RBFA

Summary

RBFA (ribosome binding factor A, HGNC:26120) is a protein-coding gene on chromosome 18q23, encoding Putative ribosome-binding factor A, mitochondrial (Q8N0V3).

Predicted to be involved in rRNA processing. Located in mitochondrion.

Source: NCBI Gene 79863 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 79 total — 1 pathogenic
• MANE Select transcript: NM_024805

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26120
Approved symbol	RBFA
Name	ribosome binding factor A
Location	18q23
Locus type	gene with protein product
Status	Approved
Aliases	FLJ21172, HsT169
Ensembl gene	ENSG00000101546
Ensembl biotype	protein_coding
OMIM	620768
Entrez	79863

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 2 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000262197, ENST00000306735, ENST00000586847, ENST00000591612, ENST00000593019

RefSeq mRNA: 2 — MANE Select: NM_024805 NM_001171967, NM_024805

CCDS: CCDS12021, CCDS54194

Canonical transcript exons

ENST00000306735 — 7 exons

Exon	Start	End
ENSE00000670868	80037330	80037506
ENSE00000950389	80038505	80038617
ENSE00000950390	80042135	80042219
ENSE00001274338	80034434	80034653
ENSE00002788608	80045774	80050651
ENSE00003563209	80044212	80044285
ENSE00003593639	80036668	80036710

Expression profiles

Bgee: expression breadth ubiquitous, 240 present calls, max score 92.56.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.3747 / max 164.6384, expressed in 1803 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
170921	18.6302	1790
170920	2.7062	1433
170919	1.0383	652

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tendon of biceps brachii	UBERON:0008188	92.56	gold quality
apex of heart	UBERON:0002098	89.42	gold quality
right lobe of liver	UBERON:0001114	89.33	gold quality
cortical plate	UBERON:0005343	88.55	gold quality
right adrenal gland cortex	UBERON:0035827	88.52	gold quality
right adrenal gland	UBERON:0001233	88.48	gold quality
skin of abdomen	UBERON:0001416	88.42	gold quality
left adrenal gland	UBERON:0001234	88.11	gold quality
left adrenal gland cortex	UBERON:0035825	87.99	gold quality
skin of leg	UBERON:0001511	87.84	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.67	gold quality
adrenal cortex	UBERON:0001235	87.23	gold quality
tibial artery	UBERON:0007610	86.99	gold quality
popliteal artery	UBERON:0002250	86.98	gold quality
gastrocnemius	UBERON:0001388	86.90	gold quality
cerebellar hemisphere	UBERON:0002245	86.79	gold quality
right hemisphere of cerebellum	UBERON:0014890	86.72	gold quality
body of pancreas	UBERON:0001150	86.69	gold quality
cerebellar cortex	UBERON:0002129	86.67	gold quality
aorta	UBERON:0000947	86.62	gold quality
adrenal gland	UBERON:0002369	86.58	gold quality
muscle of leg	UBERON:0001383	86.53	gold quality
right coronary artery	UBERON:0001625	86.51	gold quality
ganglionic eminence	UBERON:0004023	86.49	gold quality
left coronary artery	UBERON:0001626	86.46	gold quality
omental fat pad	UBERON:0010414	86.45	gold quality
peritoneum	UBERON:0002358	86.42	gold quality
heart left ventricle	UBERON:0002084	86.35	gold quality
ascending aorta	UBERON:0001496	86.34	gold quality
thoracic aorta	UBERON:0001515	86.30	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.48

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

89 targeting RBFA, 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-432-3P	100.00	67.86	705
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-4493	99.90	66.48	977
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-8067	99.86	69.59	2260

Literature-anchored findings (GeneRIF, showing 2)

• (1)H, (13)C, and (15)N resonance assignments and solution structures of the KH domain of human ribosome binding factor A, mtRbfA, involved in mitochondrial ribosome biogenesis. (PMID:35666428)
• The recognition mode between hsRBFA and mitoribosome 12S rRNA during mitoribosomal biogenesis. (PMID:36620886)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	rbfa	ENSDARG00000073705
mus_musculus	Rbfa	ENSMUSG00000024570
rattus_norvegicus	Rbfa	ENSRNOG00000055647
drosophila_melanogaster	CG15916	FBGN0030704
caenorhabditis_elegans		WBGENE00007731

Protein

Protein identifiers

Putative ribosome-binding factor A, mitochondrial — Q8N0V3 (reviewed: Q8N0V3)

All UniProt accessions (1): Q8N0V3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Mitochondrion.

Similarity. Belongs to the RbfA family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N0V3-1	1, p38	yes
Q8N0V3-2	2, p27

RefSeq proteins (2): NP_001165438, NP_079081* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000238	RbfA	Family
IPR015946	KH_dom-like_a/b	Homologous_superfamily
IPR020053	Ribosome-bd_factorA_CS	Conserved_site
IPR023799	RbfA_dom_sf	Homologous_superfamily
IPR039212	RBFA_mitochondrial	Family

Pfam: PF02033

UniProt features (23 total): helix 6, strand 4, sequence variant 3, region of interest 2, compositionally biased region 2, splice variant 2, transit peptide 1, chain 1, sequence conflict 1, turn 1

Structure

Experimental structures (PDB)

20 structures.

PDB	Method	Resolution (Å)
8IPL	X-RAY DIFFRACTION	2.2
8CSS	ELECTRON MICROSCOPY	2.36
8CSR	ELECTRON MICROSCOPY	2.54
7PNX	ELECTRON MICROSCOPY	2.76
8CST	ELECTRON MICROSCOPY	2.85
7PO0	ELECTRON MICROSCOPY	2.9
9G5C	ELECTRON MICROSCOPY	3
9G5D	ELECTRON MICROSCOPY	3
9H54	ELECTRON MICROSCOPY	3
8CSU	ELECTRON MICROSCOPY	3.03
7PNY	ELECTRON MICROSCOPY	3.06
7PNZ	ELECTRON MICROSCOPY	3.09
8IPM	X-RAY DIFFRACTION	3.1
9H51	ELECTRON MICROSCOPY	3.1
9G5B	ELECTRON MICROSCOPY	3.2
9H55	ELECTRON MICROSCOPY	3.4
9IGU	ELECTRON MICROSCOPY	3.64
9IGT	ELECTRON MICROSCOPY	5.96
2E7G	SOLUTION NMR
7X9U	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N0V3-F1	66.00	0.25

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 106 (showing top): GOBP_RIBOSOME_BIOGENESIS, GOBP_RIBOSOME_ASSEMBLY, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_ORGANELLE_ASSEMBLY, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOBP_RIBOSOMAL_SMALL_SUBUNIT_ASSEMBLY, PARENT_MTOR_SIGNALING_UP, GOCC_MITOCHONDRIAL_MATRIX, LEE_LIVER_CANCER_MYC_DN, GOMF_RIBOSOMAL_SMALL_SUBUNIT_BINDING, GOMF_RIBONUCLEOPROTEIN_COMPLEX_BINDING, GOMF_RRNA_BINDING, GOMF_RIBOSOME_BINDING, KASLER_HDAC7_TARGETS_1_UP

GO Biological Process (3): rRNA processing (GO:0006364), mitochondrial small ribosomal subunit assembly (GO:0180026), biological_process (GO:0008150)

GO Molecular Function (3): rRNA binding (GO:0019843), ribosomal small subunit binding (GO:0043024), protein binding (GO:0005515)

GO Cellular Component (2): mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	1
rRNA metabolic process	1
ribosome biogenesis	1
ribosomal small subunit assembly	1
mitochondrial ribosome assembly	1
RNA binding	1
ribosome binding	1
binding	1
cytoplasm	1
intracellular membrane-bounded organelle	1
mitochondrion	1
intracellular organelle lumen	1

Protein interactions and networks

STRING

702 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RBFA	ERAL1	O75616	635
RBFA	SLC66A2	Q8N2U9	594
RBFA	METTL15	A6NJ78	592
RBFA	ATP5IF1	Q9UII2	578
RBFA	TFB1M	Q8WVM0	575
RBFA	TRMT2B	Q96GJ1	571
RBFA	MTIF3	Q9H2K0	553
RBFA	NSUN4	Q96CB9	543
RBFA	MRM3	Q9HC36	526
RBFA	MTG2	Q9H4K7	516
RBFA	TXNL4A	P83876	503
RBFA	MRPL54	Q6P161	496
RBFA	GTPBP10	A4D1E9	489
RBFA	MTERF4	Q7Z6M4	487
RBFA	ZNF24	P17028	479

IntAct

104 interactions, top by confidence:

A	B	Type	Score
KBTBD7	METTL15	psi-mi:“MI:0914”(association)	0.730
SCN2B	EXOC5	psi-mi:“MI:0914”(association)	0.640
GYPA	TCAF2	psi-mi:“MI:0914”(association)	0.640
CMTM5	RBFA	psi-mi:“MI:0915”(physical association)	0.560
RBFA	CMTM5	psi-mi:“MI:0915”(physical association)	0.560
ERLIN1	RBFA	psi-mi:“MI:0915”(physical association)	0.560
RBFA	FATE1	psi-mi:“MI:0915”(physical association)	0.560
AGTRAP	RBFA	psi-mi:“MI:0915”(physical association)	0.560
RBFA	DERL2	psi-mi:“MI:0915”(physical association)	0.560
LEPROTL1	RBFA	psi-mi:“MI:0915”(physical association)	0.560
HIGD1C	RBFA	psi-mi:“MI:0915”(physical association)	0.560
CAV3	RBFA	psi-mi:“MI:0915”(physical association)	0.560
YIF1A	RBFA	psi-mi:“MI:0915”(physical association)	0.560
SMIM5	RBFA	psi-mi:“MI:0915”(physical association)	0.560
RBFA	GPX8	psi-mi:“MI:0915”(physical association)	0.560
ANK1	RBFA	psi-mi:“MI:0915”(physical association)	0.560
SYPL1	RBFA	psi-mi:“MI:0915”(physical association)	0.560
MDK	RBFA	psi-mi:“MI:0915”(physical association)	0.560
RBFA	CACFD1	psi-mi:“MI:0915”(physical association)	0.560
RHEX	RBFA	psi-mi:“MI:0915”(physical association)	0.560
PEX12	RBFA	psi-mi:“MI:0915”(physical association)	0.560
RBFA	FKBP7	psi-mi:“MI:0915”(physical association)	0.560
RBFA	CMTM6	psi-mi:“MI:0915”(physical association)	0.560
SYP	RBFA	psi-mi:“MI:0915”(physical association)	0.560
RBFA	GPR152	psi-mi:“MI:0915”(physical association)	0.560
RBFA	ABHD5	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (83): CMTM5 (Two-hybrid), RBFA (Affinity Capture-MS), RBFA (Affinity Capture-MS), KBTBD7 (Affinity Capture-MS), METTL15 (Affinity Capture-MS), RBFA (Affinity Capture-MS), RBFA (Affinity Capture-MS), ZZEF1 (Affinity Capture-MS), TRIM69 (Affinity Capture-MS), RBFA (Affinity Capture-MS), SIRT1 (Affinity Capture-MS), HECTD3 (Affinity Capture-MS), KBTBD6 (Affinity Capture-MS), ZNF638 (Affinity Capture-MS), RBFA (Affinity Capture-MS)

ESM2 similar proteins: A2A8U2, A6H773, A6QPI4, D4A6L0, E1BBQ2, O60232, P54098, Q05B67, Q08BI9, Q148E1, Q2KI76, Q2KJ58, Q2NL34, Q32Q90, Q4R4I0, Q5C9Z4, Q5RE99, Q5SNT2, Q5T6X4, Q5T848, Q5VUE5, Q5XIJ4, Q5ZLJ4, Q6DVA0, Q6P3B9, Q7T076, Q80YR4, Q86UK7, Q8C419, Q8CEG5, Q8IYL2, Q8N0V3, Q8NC56, Q8TBN0, Q8VDV3, Q8VE22, Q8VHV8, Q921N7, Q96IL0, Q96ND0

Diamond homologs: A5FL10, Q6P3B9, Q8N0V3, Q31D68

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	54
Likely benign	15
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
152854	GRCh38/hg38 18q23(chr18:75875505-80252090)x1	Pathogenic

SpliceAI

1681 predictions. Top by Δscore:

Variant	Effect	Δscore
18:80034654:G:GG	donor_gain	1.0000
18:80034650:CCAAG:C	donor_loss	0.9900
18:80034651:CAAG:C	donor_loss	0.9900
18:80034652:AAGTA:A	donor_loss	0.9900
18:80034653:AGTAA:A	donor_loss	0.9900
18:80034655:T:A	donor_loss	0.9900
18:80036665:A:G	acceptor_gain	0.9900
18:80036666:A:AG	acceptor_gain	0.9900
18:80036667:G:GG	acceptor_gain	0.9900
18:80037322:T:A	acceptor_gain	0.9900
18:80037325:T:TA	acceptor_gain	0.9900
18:80037326:G:A	acceptor_gain	0.9900
18:80044207:TGTA:T	acceptor_loss	0.9900
18:80044208:GTA:G	acceptor_loss	0.9900
18:80044209:TA:T	acceptor_loss	0.9900
18:80044210:A:AG	acceptor_gain	0.9900
18:80044210:AG:A	acceptor_loss	0.9900
18:80044211:G:GG	acceptor_gain	0.9900
18:80044211:G:GT	acceptor_loss	0.9900
18:80044211:GCTT:G	acceptor_gain	0.9900
18:80046149:G:GT	donor_gain	0.9900
18:80034653:AG:A	donor_loss	0.9800
18:80036664:A:AG	acceptor_gain	0.9800
18:80045768:TCCCA:T	acceptor_loss	0.9800
18:80045769:CCCA:C	acceptor_loss	0.9800
18:80045770:CCAG:C	acceptor_loss	0.9800
18:80045771:CAG:C	acceptor_loss	0.9800
18:80045772:A:AC	acceptor_loss	0.9800
18:80034649:ACCAA:A	donor_gain	0.9700
18:80044211:GC:G	acceptor_gain	0.9700

AlphaMissense

2240 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
18:80042185:T:C	F181S	0.990
18:80042184:T:C	F181L	0.987
18:80042186:T:A	F181L	0.987
18:80042186:T:G	F181L	0.987
18:80042179:T:A	I179K	0.983
18:80038544:T:A	W140R	0.979
18:80038544:T:C	W140R	0.979
18:80038546:G:C	W140C	0.978
18:80038546:G:T	W140C	0.978
18:80042143:T:C	L167S	0.976
18:80042185:T:G	F181C	0.975
18:80037448:T:C	L107P	0.974
18:80038532:T:C	C136R	0.974
18:80038536:G:C	R137P	0.972
18:80042179:T:G	I179R	0.972
18:80042135:G:C	R164S	0.969
18:80042135:G:T	R164S	0.969
18:80037439:T:C	L104P	0.966
18:80038617:G:T	R164M	0.963
18:80042173:C:A	P177Q	0.963
18:80038534:C:G	C136W	0.961
18:80045866:T:C	I248T	0.961
18:80038617:G:C	R164T	0.959
18:80038545:G:C	W140S	0.957
18:80038593:T:C	L156P	0.957
18:80037418:A:T	N97I	0.955
18:80037499:T:A	L124H	0.954
18:80042140:T:C	L166P	0.950
18:80042173:C:G	P177R	0.950
18:80045879:A:C	K252N	0.950

dbSNP variants (sampled 300 via entrez): RS1000052986 (18:80048544 A>G), RS1000302398 (18:80041945 C>T), RS1000309384 (18:80037342 T>C), RS1000471081 (18:80040260 C>G,T), RS1000919922 (18:80036871 C>A,T), RS1001105098 (18:80042019 C>T), RS1001311303 (18:80042380 C>T), RS1001320106 (18:80035907 G>A), RS1001368912 (18:80046972 A>G), RS1001460809 (18:80046792 A>G), RS1001900867 (18:80051000 G>T), RS1002123812 (18:80047068 T>C), RS1002310232 (18:80037425 C>T), RS1002406824 (18:80047321 G>A), RS1002757325 (18:80041830 C>T)

Disease associations

OMIM: gene MIM:620768 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, increases methylation, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Silicon Dioxide	increases expression, decreases expression	2
Valproic Acid	affects expression, increases expression	2
aristolochic acid I	decreases expression	1
sodium arsenite	decreases expression	1
cobaltous chloride	decreases expression	1
benzo(e)pyrene	increases methylation	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
jinfukang	increases expression	1
NSC 689534	affects binding, decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Benzo(a)pyrene	increases methylation	1
Copper	affects binding, decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Formaldehyde	decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Methapyrilene	increases methylation	1
Methyl Methanesulfonate	decreases expression	1
Ribonucleotides	affects binding	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tunicamycin	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	decreases expression	1
Thapsigargin	decreases expression	1

Clinical trials (associated diseases)

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