_147, MODULE_356, AAGCACA_MIR218, STEIN_ESRRA_TARGETS_DN, ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP, BENPORATH_ES_1, MIKKELSEN_MCV6_HCP_WITH_H3K27ME3, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, DELACROIX_RARG_BOUND_MEF, BONOME_OVARIAN_CANCER_SURVIVAL_SUBOPTIMAL_DEBULKING

GO Biological Process (1): regulation of signal transduction (GO:0009966)

GO Molecular Function (0):

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
signal transduction	1
regulation of cell communication	1
regulation of signaling	1
regulation of response to stimulus	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

442 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DBNDD1	DEF8	Q6ZN54	668
DBNDD1	DTNB	O60941	598
DBNDD1	SPATA33	Q96N06	557
DBNDD1	SPIRE2	Q8WWL2	527
DBNDD1	FANCA	O15360	505
DBNDD1	VPS9D1	Q9Y2B5	503
DBNDD1	DBNDD2	Q9BQY9	491
DBNDD1	CDK10	Q15131	481
DBNDD1	SPATA2L	Q8IUW3	479
DBNDD1	ZNF276	Q8N554	460
DBNDD1	TCF25	Q9BQ70	452
DBNDD1	DNAL4	O96015	442
DBNDD1	DRC4	O95995	429
DBNDD1	MNS1	Q8NEH6	420
DBNDD1	CPNE7	Q9UBL6	408

IntAct

3 interactions, top by confidence:

A	B	Type	Score
CSNK1D	TMEM131L	psi-mi:“MI:0914”(association)	0.350
DBNDD1	CSNK1A1	psi-mi:“MI:0914”(association)	0.350

BioGRID (4): CSNK1E (Affinity Capture-MS), CSNK1A1 (Affinity Capture-MS), CSNK1D (Affinity Capture-MS), DBNDD1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0U1RRK4, A0A1W2PPE3, A0A1W2PR82, A0A2Z4LIS9, A2VE02, A4D1S0, A5PKC7, A5PL33, A6H7B4, A6NEL2, A6QP24, A6QPM6, A8MTW9, A8MYA2, D3ZAQ5, D4AAA5, E7EW31, O75474, O75638, O89113, O94850, P0C7X2, P14652, P50617, P70339, Q2KIS6, Q3UN58, Q5JPB2, Q5VZ46, Q6GQX2, Q6NZ36, Q6ZSJ8, Q6ZW13, Q76NI1, Q7TNS8, Q80TS7, Q86UU5, Q8IWN7, Q8N6K4, Q8N944

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

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
TRIM32	“down-regulates quantity by destabilization”	DBNDD1	ubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	35
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

691 predictions. Top by Δscore:

Variant	Effect	Δscore
16:90008779:CTCAC:C	donor_loss	1.0000
16:90008780:TCA:T	donor_loss	1.0000
16:90008782:A:AT	donor_loss	1.0000
16:90008783:C:CA	donor_loss	1.0000
16:90008783:CCTG:C	donor_gain	1.0000
16:90008920:AGGCT:A	acceptor_gain	1.0000
16:90008921:GGCT:G	acceptor_gain	1.0000
16:90008923:CT:C	acceptor_gain	1.0000
16:90008924:TCTGA:T	acceptor_loss	1.0000
16:90008925:C:CC	acceptor_gain	1.0000
16:90008925:CTG:C	acceptor_loss	1.0000
16:90008926:T:A	acceptor_loss	1.0000
16:90009282:ACG:A	donor_gain	1.0000
16:90009283:CGC:C	donor_gain	1.0000
16:90009283:CGCCT:C	donor_gain	1.0000
16:90019306:CTCA:C	donor_loss	1.0000
16:90019307:TCA:T	donor_loss	1.0000
16:90019308:CACC:C	donor_loss	1.0000
16:90019309:A:AC	donor_gain	1.0000
16:90019309:ACCT:A	donor_gain	1.0000
16:90019310:C:CC	donor_gain	1.0000
16:90019310:C:CT	donor_loss	1.0000
16:90019310:CCT:C	donor_gain	1.0000
16:90019310:CCTC:C	donor_gain	1.0000
16:90008782:A:AC	donor_gain	0.9900
16:90008783:C:CC	donor_gain	0.9900
16:90008899:C:CT	acceptor_gain	0.9900
16:90008922:GCTCT:G	acceptor_gain	0.9900
16:90009282:A:AC	donor_gain	0.9900
16:90009282:ACGC:A	donor_gain	0.9900

AlphaMissense

1016 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:90008827:A:C	F92L	0.997
16:90008827:A:T	F92L	0.997
16:90008829:A:G	F92L	0.997
16:90008887:G:C	F72L	0.997
16:90008887:G:T	F72L	0.997
16:90008889:A:G	F72L	0.997
16:90008911:G:C	S64R	0.997
16:90008911:G:T	S64R	0.997
16:90008913:T:G	S64R	0.997
16:90008873:A:G	L77P	0.996
16:90008864:A:G	L80P	0.994
16:90008882:A:G	L74P	0.994
16:90008828:A:G	F92S	0.993
16:90008828:A:C	F92C	0.992
16:90008888:A:G	F72S	0.992
16:90008885:T:A	D73V	0.990
16:90008900:A:G	L68P	0.990
16:90008840:A:G	L88P	0.989
16:90008896:C:A	E69D	0.989
16:90008896:C:G	E69D	0.989
16:90008897:T:A	E69V	0.989
16:90008909:A:T	V65D	0.989
16:90008864:A:T	L80H	0.987
16:90008885:T:C	D73G	0.987
16:90008885:T:G	D73A	0.987
16:90008898:C:T	E69K	0.987
16:90008894:A:T	V70D	0.985
16:90008849:T:A	D85V	0.983
16:90008879:A:G	L75P	0.983
16:90008884:G:C	D73E	0.982

dbSNP variants (sampled 300 via entrez): RS1000362619 (16:90011815 G>A), RS1000490566 (16:90005359 G>T), RS1000530300 (16:90005563 G>A), RS1000684387 (16:90010897 GTCTA>G), RS1000816639 (16:90011987 C>T), RS1001057600 (16:90019950 GGGGAT>G), RS1001141217 (16:90019668 C>T), RS1001577333 (16:90019125 G>A), RS1001629596 (16:90018901 G>A), RS1001672603 (16:90020215 G>C), RS1001702543 (16:90006806 TC>T,TCC), RS1001784050 (16:90008024 C>T), RS1001813807 (16:90010553 G>T), RS1001851793 (16:90015264 A>G), RS1002185807 (16:90015914 TTAGA>T)

Disease associations

OMIM: gene MIM:620388 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST005897_4	Low tan response	0.000000e+00
GCST006988_110	Blond vs. brown/black hair color	5.000000e-08
GCST010703_280	Brain morphology (MOSTest)	2.000000e-15
GCST90020028_1507	Hip circumference adjusted for BMI	3.000000e-10
GCST90020029_814	Waist circumference adjusted for body mass index	7.000000e-10

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004279	suntan
EFO:0003924	hair color
EFO:0004346	neuroimaging measurement
EFO:0008039	BMI-adjusted hip circumference
EFO:0007789	BMI-adjusted waist circumference

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
Benzo(a)pyrene	affects methylation, increases expression	3
Air Pollutants	decreases expression, increases abundance, increases expression	2
Estradiol	affects cotreatment, decreases expression, increases expression	2
Smoke	increases abundance, increases expression, decreases expression	2
Aflatoxin B1	affects expression, increases expression	2
aristolochic acid I	decreases expression	1
FR900359	decreases phosphorylation	1
methyleugenol	increases expression	1
lead acetate	decreases expression	1
sodium arsenite	decreases expression, increases abundance	1
perfluorooctanoic acid	increases expression	1
di-n-butylphosphoric acid	affects expression	1
ICG 001	increases expression	1
abrine	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
(+)-JQ1 compound	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Sunitinib	decreases expression	1
Amiodarone	increases expression	1
Arsenic	decreases expression, increases abundance	1
Calcitriol	increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Copper	increases expression, affects cotreatment	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Mustard Gas	increases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1

Clinical trials (associated diseases)

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