BSDC1

Summary

BSDC1 (BSD domain containing 1, HGNC:25501) is a protein-coding gene on chromosome 1p35.1, encoding BSD domain-containing protein 1 (Q9NW68).

Predicted to be active in cytoplasm.

Source: NCBI Gene 55108 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 76 total
• MANE Select transcript: NM_018045

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25501
Approved symbol	BSDC1
Name	BSD domain containing 1
Location	1p35.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10276, RP4-811H24.7
Ensembl gene	ENSG00000160058
Ensembl biotype	protein_coding
OMIM	617518
Entrez	55108

Gene structure

Transcript identifiers

Ensembl transcripts: 35 — 26 protein_coding, 5 retained_intron, 3 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000341071, ENST00000373520, ENST00000419121, ENST00000444377, ENST00000446293, ENST00000455895, ENST00000463967, ENST00000474414, ENST00000526031, ENST00000527163, ENST00000527513, ENST00000530485, ENST00000530753, ENST00000530876, ENST00000531222, ENST00000533084, ENST00000882342, ENST00000882343, ENST00000882344, ENST00000882345, ENST00000882346, ENST00000882347, ENST00000882348, ENST00000882349, ENST00000882350, ENST00000882351, ENST00000882352, ENST00000882353, ENST00000882354, ENST00000930010, ENST00000930011, ENST00000945396, ENST00000945397, ENST00000945398, ENST00000945399

RefSeq mRNA: 5 — MANE Select: NM_018045 NM_001143888, NM_001143889, NM_001143890, NM_001300958, NM_018045

CCDS: CCDS363, CCDS44101, CCDS44102, CCDS44103, CCDS72752

Canonical transcript exons

ENST00000455895 — 11 exons

Exon	Start	End
ENSE00001750375	32383830	32383997
ENSE00001821639	32364633	32366654
ENSE00002179014	32394404	32394441
ENSE00003495160	32378215	32378283
ENSE00003502523	32381214	32381268
ENSE00003508245	32377970	32378048
ENSE00003520640	32378724	32378839
ENSE00003539250	32368447	32368550
ENSE00003581859	32394080	32394140
ENSE00003599147	32386779	32386895
ENSE00003658217	32376262	32376741

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 96.20.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.2068 / max 250.9195, expressed in 1820 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
11545	23.7021	1819
11544	0.5047	54

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	96.20	gold quality
nipple	UBERON:0002030	95.73	gold quality
trabecular bone tissue	UBERON:0002483	95.27	gold quality
ganglionic eminence	UBERON:0004023	95.19	gold quality
right adrenal gland cortex	UBERON:0035827	95.08	gold quality
left adrenal gland	UBERON:0001234	95.02	gold quality
adrenal cortex	UBERON:0001235	95.00	gold quality
prefrontal cortex	UBERON:0000451	94.95	gold quality
pylorus	UBERON:0001166	94.91	gold quality
left adrenal gland cortex	UBERON:0035825	94.89	gold quality
cardia of stomach	UBERON:0001162	94.87	gold quality
right adrenal gland	UBERON:0001233	94.86	gold quality
adrenal gland	UBERON:0002369	94.82	gold quality
adrenal tissue	UBERON:0018303	94.81	gold quality
left ovary	UBERON:0002119	94.33	gold quality
right frontal lobe	UBERON:0002810	94.33	gold quality
body of pancreas	UBERON:0001150	94.31	gold quality
cingulate cortex	UBERON:0003027	94.31	gold quality
anterior cingulate cortex	UBERON:0009835	94.31	gold quality
corpus callosum	UBERON:0002336	94.30	gold quality
right testis	UBERON:0004534	94.30	gold quality
ventricular zone	UBERON:0003053	94.23	gold quality
renal medulla	UBERON:0000362	94.21	gold quality
adult organism	UBERON:0007023	94.19	gold quality
cortical plate	UBERON:0005343	94.15	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	94.15	gold quality
left testis	UBERON:0004533	94.13	gold quality
right hemisphere of cerebellum	UBERON:0014890	94.05	gold quality
spinal cord	UBERON:0002240	94.03	gold quality
gall bladder	UBERON:0002110	93.96	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

124 targeting BSDC1, 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-3613-3P	100.00	76.36	7965
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4425	100.00	67.59	1049
HSA-MIR-6798-5P	100.00	65.77	699
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	bsdc1	ENSDARG00000052623
mus_musculus	Bsdc1	ENSMUSG00000040859
rattus_norvegicus	Bsdc1	ENSRNOG00000008338
caenorhabditis_elegans		WBGENE00022401

Paralogs (1): SYAP1 (ENSG00000169895)

Protein

Protein identifiers

BSD domain-containing protein 1 — Q9NW68 (reviewed: Q9NW68)

All UniProt accessions (5): Q9NW68, E9PNA9, E9PQA7, E9PS77, F8W6C6

Isoforms (9)

UniProt ID	Names	Canonical?
Q9NW68-1	1	yes
Q9NW68-2	2
Q9NW68-3	3
Q9NW68-4	4
Q9NW68-5	5
Q9NW68-6	6
Q9NW68-7	7
Q9NW68-8	8
Q9NW68-9	9

RefSeq proteins (5): NP_001137360, NP_001137361, NP_001137362, NP_001287887, NP_060515* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005607	BSD_dom	Domain
IPR035925	BSD_dom_sf	Homologous_superfamily
IPR051494	BSD_domain-containing	Family

Pfam: PF03909

UniProt features (31 total): splice variant 11, sequence conflict 7, modified residue 6, compositionally biased region 3, region of interest 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NW68-F1	62.91	0.20

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 (6): 387, 388, 418, 92, 166, 356

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 185 (showing top): MODULE_255, TTTGTAG_MIR520D, GCM_ZNF198, MODULE_317, TATTATA_MIR374, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX1_UP, ACATTCC_MIR1_MIR206, HNF4_01, TGACATY_UNKNOWN, ATF3_Q6, GCM_SUFU, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, CCCAGAG_MIR326, CTTTGTA_MIR524

GO Biological Process (0):

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

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

562 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BSDC1	KIF26B	Q2KJY2	531
BSDC1	PPP4R3B	Q5MIZ7	491
BSDC1	SHC3	Q92529	462
BSDC1	ARL2BP	Q9Y2Y0	455
BSDC1	FAM219B	Q5XKK7	451
BSDC1	SCN3B	Q9NY72	446
BSDC1	HSDL2	Q6YN16	433
BSDC1	FAM117A	Q9C073	432
BSDC1	POLR3D	P05423	428
BSDC1	LRRC42	Q9Y546	418
BSDC1	PLCB1	Q9NQ66	415
BSDC1	HPSE	Q9Y251	409
BSDC1	TMEM244	Q5VVB8	401
BSDC1	SDC1	P18827	400
BSDC1	EPYC	Q99645	396

IntAct

27 interactions, top by confidence:

A	B	Type	Score
GABARAPL2	BSDC1	psi-mi:“MI:0915”(physical association)	0.560
GABARAPL1	BSDC1	psi-mi:“MI:0915”(physical association)	0.560
BSDC1	TRAPPC2L	psi-mi:“MI:0915”(physical association)	0.560
EMP3	BSDC1	psi-mi:“MI:0915”(physical association)	0.540
EMP3	BSDC1	psi-mi:“MI:2364”(proximity)	0.540
SERPINB13	TTC4	psi-mi:“MI:0914”(association)	0.530
NRAS	ESYT2	psi-mi:“MI:2364”(proximity)	0.480
Bsdc1	BSDC1	psi-mi:“MI:0915”(physical association)	0.400
BSDC1	Klc1	psi-mi:“MI:0915”(physical association)	0.400
Klc2	BSDC1	psi-mi:“MI:0915”(physical association)	0.400
BSDC1	HOXA1	psi-mi:“MI:0915”(physical association)	0.370
hspa1a_hspa1b_human-1	SHTN1	psi-mi:“MI:0914”(association)	0.350
TMEM216	SNAP23	psi-mi:“MI:2364”(proximity)	0.270
KRAS	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
HRAS	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
FHIP2A	MED19	psi-mi:“MI:2364”(proximity)	0.270
FHIP2B	VWA8	psi-mi:“MI:2364”(proximity)	0.270
GABARAPL2	BSDC1	psi-mi:“MI:0915”(physical association)	0.000
TRAPPC2L	BSDC1	psi-mi:“MI:0915”(physical association)	0.000
GABARAPL1	BSDC1	psi-mi:“MI:0915”(physical association)	0.000
	BSDC1	psi-mi:“MI:0915”(physical association)	0.000
PHC2	BSDC1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (38): BSDC1 (Proximity Label-MS), BSDC1 (Affinity Capture-MS), BSDC1 (Proximity Label-MS), BSDC1 (Proximity Label-MS), BSDC1 (Proximity Label-MS), BSDC1 (Proximity Label-MS), BSDC1 (Proximity Label-MS), BSDC1 (Two-hybrid), BSDC1 (Two-hybrid), BSDC1 (Two-hybrid), TRAPPC2L (Two-hybrid), BSDC1 (Proximity Label-MS), BSDC1 (Proximity Label-MS), BSDC1 (Proximity Label-MS), BSDC1 (Proximity Label-MS)

ESM2 similar proteins: A0JNJ3, A0M8T5, A0PJT0, A2BIJ3, D3ZTQ1, O35867, O94876, P42566, P42567, P97578, Q00PJ1, Q02225, Q09YI1, Q09YK4, Q09YM8, Q16643, Q2IBF8, Q2QL82, Q2QLA2, Q2QLG9, Q2T9N1, Q3SX22, Q3UQU0, Q3USH5, Q5BJ78, Q5RDH2, Q5T1M5, Q5U3K5, Q5ZIK6, Q68EF0, Q69ZZ6, Q6INU2, Q6NTW1, Q6P9Q6, Q6TYB5, Q6ZPJ0, Q80Y55, Q8IWB9, Q8IWE2, Q8N0X7

Diamond homologs: A2BIJ3, Q3SX22, Q5BJ78, Q5ZIK6, Q6INU2, Q6NTW1, Q80Y55, Q9NW68, P54858

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	60
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1995 predictions. Top by Δscore:

Variant	Effect	Δscore
1:32368443:TCA:T	donor_loss	1.0000
1:32368444:CAC:C	donor_loss	1.0000
1:32368446:C:CA	donor_loss	1.0000
1:32376737:CTCCT:C	acceptor_gain	1.0000
1:32376738:TCCT:T	acceptor_gain	1.0000
1:32376739:CCTC:C	acceptor_gain	1.0000
1:32376742:C:CC	acceptor_gain	1.0000
1:32377965:CTTA:C	donor_loss	1.0000
1:32377967:TA:T	donor_loss	1.0000
1:32377968:A:C	donor_loss	1.0000
1:32377968:ACCTT:A	donor_gain	1.0000
1:32377969:CC:C	donor_loss	1.0000
1:32377969:CCTTC:C	donor_gain	1.0000
1:32377972:T:A	donor_gain	1.0000
1:32378046:CTC:C	acceptor_gain	1.0000
1:32378053:A:AC	acceptor_gain	1.0000
1:32378053:A:C	acceptor_gain	1.0000
1:32378055:G:C	acceptor_gain	1.0000
1:32378055:G:GC	acceptor_gain	1.0000
1:32378723:CCAT:C	donor_gain	1.0000
1:32378837:GCCC:G	acceptor_loss	1.0000
1:32378839:CCTG:C	acceptor_loss	1.0000
1:32378840:C:A	acceptor_loss	1.0000
1:32378840:C:CC	acceptor_gain	1.0000
1:32378841:T:C	acceptor_loss	1.0000
1:32381213:CCAT:C	donor_gain	1.0000
1:32386771:GTACT:G	donor_loss	1.0000
1:32386773:A:AC	donor_gain	1.0000
1:32386773:AC:A	donor_loss	1.0000
1:32386774:C:CC	donor_gain	1.0000

AlphaMissense

2793 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:32378253:A:G	W187R	1.000
1:32378253:A:T	W187R	1.000
1:32378255:A:G	F186S	1.000
1:32378270:A:T	V181D	1.000
1:32381232:A:C	Y132D	1.000
1:32386852:A:G	F39S	1.000
1:32386861:A:G	L36P	1.000
1:32368524:A:G	W395R	0.999
1:32368524:A:T	W395R	0.999
1:32378244:A:C	Y190D	0.999
1:32378246:C:G	R189P	0.999
1:32378254:G:C	F186L	0.999
1:32378254:G:T	F186L	0.999
1:32378256:A:G	F186L	0.999
1:32378282:A:T	V177D	0.999
1:32381232:A:T	Y132N	0.999
1:32381252:A:G	L125P	0.999
1:32386804:G:T	A55D	0.999
1:32386805:C:G	A55P	0.999
1:32386816:A:T	I51N	0.999
1:32386864:T:G	D35A	0.999
1:32368522:C:A	W395C	0.998
1:32368522:C:G	W395C	0.998
1:32378251:C:A	W187C	0.998
1:32378251:C:G	W187C	0.998
1:32378252:C:G	W187S	0.998
1:32378255:A:C	F186C	0.998
1:32378273:G:T	A180D	0.998
1:32381231:T:G	Y132S	0.998
1:32381232:A:G	Y132H	0.998

dbSNP variants (sampled 300 via entrez): RS1000111835 (1:32365024 C>G,T), RS1000214902 (1:32380138 G>A), RS1000333514 (1:32371217 A>C), RS1000365399 (1:32389161 A>G), RS1000540497 (1:32385599 C>A,T), RS1000547561 (1:32378903 G>A), RS1000756984 (1:32372972 G>A), RS1000885414 (1:32395883 A>G), RS1000896062 (1:32384583 C>T), RS1000921759 (1:32390772 G>A,C), RS1000947624 (1:32377749 T>C), RS1001051466 (1:32379111 TG>T), RS1001264637 (1:32384238 G>C), RS1001266898 (1:32382013 G>A), RS1001422779 (1:32375877 G>A)

Disease associations

OMIM: gene MIM:617518 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST008152_180	Weight	8.000000e-06
GCST008758_22	Pre-treatment viral load in HIV-1 infection	4.000000e-16
GCST011742_40	Triglyceride levels in HIV infection	9.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004338	body weight
EFO:0010125	viral load
EFO:0004530	triglyceride measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects cotreatment, increases abundance, increases expression	2
cobaltous chloride	increases expression	2
Methyl Methanesulfonate	increases expression	2
Valproic Acid	affects expression, decreases expression	2
FR900359	affects phosphorylation	1
alpha-pinene	affects cotreatment, decreases expression, increases abundance	1
butyraldehyde	decreases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, decreases expression	1
coumarin	increases phosphorylation	1
methacrylaldehyde	decreases expression, increases abundance, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
K 7174	increases expression	1
ICG 001	increases expression	1
abrine	increases expression	1
Grape Seed Proanthocyanidins	decreases expression, affects cotreatment	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Bortezomib	increases expression	1
Acrolein	affects cotreatment, decreases expression, increases abundance	1
Air Pollutants	affects cotreatment, decreases expression, increases abundance	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Cadmium	increases abundance, increases expression	1
Caffeine	increases phosphorylation	1
Catechin	affects cotreatment, decreases expression	1
Coumestrol	affects cotreatment, decreases expression	1
Dactinomycin	increases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Enzyme Inhibitors	increases O-linked glycosylation, decreases activity	1
Estradiol	decreases expression	1
Ethyl Methanesulfonate	increases expression	1

Clinical trials (associated diseases)

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