RTBDN

Summary

RTBDN (retbindin, HGNC:30310) is a protein-coding gene on chromosome 19p13.13, encoding Retbindin (Q9BSG5). Riboflavin-binding protein which might have a role in retinal flavin transport.

This gene was first identified in a study of human eye tissues. The protein encoded by this gene is preferentially expressed in the retina and may play a role in binding retinoids and other carotenoids as it shares homology with riboflavin binding proteins. Alternative splicing results in multiple transcript variants and protein isoforms.

Source: NCBI Gene 83546 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 35 total
• MANE Select transcript: NM_001270441

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30310
Approved symbol	RTBDN
Name	retbindin
Location	19p13.13
Locus type	gene with protein product
Status	Approved
Aliases	FLJ36353
Ensembl gene	ENSG00000132026
Ensembl biotype	protein_coding
OMIM	609553
Entrez	83546

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 27 protein_coding

ENST00000322912, ENST00000393233, ENST00000458671, ENST00000585384, ENST00000586969, ENST00000587549, ENST00000589272, ENST00000589567, ENST00000589681, ENST00000589808, ENST00000590404, ENST00000591512, ENST00000592204, ENST00000674343, ENST00000866320, ENST00000866321, ENST00000866322, ENST00000934867, ENST00000934868, ENST00000934869, ENST00000965056, ENST00000965057, ENST00000965058, ENST00000965059, ENST00000965060, ENST00000965061, ENST00000965062

RefSeq mRNA: 8 — MANE Select: NM_001270441 NM_001080997, NM_001270440, NM_001270441, NM_001270442, NM_001270443, NM_001270444, NM_001270445, NM_031429

CCDS: CCDS12283, CCDS45994, CCDS59356

Canonical transcript exons

ENST00000674343 — 6 exons

Exon	Start	End
ENSE00002854337	12825482	12825933
ENSE00003729012	12828657	12828767
ENSE00003732585	12826775	12826871
ENSE00003735817	12828869	12828953
ENSE00003748087	12829811	12829997
ENSE00003898798	12834489	12834579

Expression profiles

Bgee: expression breadth ubiquitous, 107 present calls, max score 86.78.

FANTOM5 (CAGE): breadth broad, TPM avg 1.9237 / max 781.1282, expressed in 265 samples.

FANTOM5 promoters (12 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179401	1.0971	69
179406	0.2226	87
179409	0.2055	110
179403	0.0844	9
179400	0.0760	8
179402	0.0756	10
179405	0.0508	30
179407	0.0436	25
179408	0.0337	11
179397	0.0173	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pituitary gland	UBERON:0000007	86.78	gold quality
adenohypophysis	UBERON:0002196	86.76	gold quality
prefrontal cortex	UBERON:0000451	82.09	gold quality
anterior cingulate cortex	UBERON:0009835	80.79	gold quality
right frontal lobe	UBERON:0002810	80.73	gold quality
Brodmann (1909) area 9	UBERON:0013540	80.70	gold quality
amygdala	UBERON:0001876	79.46	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	79.26	gold quality
cardiac muscle of right atrium	UBERON:0003379	77.86	gold quality
frontal cortex	UBERON:0001870	77.85	gold quality
left ventricle myocardium	UBERON:0006566	77.58	gold quality
islet of Langerhans	UBERON:0000006	76.97	gold quality
neocortex	UBERON:0001950	76.94	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	75.80	gold quality
cerebral cortex	UBERON:0000956	75.07	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	74.61	silver quality
hypothalamus	UBERON:0001898	73.49	gold quality
temporal lobe	UBERON:0001871	72.58	gold quality
Ammon’s horn	UBERON:0001954	72.25	gold quality
cerebellar hemisphere	UBERON:0002245	71.11	gold quality
cerebellar cortex	UBERON:0002129	71.07	gold quality
right hemisphere of cerebellum	UBERON:0014890	71.07	gold quality
forebrain	UBERON:0001890	70.27	gold quality
brain	UBERON:0000955	69.29	gold quality
cerebellum	UBERON:0002037	69.11	gold quality
superior frontal gyrus	UBERON:0002661	66.86	gold quality
upper arm skin	UBERON:0004263	66.35	gold quality
kidney epithelium	UBERON:0004819	65.83	gold quality
entorhinal cortex	UBERON:0002728	65.22	silver quality
epithelial cell of pancreas	CL:0000083	64.10	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-7316	yes	59.58
E-MTAB-6379	no	1.55
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting RTBDN, 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-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-1323	99.83	69.89	2471
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-548O-3P	99.74	69.30	2228
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-5584-5P	99.49	68.22	2814
HSA-MIR-10399-5P	99.17	69.87	2610
HSA-MIR-6504-3P	99.17	69.31	2891
HSA-MIR-4254	99.11	65.15	1315
HSA-MIR-6776-5P	98.54	67.43	1304
HSA-MIR-6873-5P	98.45	66.14	1417
HSA-MIR-490-3P	97.79	65.54	606
HSA-MIR-4314	97.50	67.30	1369
HSA-MIR-5194	96.77	63.91	1021
HSA-MIR-6738-5P	96.33	63.61	815
HSA-MIR-1914-3P	95.07	63.37	762

Literature-anchored findings (GeneRIF, showing 2)

• retbindin is an excellent candidate for binding retinal flavins and possibly participating in their transport from the extracellular space to the photoreceptors. (PMID:25542898)
• Retbindin is capable of flavin binding. This characteristic can protect photoreceptors from flavin-sensitized light damage. Human retbindin in the culture media of a riboflavin-sensitized transgenic mouse cone cell line protected it from a 1-hour light-box exposure at 12,000 lux. (PMID:29721980)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	rtbdn	ENSDARG00000103413
mus_musculus	Rtbdn	ENSMUSG00000048617
rattus_norvegicus	Rtbdn	ENSRNOG00000043215

Paralogs (4): FOLR1 (ENSG00000110195), FOLR3 (ENSG00000110203), FOLR2 (ENSG00000165457), IZUMO1R (ENSG00000183560)

Protein

Protein identifiers

Retbindin — Q9BSG5 (reviewed: Q9BSG5)

All UniProt accessions (10): Q9BSG5, K7EIS2, K7EKV3, K7EM70, K7EN64, K7ENA4, K7EQL9, K7ES48, K7ESG0, K7ESL8

UniProt curated annotations — full annotation on UniProt →

Function. Riboflavin-binding protein which might have a role in retinal flavin transport.

Subcellular location. Secreted. Extracellular space. Extracellular matrix. Interphotoreceptor matrix. Cell membrane.

Tissue specificity. Expressed in peripheral retina (at protein level).

Post-translational modifications. Not N-glycosylated.

Similarity. Belongs to the folate receptor family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9BSG5-1	1	yes
Q9BSG5-2	2
Q9BSG5-3	3

RefSeq proteins (8): NP_001074466, NP_001257369, NP_001257370, NP_001257371, NP_001257372, NP_001257373, NP_001257374, NP_113617 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004269	Folate_rcpt	Family
IPR018143	Folate_rcpt-like	Domain

Pfam: PF03024

UniProt features (11 total): disulfide bond 4, splice variant 2, signal peptide 1, chain 1, sequence variant 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BSG5-F1	66.17	0.16

Functional residue map

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

Disulfide bonds (4): 79–149, 86–126, 119–163, 132–145

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 77 (showing top): RNGTGGGC_UNKNOWN, BENPORATH_ES_WITH_H3K27ME3, TGCGCANK_UNKNOWN, E2F4DP1_01, GOCC_CELL_SURFACE, E2F1DP1_01, E2F1DP2_01, GOBP_ORGANIC_ANION_TRANSPORT, GCM_DDX11, GOBP_VITAMIN_TRANSPORT, TGGNNNNNNKCCAR_UNKNOWN, GCM_NF2, MEF2_03, GOCC_SIDE_OF_MEMBRANE, chr19p13

GO Biological Process (1): riboflavin transport (GO:0032218)

GO Molecular Function (3): riboflavin transmembrane transporter activity (GO:0032217), signaling receptor activity (GO:0038023), riboflavin binding (GO:1902444)

GO Cellular Component (5): external side of plasma membrane (GO:0009897), interphotoreceptor matrix (GO:0033165), extracellular region (GO:0005576), plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
vitamin transport	1
nitrogen compound transport	1
riboflavin transport	1
vitamin transmembrane transporter activity	1
molecular transducer activity	1
anion binding	1
heterocyclic compound binding	1
plasma membrane	1
cell surface	1
side of membrane	1
specialized extracellular matrix	1
membrane	1
cell periphery	1

Protein interactions and networks

STRING

268 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RTBDN	OPTC	Q9UBM4	560
RTBDN	ZNF256	Q9Y2P7	541
RTBDN	GUCY1A2	P33402	503
RTBDN	BEST2	Q8NFU1	472
RTBDN	GUCA2B	Q16661	460
RTBDN	PRPH2	P23942	428
RTBDN	RAD18	Q9NS91	423
RTBDN	KCNB1	Q14721	410
RTBDN	TTC9B	Q8N6N2	401
RTBDN	SLC24A1	O60721	377
RTBDN	FLAD1	Q8NFF5	375
RTBDN	RAD17	O75943	371
RTBDN	FANCL	Q9NW38	361
RTBDN	ERICH1	Q86X53	350
RTBDN	PTGR3	Q8N4Q0	348

IntAct

3 interactions, top by confidence:

A	B	Type	Score
RTBDN	COL6A1	psi-mi:“MI:0914”(association)	0.350

BioGRID (24): TSEN2 (Affinity Capture-MS), TTC19 (Affinity Capture-MS), UBAC1 (Affinity Capture-MS), ZER1 (Affinity Capture-MS), DDX19B (Affinity Capture-MS), BIRC6 (Affinity Capture-MS), GAS6 (Affinity Capture-MS), COL6A1 (Affinity Capture-MS), AMD1 (Affinity Capture-MS), GAS6 (Affinity Capture-MS), ZER1 (Affinity Capture-MS), TTC19 (Affinity Capture-MS), COL6A1 (Affinity Capture-MS), AMD1 (Affinity Capture-MS), UBAC1 (Affinity Capture-MS)

ESM2 similar proteins: A0A8M9PDM1, A0A8M9QN10, A1L3I3, A2AWH2, A2CI97, A2CI98, A4IFM1, A4IHZ3, A7E2V4, A7E305, B1AL88, B6CKP4, E7F211, F8W3R9, O55034, O94901, P35054, P51864, P86275, P98153, P98154, Q0VCT2, Q3UHH1, Q498C7, Q4KM46, Q4TUC0, Q58T08, Q5EB20, Q5HZE8, Q5RD34, Q5VUB5, Q6UW32, Q6V9Y8, Q7TNI2, Q7Z5A8, Q80ZA7, Q86VZ4, Q8CB67, Q8CCS2, Q8N0W7

Diamond homologs: Q4TUC0, Q5DRQ5, Q8QZY4, Q9BSG5, F1M928, Q9EQF4, P02752

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	28
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1201 predictions. Top by Δscore:

Variant	Effect	Δscore
19:12828773:C:CT	acceptor_gain	1.0000
19:12828774:G:C	acceptor_gain	1.0000
19:12828775:T:TC	acceptor_gain	1.0000
19:12828863:A:AC	donor_gain	1.0000
19:12828864:C:CC	donor_gain	1.0000
19:12828865:TCA:T	donor_loss	1.0000
19:12828866:CA:C	donor_loss	1.0000
19:12828867:A:AC	donor_gain	1.0000
19:12828867:ACTCA:A	donor_loss	1.0000
19:12828868:C:CA	donor_gain	1.0000
19:12828868:CT:C	donor_gain	1.0000
19:12825930:AGGT:A	acceptor_gain	0.9900
19:12825933:TCTAG:T	acceptor_loss	0.9900
19:12825934:C:CC	acceptor_gain	0.9900
19:12826772:CA:C	donor_loss	0.9900
19:12826774:C:CG	donor_loss	0.9900
19:12826870:ACCT:A	acceptor_loss	0.9900
19:12826878:A:C	acceptor_gain	0.9900
19:12826882:C:CT	acceptor_gain	0.9900
19:12828652:CCTAC:C	donor_loss	0.9900
19:12828653:CTAC:C	donor_loss	0.9900
19:12828655:A:AC	donor_gain	0.9900
19:12828655:ACCAG:A	donor_loss	0.9900
19:12828656:C:CC	donor_gain	0.9900
19:12828656:CCAGG:C	donor_gain	0.9900
19:12828763:CGCAT:C	acceptor_gain	0.9900
19:12828765:CAT:C	acceptor_gain	0.9900
19:12828768:C:CA	acceptor_loss	0.9900
19:12828768:C:CC	acceptor_gain	0.9900
19:12828774:G:GC	acceptor_gain	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000163967 (19:12837150 T>A), RS1000568610 (19:12830590 C>T), RS1000667526 (19:12830941 CTGTG>C,CTG,CTGTGTG), RS1001122229 (19:12831213 T>A,C), RS1001158221 (19:12837125 G>A), RS1001232541 (19:12833283 G>A), RS1001242350 (19:12833683 A>C), RS1001961650 (19:12836568 A>G,T), RS1002083118 (19:12826749 C>T), RS1002165663 (19:12830596 G>A), RS1002241512 (19:12831758 T>C), RS1002249621 (19:12832123 C>G,T), RS1002837514 (19:12829346 C>A,T), RS1002855374 (19:12834783 A>G), RS1002917514 (19:12835513 G>A,T)

Disease associations

OMIM: gene MIM:609553 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST000503_11	Mean corpuscular volume	2.000000e-12

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
ethyl-p-hydroxybenzoate	decreases expression	1
CGP 52608	affects binding, increases reaction	1
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Silicon Dioxide	decreases methylation	1
Valproic Acid	increases expression	1

Clinical trials (associated diseases)

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