RSBN1L

Summary

RSBN1L (round spermatid basic protein 1 like, HGNC:24765) is a protein-coding gene on chromosome 7q11.23, encoding Lysine-specific demethylase RSBN1L (Q6PCB5). Lysine-specific demethylase that specifically demethylates methylated lysine residues of proteins.

Predicted to enable dioxygenase activity and metal ion binding activity. Predicted to be active in nucleus.

Source: NCBI Gene 222194 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 94 total
• MANE Select transcript: NM_198467

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24765
Approved symbol	RSBN1L
Name	round spermatid basic protein 1 like
Location	7q11.23
Locus type	gene with protein product
Status	Approved
Aliases	FLJ42526, FLJ45813, MGC71764
Ensembl gene	ENSG00000187257
Ensembl biotype	protein_coding
Entrez	222194

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 5 protein_coding, 2 retained_intron

ENST00000334955, ENST00000441514, ENST00000445288, ENST00000445512, ENST00000462800, ENST00000468035, ENST00000935350

RefSeq mRNA: 1 — MANE Select: NM_198467 NM_198467

CCDS: CCDS43607

Canonical transcript exons

ENST00000334955 — 8 exons

Exon	Start	End
ENSE00001332942	77696459	77697055
ENSE00001376749	77773147	77773314
ENSE00001383884	77778338	77778446
ENSE00001388626	77778530	77783022
ENSE00003472491	77765495	77765632
ENSE00003497082	77768661	77768803
ENSE00003529948	77736410	77736526
ENSE00003680399	77749424	77750064

Expression profiles

Bgee: expression breadth ubiquitous, 252 present calls, max score 95.65.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.2487 / max 229.6578, expressed in 1784 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
79218	16.2487	1784

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tendon of biceps brachii	UBERON:0008188	95.65	silver quality
calcaneal tendon	UBERON:0003701	93.39	gold quality
tendon	UBERON:0000043	92.97	gold quality
epithelial cell of pancreas	CL:0000083	91.24	gold quality
pancreatic ductal cell	CL:0002079	90.53	silver quality
buccal mucosa cell	CL:0002336	90.41	silver quality
nasal cavity epithelium	UBERON:0005384	90.25	silver quality
cortical plate	UBERON:0005343	89.27	gold quality
oocyte	CL:0000023	88.45	gold quality
endothelial cell	CL:0000115	88.39	gold quality
corpus callosum	UBERON:0002336	88.01	gold quality
pigmented layer of retina	UBERON:0001782	87.93	gold quality
colonic epithelium	UBERON:0000397	87.91	gold quality
myocardium	UBERON:0002349	87.82	silver quality
leukocyte	CL:0000738	87.76	gold quality
blood	UBERON:0000178	87.74	gold quality
monocyte	CL:0000576	87.70	gold quality
ganglionic eminence	UBERON:0004023	87.23	gold quality
cauda epididymis	UBERON:0004360	87.05	gold quality
bronchial epithelial cell	CL:0002328	86.95	gold quality
adrenal tissue	UBERON:0018303	86.80	gold quality
bronchus	UBERON:0002185	86.65	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.53	gold quality
lymph node	UBERON:0000029	86.39	gold quality
ventricular zone	UBERON:0003053	86.38	gold quality
islet of Langerhans	UBERON:0000006	86.11	gold quality
epithelium of nasopharynx	UBERON:0001951	85.98	gold quality
oviduct epithelium	UBERON:0004804	85.91	gold quality
corpus epididymis	UBERON:0004359	85.76	gold quality
bone marrow cell	CL:0002092	85.62	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)

119 targeting RSBN1L, 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-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-512-3P	99.97	67.35	1049
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-9718	99.94	68.91	918
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-613	99.91	71.50	1710
HSA-MIR-302A-3P	99.89	71.23	1777
HSA-MIR-302B-3P	99.89	71.23	1777
HSA-MIR-302C-3P	99.89	71.20	1778

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Rsbn1l	ENSMUSG00000039968
rattus_norvegicus	Rsbn1l	ENSRNOG00000013431
drosophila_melanogaster	CG10600	FBGN0032717
caenorhabditis_elegans		WBGENE00001080

Paralogs (1): RSBN1 (ENSG00000081019)

Protein

Protein identifiers

Lysine-specific demethylase RSBN1L — Q6PCB5 (reviewed: Q6PCB5)

Alternative names: Round spermatid basic protein 1-like protein

All UniProt accessions (3): C9JM20, H7C2D3, Q6PCB5

UniProt curated annotations — full annotation on UniProt →

Function. Lysine-specific demethylase that specifically demethylates methylated lysine residues of proteins.

Subcellular location. Nucleus.

Cofactor. Binds 1 Fe(2+) ion per subunit.

Similarity. Belongs to the round spermatid basic protein 1 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6PCB5-1	1	yes
Q6PCB5-2	2

RefSeq proteins (1): NP_940869* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026306	RSBN1/Dpy-2/CEP530	Family

UniProt features (36 total): compositionally biased region 8, binding site 5, region of interest 5, modified residue 5, cross-link 5, sequence conflict 5, initiator methionine 1, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6PCB5-F1	62.95	0.34

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (5): 568; 571; 573; 665; 673

Post-translational modifications (10): 2, 6, 28, 32, 315, 223, 548, 753, 763, 814

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 106 (showing top): GATA6_01, ACATTCC_MIR1_MIR206, chr7q11, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_MAGENTA_DN, GOCC_NUCLEAR_SPECK, GOCC_NUCLEAR_BODY, GOCC_RIBONUCLEOPROTEIN_GRANULE, ATGTAGC_MIR221_MIR222, GOMF_DEMETHYLASE_ACTIVITY, GEORGES_TARGETS_OF_MIR192_AND_MIR215, GOMF_DIOXYGENASE_ACTIVITY, CTGTTAC_MIR194, GAGCCAG_MIR149, CHICAS_RB1_TARGETS_CONFLUENT, GOCC_SUPRAMOLECULAR_COMPLEX

GO Biological Process (0):

GO Molecular Function (3): metal ion binding (GO:0046872), dioxygenase activity (GO:0051213), oxidoreductase activity (GO:0016491)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cation binding	1
oxidoreductase activity	1
catalytic activity	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

561 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RSBN1L	C2orf42	Q9NWW7	666
RSBN1L	DGKK	Q5KSL6	526
RSBN1L	ERICH1	Q86X53	448
RSBN1L	PXDC1	Q5TGL8	437
RSBN1L	PCNX3	Q9H6A9	401
RSBN1L	CYFIP1	Q7L576	392
RSBN1L	H3BQ15	H3BQ15	386
RSBN1L	HTR2C	P28335	384
RSBN1L	HERC1	Q15751	384
RSBN1L	AMDHD2	Q9Y303	383
RSBN1L	NLGN3	Q9NZ94	378
RSBN1L	PCIF1	Q9H4Z3	371
RSBN1L	PTPN12	Q05209	370
RSBN1L	ADAMTS10	Q9H324	366
RSBN1L	SLC22A23	A1A5C7	360

IntAct

89 interactions, top by confidence:

A	B	Type	Score
EAF1	ELL2	psi-mi:“MI:0914”(association)	0.840
DYNLL1	BLTP3B	psi-mi:“MI:0914”(association)	0.730
DYNLL2	BLTP3B	psi-mi:“MI:0914”(association)	0.640
RPL14	RRP8	psi-mi:“MI:0914”(association)	0.640
LIN28A	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
ZRANB2	PIP4K2A	psi-mi:“MI:0914”(association)	0.610
KSR2	POLR3A	psi-mi:“MI:0914”(association)	0.530
MAP4K4	STRN	psi-mi:“MI:0914”(association)	0.530
RPS3	ZNF316	psi-mi:“MI:0914”(association)	0.530
MAGEB2	POLRMT	psi-mi:“MI:0914”(association)	0.530
RBM34	NVL	psi-mi:“MI:0914”(association)	0.530
NIFK	RSL1D1	psi-mi:“MI:0914”(association)	0.530
RPL13	RRP8	psi-mi:“MI:0914”(association)	0.530
H3C1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.410
ZDHHC17	RSBN1L	psi-mi:“MI:0915”(physical association)	0.370
AKAP5	MRPL43	psi-mi:“MI:0914”(association)	0.350
PAPD5	UNC119B	psi-mi:“MI:0914”(association)	0.350
SAMHD1	SF1	psi-mi:“MI:0914”(association)	0.350
NEIL3	SF3B2	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
N	POLRMT	psi-mi:“MI:0914”(association)	0.350
GRHL1	POLRMT	psi-mi:“MI:0914”(association)	0.350

BioGRID (143): RSBN1L (Two-hybrid), RSBN1L (Affinity Capture-MS), RSBN1L (Affinity Capture-MS), RSBN1L (Affinity Capture-MS), RSBN1L (Affinity Capture-MS), RSBN1L (Affinity Capture-MS), RSBN1L (Affinity Capture-MS), RSBN1L (Proximity Label-MS), RSBN1L (Affinity Capture-MS), RSBN1L (Affinity Capture-MS), RSBN1L (Affinity Capture-MS), RSBN1L (Affinity Capture-MS), RSBN1L (Synthetic Lethality), RSBN1 (Affinity Capture-MS), RSBN1L (Affinity Capture-MS)

ESM2 similar proteins: A0JMZ4, A2AWL7, A8MW92, B0S6S9, D3Z3C6, E7FAP1, F1QB81, O60284, P0C2N5, P29352, P52551, P62287, P62288, P62289, P62296, Q13029, Q28DE6, Q3U285, Q3U8K7, Q4FZB7, Q4V7H1, Q5EXX3, Q5RJX8, Q5SPL2, Q5SW75, Q5U3H2, Q5ZJK5, Q5ZLE9, Q63755, Q6GP17, Q6KAQ7, Q6NRK3, Q6PCB5, Q6PJP8, Q76I76, Q76I79, Q80TY4, Q86XD8, Q8BLG0, Q8CCJ9

Diamond homologs: Q28DE6, Q5VWQ0, Q6PCB5, Q80T69, Q9GRZ3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 108 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Peptide chain elongation	16	28.2×	2e-17
Viral mRNA Translation	16	28.2×	2e-17
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	16	27.9×	2e-17
Selenocysteine synthesis	16	26.7×	2e-17
Eukaryotic Translation Termination	16	26.7×	2e-17
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	16	26.2×	2e-17
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA	16	26.2×	2e-17
SRP-dependent cotranslational protein targeting to membrane	18	25.0×	2e-18

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of mRNA splicing, via spliceosome	6	46.0×	3e-07
cytoplasmic translation	18	33.3×	3e-20
ribosomal large subunit biogenesis	7	31.0×	3e-07
translation	16	16.4×	5e-13
regulation of alternative mRNA splicing, via spliceosome	6	14.7×	2e-04
negative regulation of translation	7	13.7×	6e-05
ribosomal small subunit biogenesis	5	11.4×	5e-03
rRNA processing	8	11.3×	5e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	80
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2120 predictions. Top by Δscore:

Variant	Effect	Δscore
7:77719117:G:GT	donor_gain	1.0000
7:77736395:T:TA	acceptor_gain	1.0000
7:77736400:T:TA	acceptor_gain	1.0000
7:77736405:TCCA:T	acceptor_loss	1.0000
7:77736406:CCA:C	acceptor_loss	1.0000
7:77736407:CA:C	acceptor_loss	1.0000
7:77736408:A:AG	acceptor_gain	1.0000
7:77736409:G:GA	acceptor_gain	1.0000
7:77736409:GA:G	acceptor_gain	1.0000
7:77736409:GAT:G	acceptor_gain	1.0000
7:77736409:GATA:G	acceptor_gain	1.0000
7:77736409:GATAA:G	acceptor_gain	1.0000
7:77736522:GAAAA:G	donor_gain	1.0000
7:77736523:AAAA:A	donor_gain	1.0000
7:77736524:AAA:A	donor_gain	1.0000
7:77736525:AA:A	donor_gain	1.0000
7:77736526:AG:A	donor_loss	1.0000
7:77736527:G:GG	donor_gain	1.0000
7:77736527:GTA:G	donor_loss	1.0000
7:77736528:TAA:T	donor_loss	1.0000
7:77737564:GCT:G	donor_gain	1.0000
7:77737566:T:G	donor_gain	1.0000
7:77737566:T:TG	donor_gain	1.0000
7:77765631:AA:A	donor_gain	1.0000
7:77765632:AG:A	donor_loss	1.0000
7:77765633:G:GG	donor_gain	1.0000
7:77765633:GT:G	donor_loss	1.0000
7:77765634:T:G	donor_loss	1.0000
7:77768659:A:AG	acceptor_gain	1.0000
7:77768660:G:GA	acceptor_gain	1.0000

AlphaMissense

5592 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:77749790:G:A	G357E	1.000
7:77750000:T:A	V427E	1.000
7:77750002:A:G	K428E	1.000
7:77750004:A:C	K428N	1.000
7:77750004:A:T	K428N	1.000
7:77750030:T:A	I437K	1.000
7:77765522:T:G	Y458D	1.000
7:77765531:G:C	G461R	1.000
7:77765532:G:A	G461D	1.000
7:77765549:A:C	S467R	1.000
7:77765551:C:A	S467R	1.000
7:77765551:C:G	S467R	1.000
7:77765571:A:T	E474V	1.000
7:77765572:A:C	E474D	1.000
7:77765572:A:T	E474D	1.000
7:77765579:G:A	G477R	1.000
7:77765579:G:C	G477R	1.000
7:77765580:G:A	G477E	1.000
7:77768673:T:A	W499R	1.000
7:77768673:T:C	W499R	1.000
7:77768675:G:C	W499C	1.000
7:77768675:G:T	W499C	1.000
7:77768715:A:C	S513R	1.000
7:77768717:T:A	S513R	1.000
7:77768717:T:G	S513R	1.000
7:77768721:G:C	D515H	1.000
7:77768722:A:T	D515V	1.000
7:77768724:G:C	G516R	1.000
7:77768724:G:T	G516C	1.000
7:77768725:G:A	G516D	1.000

dbSNP variants (sampled 300 via entrez): RS1000013903 (7:77753297 T>C), RS1000136615 (7:77714652 A>G), RS1000158627 (7:77750476 A>G), RS1000206422 (7:77776543 G>A), RS1000220392 (7:77754408 G>A), RS1000241845 (7:77722398 G>A,C), RS1000273797 (7:77750766 T>A), RS1000312259 (7:77725677 C>T), RS1000319368 (7:77776773 T>G), RS1000331154 (7:77716427 A>C,G), RS1000362687 (7:77725443 C>G), RS1000388762 (7:77770947 G>GT), RS1000402413 (7:77764721 G>T), RS1000403676 (7:77715011 C>T), RS1000424872 (7:77757319 C>A,G,T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST000649_15	Chronic kidney disease	2.000000e-09
GCST001762_549	Obesity-related traits	6.000000e-06
GCST002647_69	Height	4.000000e-13
GCST009309_3	Face memory	4.000000e-06
GCST012216_5	Vegetable consumption	1.000000e-08
GCST90002381_239	Eosinophil count	1.000000e-11
GCST90002382_152	Eosinophil percentage of white cells	3.000000e-10
GCST90020025_1118	Waist-to-hip ratio adjusted for BMI	1.000000e-09
GCST90020027_1400	Waist-hip index	2.000000e-09

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0003939	energy intake
EFO:0004874	memory performance
EFO:0008111	diet measurement
EFO:0004842	eosinophil count
EFO:0007991	eosinophil percentage of leukocytes
EFO:0007788	BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	affects expression, decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	decreases phosphorylation	1
triphenyl phosphate	affects expression	1
manganese chloride	increases abundance, increases expression	1
beta-methylcholine	affects expression	1
avobenzone	increases expression	1
ICG 001	decreases expression	1
bisphenol S	affects cotreatment, decreases methylation	1
PCI 5002	affects cotreatment, increases expression	1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-ol	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Leflunomide	increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants, Occupational	decreases expression	1
Benzo(a)pyrene	decreases expression	1
Caffeine	increases phosphorylation	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Formaldehyde	decreases expression	1
Manganese	increases abundance, increases expression	1
Nickel	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Rotenone	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	decreases expression	1
Zinc	affects cotreatment, increases expression	1
Cyclosporine	increases expression	1

Clinical trials (associated diseases)

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