RBM47

Summary

RBM47 (RNA binding motif protein 47, HGNC:30358) is a protein-coding gene on chromosome 4p14, encoding RNA-binding protein 47 (A0AV96). Single-stranded RNA-binding protein that functions in a variety of RNA processes, including alternative splicing, RNA stabilization, and RNA editing.

Enables enzyme binding activity; enzyme-substrate adaptor activity; and mRNA 3’-UTR binding activity. Involved in cytidine to uridine editing; positive regulation of type I interferon-mediated signaling pathway; and regulation of mRNA metabolic process. Located in cytoplasm and nucleus. Part of apolipoprotein B mRNA editing enzyme complex.

Source: NCBI Gene 54502 — RefSeq curated summary.

At a glance

• GWAS associations: 11
• Clinical variants (ClinVar): 91 total
• MANE Select transcript: NM_001098634

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30358
Approved symbol	RBM47
Name	RNA binding motif protein 47
Location	4p14
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20273, NET18
Ensembl gene	ENSG00000163694
Ensembl biotype	protein_coding
OMIM	619104
Entrez	54502

Gene structure

Transcript identifiers

Ensembl transcripts: 47 — 44 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000295971, ENST00000381793, ENST00000381795, ENST00000505220, ENST00000505414, ENST00000507180, ENST00000510871, ENST00000511598, ENST00000511902, ENST00000513044, ENST00000513473, ENST00000514014, ENST00000514782, ENST00000515053, ENST00000515809, ENST00000910696, ENST00000910697, ENST00000910698, ENST00000910699, ENST00000910700, ENST00000910701, ENST00000910702, ENST00000910703, ENST00000910704, ENST00000910705, ENST00000910706, ENST00000910707, ENST00000910708, ENST00000910709, ENST00000910710, ENST00000910711, ENST00000912900, ENST00000912901, ENST00000912902, ENST00000912903, ENST00000912904, ENST00000912905, ENST00000912906, ENST00000912907, ENST00000912908, ENST00000912909, ENST00000912910, ENST00000950955, ENST00000950956, ENST00000950957, ENST00000950958, ENST00000950959

RefSeq mRNA: 4 — MANE Select: NM_001098634 NM_001098634, NM_001371113, NM_001371114, NM_019027

CCDS: CCDS3460, CCDS43223, CCDS93492

Canonical transcript exons

ENST00000295971 — 7 exons

Exon	Start	End
ENSE00001077384	40437771	40438924
ENSE00001077385	40466577	40466699
ENSE00001259908	40436441	40436647
ENSE00001489860	40544422	40544506
ENSE00002025290	40629396	40629864
ENSE00002050228	40423280	40426143
ENSE00003493188	40432651	40432862

Expression profiles

Bgee: expression breadth ubiquitous, 247 present calls, max score 99.45.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.3017 / max 725.1913, expressed in 1162 samples.

FANTOM5 promoters (22 alternative TSS)

Promoter ID	TPM avg	Samples expressed
51919	6.1087	611
51912	4.6794	874
51908	1.9945	521
51921	1.2979	304
51911	1.0649	482
51917	0.5446	257
51910	0.5321	291
51895	0.4579	85
51907	0.4538	189
51899	0.4017	164

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
renal medulla	UBERON:0000362	99.45	gold quality
mucosa of sigmoid colon	UBERON:0004993	99.45	gold quality
colonic mucosa	UBERON:0000317	99.38	gold quality
ileal mucosa	UBERON:0000331	99.17	gold quality
parotid gland	UBERON:0001831	99.15	gold quality
jejunal mucosa	UBERON:0000399	98.78	gold quality
bronchial epithelial cell	CL:0002328	98.43	gold quality
epithelium of bronchus	UBERON:0002031	98.33	gold quality
bronchus	UBERON:0002185	98.24	gold quality
buccal mucosa cell	CL:0002336	98.19	gold quality
nasal cavity epithelium	UBERON:0005384	98.15	gold quality
esophagus squamous epithelium	UBERON:0006920	98.05	gold quality
nephron tubule	UBERON:0001231	97.96	gold quality
corpus epididymis	UBERON:0004359	97.58	gold quality
duodenum	UBERON:0002114	97.57	gold quality
palpebral conjunctiva	UBERON:0001812	97.40	gold quality
pharyngeal mucosa	UBERON:0000355	97.26	gold quality
pylorus	UBERON:0001166	97.26	gold quality
eye	UBERON:0000970	97.20	gold quality
adrenal tissue	UBERON:0018303	97.20	gold quality
nasal cavity mucosa	UBERON:0001826	97.13	gold quality
caput epididymis	UBERON:0004358	97.00	gold quality
pigmented layer of retina	UBERON:0001782	96.67	gold quality
retina	UBERON:0000966	96.64	gold quality
epithelium of esophagus	UBERON:0001976	96.56	gold quality
kidney epithelium	UBERON:0004819	96.36	gold quality
seminal vesicle	UBERON:0000998	96.07	gold quality
mucosa of transverse colon	UBERON:0004991	96.07	gold quality
trachea	UBERON:0003126	96.04	gold quality
oral cavity	UBERON:0000167	95.96	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-ANND-2	yes	6496.11
E-HCAD-35	yes	35.77
E-HCAD-10	yes	26.62
E-ANND-3	yes	19.99
E-GEOD-125970	yes	14.89
E-MTAB-7249	no	53.02

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

135 targeting RBM47, 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-3163	100.00	77.23	8605
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-548AT-5P	99.96	70.83	2666
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

Literature-anchored findings (GeneRIF, showing 13)

• RBM47 is an RNA-binding protein that can suppress breast cancer progression (PMID:24898756)
• Our findings, together with the enhanced tumor formation and metastasis of xenografted mice by knockdown of the RBM47 expression, suggested tumor-suppressive roles for RBM47 through the inhibition of Nrf2 activity (PMID:26923328)
• Results show that down-regulation of RBM47 is associated with and functionally important for colorectal cancer (CRC) progression. Therefore, detection of RBM47 down-regulation may serve as a new prognostic marker for CRC and might represent an important diagnostic option to identify patients with poor prognosis. (PMID:28680090)
• miR-25 could directly target the RNA-binding motif protein 47 (RBM47). RBM47 is a promising target for the treatment of melanoma. (PMID:30403177)
• Results identified and confirmed to have downregulated gene expression of SFRP5 in sporadic nonfunctioning pancreatic neuroendocrine tumors (NFPanNETs) and CDCA7L and RBM47 in MEN1-related NFPanNETs. (PMID:30620390)
• The first RNA recognition motif (RRM) domain of RBM47 is critical in the regulation of alternative splicing and its recognition to pre-mRNA of TJP1. Furthermore, the TJP1-alpha- isoform enhances the assembly of actin stress fibers, thereby promoting cellular migration in a wound healing assay, providing a basis for studies related to the modulation of epithelial-to-mesenchymal transition via alternative splicing. (PMID:31358901)
• The RNA-binding protein RBM47 is a novel regulator of cell fate decisions by transcriptionally controlling the p53-p21-axis. (PMID:31511650)
• The RNA-binding protein RBM47 inhibits non-small cell lung carcinoma metastasis through modulation of AXIN1 mRNA stability and Wnt/beta-catentin signaling. (PMID:32891348)
• [RNA Binding Protein RBM47 Inhibits the K562 Cell Proliferation by Regulating HMGA2 mRNA Expression]. (PMID:34105460)
• RNA binding motif 47 (RBM47): emerging roles in vertebrate development, RNA editing and cancer. (PMID:34499322)
• RBM47 regulates intestinal injury and tumorigenesis by modifying proliferation, oxidative response, and inflammatory pathways. (PMID:37014710)
• RNA-Binding Motif Protein RBM47 Promotes Invasiveness of Glioblastoma Through Activation of Epithelial-to-Mesenchymal Transition Program. (PMID:38156907)
• Deubiquitinating enzyme OTUD4 stabilizes RBM47 to induce ATF3 transcription: a novel mechanism underlying the restrained malignant properties of ccRCC cells. (PMID:38553613)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	rbm47	ENSDARG00000061985
mus_musculus	Rbm47	ENSMUSG00000070780
rattus_norvegicus	Rbm47	ENSRNOG00000002408

Paralogs (36): DAZAP1 (ENSG00000071626), CIRBP (ENSG00000099622), RBM23 (ENSG00000100461), RBM3 (ENSG00000102317), NCL (ENSG00000115053), TIA1 (ENSG00000116001), HNRNPA2B1 (ENSG00000122566), RBM19 (ENSG00000122965), RBM39 (ENSG00000131051), MSI1 (ENSG00000135097), HNRNPA1 (ENSG00000135486), HNRNPD (ENSG00000138668), HNRNPA1L2 (ENSG00000139675), RBMX (ENSG00000147274), A1CF (ENSG00000148584), TIAL1 (ENSG00000151923), RBM46 (ENSG00000151962), HNRNPDL (ENSG00000152795), MSI2 (ENSG00000153944), RBMY1F (ENSG00000169800), HNRNPA3 (ENSG00000170144), RBMXL2 (ENSG00000170748), RBM4B (ENSG00000173914), RBM4 (ENSG00000173933), RBMXL3 (ENSG00000175718), HNRNPA0 (ENSG00000177733), TRNAU1AP (ENSG00000180098), HNRNPAB (ENSG00000197451), RBMXL1 (ENSG00000213516), HNRNPA1L3 (ENSG00000224578), RBMY1J (ENSG00000226941), RBMY1A1 (ENSG00000234414), RBMY1E (ENSG00000242389), RBMY1B (ENSG00000242875), RBMY1D (ENSG00000244395), DND1 (ENSG00000256453)

Protein

Protein identifiers

RNA-binding protein 47 — A0AV96 (reviewed: A0AV96)

Alternative names: RNA-binding motif protein 47

All UniProt accessions (10): A0AV96, B7Z8Z7, D6R9D6, D6R9M7, D6RA49, D6RBP6, D6RBS9, D6RCT1, D6REZ6, D6RFL5

UniProt curated annotations — full annotation on UniProt →

Function. Single-stranded RNA-binding protein that functions in a variety of RNA processes, including alternative splicing, RNA stabilization, and RNA editing. Functions as an enzyme-substrate adapter for the cytidine deaminase APOBEC1. With APOBEC1 forms an mRNA editing complex involved into cytidine to uridine editing of a variety of mRNA molecules. Through the binding of their 3’UTR, also stabilizes a variety of mRNAs and regulates the expression of genes such as the interferon alpha/beta receptor and interleukin-10. Also involved in the alternative splicing of several genes including TJP1. Binds the pre-mRNA (U)GCAUG consensus sequences in downstream intronic regions of alternative exons, regulating their exclusion and inclusion into mRNAs. Independently of its RNA-binding activity, could negatively regulate MAVS by promoting its lysosomal degradation.

Subunit / interactions. Homodimer. Interacts with A1CF. Interacts with APOBEC1; form an mRNA editing complex. Interacts with RBPMS.

Subcellular location. Nucleus. Cytoplasm.

Domain organisation. The RRM domains are required for mRNA stabilization.

Induction. Up-regulated by interferon.

Similarity. Belongs to the RRM RBM47 family.

Isoforms (2)

UniProt ID	Names	Canonical?
A0AV96-1	1, h-isoform a	yes
A0AV96-2	2, h-isoform b

RefSeq proteins (4): NP_001092104, NP_001358042, NP_001358043, NP_061900 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR006535	HnRNP_R/Q_splicing_fac	Family
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR034440	RBM47_RRM2	Domain
IPR034445	RBM47_RRM3	Domain
IPR035979	RBD_domain_sf	Homologous_superfamily
IPR047044	RBM47_RRM1	Domain

Pfam: PF00076

UniProt features (30 total): modified residue 5, strand 5, domain 3, mutagenesis site 3, sequence conflict 3, turn 3, sequence variant 2, helix 2, chain 1, splice variant 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2DIS	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0AV96-F1	64.38	0.28

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 (5): 405, 332, 394, 394, 405

Mutagenesis-validated functional residues (3):

Position	Phenotype
115	loss of function in regulation of alternative splicing. loss of pre-mrna binding activity. decreased homodimerization.
198	decreased function in regulation of alternative splicing. decreased pre-mrna binding. no effect on homodimerization.
285	decreased function in regulation of alternative splicing. no effect on pre-mrna binding.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 377 (showing top): GOBP_HEMATOPOIETIC_PROGENITOR_CELL_DIFFERENTIATION, HNF3ALPHA_Q6, GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, GOBP_RESPONSE_TO_PEPTIDE, GCANCTGNY_MYOD_Q6, TTTGTAG_MIR520D, GOBP_ALTERNATIVE_MRNA_SPLICING_VIA_SPLICEOSOME, GOBP_3_UTR_MEDIATED_MRNA_STABILIZATION, GOBP_RESPONSE_TO_TYPE_I_INTERFERON, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CYTOKINE_PRODUCTION, HNF1_Q6, GOBP_POSITIVE_REGULATION_OF_RESPONSE_TO_EXTERNAL_STIMULUS, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOBP_REGULATION_OF_IMMUNE_RESPONSE

GO Biological Process (10): regulation of alternative mRNA splicing, via spliceosome (GO:0000381), hematopoietic progenitor cell differentiation (GO:0002244), mRNA processing (GO:0006397), RNA splicing (GO:0008380), cytidine to uridine editing (GO:0016554), positive regulation of interleukin-10 production (GO:0032733), positive regulation of type I interferon-mediated signaling pathway (GO:0060340), 3’-UTR-mediated mRNA stabilization (GO:0070935), low-density lipoprotein particle clearance (GO:0034383), negative regulation of mRNA catabolic process (GO:1902373)

GO Molecular Function (7): RNA binding (GO:0003723), mRNA binding (GO:0003729), mRNA 3’-UTR binding (GO:0003730), enzyme binding (GO:0019899), enzyme-substrate adaptor activity (GO:0140767), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), cytoplasm (GO:0005737), apolipoprotein B mRNA editing enzyme complex (GO:0030895)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
binding	2
alternative mRNA splicing, via spliceosome	1
regulation of mRNA splicing, via spliceosome	1
hemopoiesis	1
cell differentiation	1
mRNA metabolic process	1
base conversion or substitution editing	1
positive regulation of cytokine production	1
interleukin-10 production	1
regulation of interleukin-10 production	1
positive regulation of cytokine-mediated signaling pathway	1
positive regulation of innate immune response	1
type I interferon-mediated signaling pathway	1
regulation of type I interferon-mediated signaling pathway	1
mRNA stabilization	1
plasma lipoprotein particle clearance	1
low-density lipoprotein particle disassembly	1
mRNA catabolic process	1
positive regulation of gene expression	1
regulation of mRNA catabolic process	1
negative regulation of RNA catabolic process	1
negative regulation of mRNA metabolic process	1
nucleic acid binding	1
RNA binding	1
mRNA binding	1
protein binding	1
protein-macromolecule adaptor activity	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1
mRNA editing complex	1
nuclear protein-containing complex	1

Protein interactions and networks

STRING

1618 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RBM47	APOBEC1	P41238	684
RBM47	ZCCHC24	Q8N2G6	591
RBM47	ESRP2	Q9H6T0	564
RBM47	ESRP1	Q6NXG1	533
RBM47	DKK1	O94907	526
RBM47	NANOG	Q9H9S0	511
RBM47	EIF4A3	P38919	469
RBM47	TMEM156	Q8N614	467
RBM47	RBFOX2	O43251	464
RBM47	SMIM14	Q96QK8	451
RBM47	N4BP2	Q86UW6	450
RBM47	LUZP4	Q9P127	447
RBM47	LIAS	O43766	435
RBM47	MBNL1	Q9NR56	428
RBM47	ELAVL1	Q15717	424

IntAct

55 interactions, top by confidence:

A	B	Type	Score
	RBM47	psi-mi:“MI:0915”(physical association)	0.560
RBM47	PCBP3	psi-mi:“MI:0915”(physical association)	0.560
RBM47	ZNF385C	psi-mi:“MI:0915”(physical association)	0.560
RBM47	CAMK2A	psi-mi:“MI:0915”(physical association)	0.560
RBM47	C1orf94	psi-mi:“MI:0915”(physical association)	0.560
RBM47	FAM22F	psi-mi:“MI:0915”(physical association)	0.560
RBM47	C10orf55	psi-mi:“MI:0915”(physical association)	0.560
RBM47	PRR13	psi-mi:“MI:0915”(physical association)	0.560
RBM47	RBFOX1	psi-mi:“MI:0915”(physical association)	0.560
RBM47	CELF5	psi-mi:“MI:0915”(physical association)	0.560
RBM47	OTX2	psi-mi:“MI:0915”(physical association)	0.560
N	RBM47	psi-mi:“MI:0914”(association)	0.530
RBM46	RBM47	psi-mi:“MI:0915”(physical association)	0.500
ATM	RBM47	psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
N	MRPL45	psi-mi:“MI:0914”(association)	0.350
N	RBM47	psi-mi:“MI:0914”(association)	0.350
ESR2		psi-mi:“MI:0914”(association)	0.350
PIP	RBM47	psi-mi:“MI:0914”(association)	0.350
DYRK2	RBM47	psi-mi:“MI:0914”(association)	0.350
RBM47	PTCD1	psi-mi:“MI:0914”(association)	0.350
PRR3	RBM47	psi-mi:“MI:0914”(association)	0.350
RBM47	IGF2BP3	psi-mi:“MI:0914”(association)	0.350
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350

BioGRID (237): C1orf94 (Two-hybrid), HSFY1 (Two-hybrid), RBM47 (Affinity Capture-MS), RBM47 (Affinity Capture-MS), RBM47 (Affinity Capture-RNA), RBM47 (Affinity Capture-RNA), RBM47 (Affinity Capture-MS), RBM47 (Two-hybrid), RBM47 (Two-hybrid), RBM47 (Two-hybrid), RBM47 (Two-hybrid), RBM47 (Two-hybrid), RBM47 (Two-hybrid), OTX2 (Two-hybrid), PCBP3 (Two-hybrid)

ESM2 similar proteins: A0A8I6B1J2, A0AV96, A8XND8, B3M3R5, B3NGA1, B4HUE4, B4IX08, B4KX02, B4LFQ9, B4MM23, B4PIS2, B4QRJ0, F2Z3T4, G5EFF1, O01367, P16914, P31367, Q0V9L3, Q24312, Q32NN2, Q56V19, Q5R4F5, Q5R5P4, Q5VZF2, Q5W9D5, Q5W9D6, Q5W9D7, Q5ZKW9, Q66H68, Q6IRN2, Q6P0D0, Q6P104, Q6Q2B2, Q7JJZ8, Q7TSY6, Q8C181, Q8MSV2, Q8R003, Q8R205, Q91WT8

Diamond homologs: A0A8M1NHK4, A0AV96, A0JM51, A4FV72, A4QUF0, A8WLV5, O01671, O04425, O43040, O43390, O60506, P28659, P33240, P86049, Q08BH5, Q08E07, Q0P4R6, Q0V9L3, Q10B98, Q14498, Q28HE9, Q2HJG2, Q2UK72, Q3UEB3, Q4QQT3, Q4R2Z0, Q4R535, Q5B630, Q5EA36, Q5R469, Q5R5P4, Q5R723, Q5R9H4, Q5RC41, Q5RC80, Q5RDA3, Q5SZQ8, Q5YD48, Q66H68, Q6DCB7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	77
Likely benign	2
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

921 predictions. Top by Δscore:

Variant	Effect	Δscore
4:40432645:CTCTA:C	donor_loss	1.0000
4:40432646:TCTA:T	donor_loss	1.0000
4:40432647:CTACC:C	donor_loss	1.0000
4:40432648:TACCT:T	donor_loss	1.0000
4:40432649:A:C	donor_loss	1.0000
4:40432650:CCT:C	donor_loss	1.0000
4:40432858:GGCTA:G	acceptor_gain	1.0000
4:40432860:CTA:C	acceptor_gain	1.0000
4:40432861:TA:T	acceptor_gain	1.0000
4:40432863:C:CC	acceptor_gain	1.0000
4:40432875:C:CT	acceptor_gain	1.0000
4:40432876:A:T	acceptor_gain	1.0000
4:40466571:ACTC:A	donor_loss	1.0000
4:40466573:TCACC:T	donor_loss	1.0000
4:40466575:A:AC	donor_gain	1.0000
4:40466575:A:T	donor_loss	1.0000
4:40466575:AC:A	donor_gain	1.0000
4:40466576:C:CT	donor_gain	1.0000
4:40466576:CC:C	donor_gain	1.0000
4:40466576:CCAA:C	donor_gain	1.0000
4:40466576:CCAAA:C	donor_gain	1.0000
4:40466695:AAATC:A	acceptor_gain	1.0000
4:40466696:AATC:A	acceptor_gain	1.0000
4:40466697:ATC:A	acceptor_gain	1.0000
4:40466698:TC:T	acceptor_gain	1.0000
4:40466699:CC:C	acceptor_gain	1.0000
4:40466700:C:CC	acceptor_gain	1.0000
4:40466700:C:CG	acceptor_loss	1.0000
4:40466701:T:C	acceptor_loss	1.0000
4:40426139:CGGCC:C	acceptor_gain	0.9900

AlphaMissense

3872 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:40437941:G:T	P318H	1.000
4:40437942:G:A	P318S	1.000
4:40437943:C:A	K317N	1.000
4:40437943:C:G	K317N	1.000
4:40437945:T:C	K317E	1.000
4:40437947:G:A	A316V	1.000
4:40437947:G:T	A316D	1.000
4:40437948:C:T	A316T	1.000
4:40437956:A:T	V313D	1.000
4:40438004:G:T	A297D	1.000
4:40438005:C:G	A297P	1.000
4:40438013:G:T	A294D	1.000
4:40438014:C:G	A294P	1.000
4:40438023:G:T	R291S	1.000
4:40438030:G:C	F288L	1.000
4:40438030:G:T	F288L	1.000
4:40438031:A:G	F288S	1.000
4:40438032:A:G	F288L	1.000
4:40438033:G:C	H287Q	1.000
4:40438033:G:T	H287Q	1.000
4:40438034:T:C	H287R	1.000
4:40438035:G:C	H287D	1.000
4:40438037:A:T	V286E	1.000
4:40438039:G:C	F285L	1.000
4:40438039:G:T	F285L	1.000
4:40438040:A:C	F285C	1.000
4:40438040:A:G	F285S	1.000
4:40438041:A:C	F285V	1.000
4:40438041:A:G	F285L	1.000
4:40438041:A:T	F285I	1.000

dbSNP variants (sampled 300 via entrez): RS1000001446 (4:40472546 G>A), RS1000003745 (4:40632038 C>G,T), RS1000028296 (4:40472502 C>T), RS10000300 (4:40464530 G>T), RS1000043007 (4:40427887 T>C), RS1000067771 (4:40631368 T>C), RS1000079679 (4:40590402 A>C,G), RS1000084254 (4:40600990 A>C,G), RS1000136593 (4:40508415 G>A), RS1000152682 (4:40515343 C>T), RS1000159242 (4:40492690 T>C), RS1000181911 (4:40527027 G>T), RS1000183962 (4:40608010 C>A), RS1000190681 (4:40448196 AAAATAAAT>A,AAAAT,AAAATAAATAAAT), RS1000193297 (4:40534479 G>A)

Disease associations

OMIM: gene MIM:619104 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

11 associations (top):

Study	Trait	p-value
GCST002575_4	Body mass index (change over time)	2.000000e-07
GCST004863_131	Mosquito bite size	1.000000e-07
GCST006020_7	Diastolic blood pressure	8.000000e-08
GCST006021_45	Systolic blood pressure	2.000000e-08
GCST006023_1	Hypertension	8.000000e-07
GCST006614_24	Total cholesterol levels	1.000000e-09
GCST009391_142	Metabolite levels	6.000000e-06
GCST010151_12	Carotid intima media thickness x smoking interaction	3.000000e-06
GCST010243_234	Apolipoprotein B levels	4.000000e-10
GCST011742_47	Triglyceride levels in HIV infection	1.000000e-06
GCST90002393_221	Monocyte count	2.000000e-13

EFO canonical traits (10, from GWAS)

EFO ID	Trait name
EFO:0005937	longitudinal BMI measurement
EFO:0008378	mosquito bite reaction size measurement
EFO:0006336	diastolic blood pressure
EFO:0006335	systolic blood pressure
EFO:0004574	total cholesterol measurement
EFO:0010475	deoxycholate measurement
EFO:0006527	smoking status measurement
EFO:0004615	apolipoprotein B measurement
EFO:0004530	triglyceride measurement
EFO:0005091	monocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, decreases methylation	7
Benzo(a)pyrene	decreases expression, increases expression, increases methylation, affects methylation	6
Air Pollutants	affects cotreatment, increases abundance, increases oxidation, affects expression, decreases expression (+1 more)	4
Cadmium Chloride	increases expression, increases abundance	3
Particulate Matter	decreases expression, increases abundance, increases expression, affects expression	3
methylmercuric chloride	decreases expression, increases expression	2
mercuric bromide	increases expression, affects cotreatment	2
entinostat	increases expression, affects cotreatment	2
Vorinostat	affects cotreatment, decreases expression	2
Acetaminophen	decreases expression	2
Ozone	affects expression, affects cotreatment, increases oxidation, increases abundance	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Tretinoin	increases expression	2
Cyclosporine	decreases expression, increases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, increases expression	2
bisphenol F	affects cotreatment, increases methylation	1
2,4,6-tribromophenol	increases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	increases oxidation, increases abundance, affects cotreatment	1
bisphenol A	decreases expression	1
decabromobiphenyl ether	decreases expression	1
sulforaphane	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
tetrabromobisphenol A	increases expression	1
benzo(e)pyrene	increases methylation	1
periodate-oxidized adenosine	affects expression	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
cyclic 3’,5’-uridine monophosphate	affects binding	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression, decreases expression	1

Clinical trials (associated diseases)

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