DDX46

Summary

DDX46 (DEAD-box helicase 46, HGNC:18681) is a protein-coding gene on chromosome 5q31.1, encoding Probable ATP-dependent RNA helicase DDX46 (Q7L014). Component of the 17S U2 SnRNP complex of the spliceosome, a large ribonucleoprotein complex that removes introns from transcribed pre-mRNAs. It is a selective cancer dependency (DepMap: 88.8% of cell lines).

This gene encodes a member of the DEAD box protein family. DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure, such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. The protein encoded by this gene is a component of the 17S U2 snRNP complex; it plays an important role in pre-mRNA splicing. Multiple alternatively spliced transcript variants have been found for this gene.

Source: NCBI Gene 9879 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 62 total
• Cancer dependency (DepMap): dependent in 88.8% of screened cell lines
• MANE Select transcript: NM_001300860

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18681
Approved symbol	DDX46
Name	DEAD-box helicase 46
Location	5q31.1
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0801, FLJ25329, PRPF5, Prp5
Ensembl gene	ENSG00000145833
Ensembl biotype	protein_coding
OMIM	617848
Entrez	9879

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 5 protein_coding, 5 retained_intron, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000354283, ENST00000452510, ENST00000503946, ENST00000505592, ENST00000506332, ENST00000507392, ENST00000509178, ENST00000509255, ENST00000513592, ENST00000513987, ENST00000628477, ENST00000876680, ENST00000939865

RefSeq mRNA: 2 — MANE Select: NM_001300860 NM_001300860, NM_014829

CCDS: CCDS34240, CCDS75306

Canonical transcript exons

ENST00000452510 — 23 exons

Exon	Start	End
ENSE00001006724	134773696	134773861
ENSE00001006729	134777574	134777725
ENSE00001006734	134781921	134782086
ENSE00001006735	134781133	134781246
ENSE00001085897	134766917	134767060
ENSE00001085904	134770903	134770999
ENSE00001085905	134763904	134764092
ENSE00001194511	134828659	134831121
ENSE00002073726	134758779	134758955
ENSE00003458916	134811221	134811358
ENSE00003465738	134784366	134784541
ENSE00003489979	134817496	134817714
ENSE00003490457	134807748	134807941
ENSE00003529761	134782945	134783065
ENSE00003532450	134788513	134788591
ENSE00003545345	134794850	134795014
ENSE00003549519	134816430	134816606
ENSE00003563490	134795988	134796150
ENSE00003589006	134811696	134811845
ENSE00003597983	134818860	134819004
ENSE00003665514	134785465	134785586
ENSE00003682645	134790470	134790552
ENSE00004473828	134826947	134827020

Expression profiles

Bgee: expression breadth ubiquitous, 294 present calls, max score 97.01.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 75.1152 / max 1923.3843, expressed in 1825 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
58608	75.1152	1825

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	97.01	gold quality
gluteal muscle	UBERON:0002000	96.20	gold quality
tibia	UBERON:0000979	95.46	gold quality
monocyte	CL:0000576	95.42	gold quality
mononuclear cell	CL:0000842	95.40	gold quality
leukocyte	CL:0000738	95.08	gold quality
tonsil	UBERON:0002372	94.59	gold quality
trabecular bone tissue	UBERON:0002483	94.47	gold quality
endometrium	UBERON:0001295	94.37	gold quality
visceral pleura	UBERON:0002401	94.33	gold quality
triceps brachii	UBERON:0001509	94.26	gold quality
esophagus squamous epithelium	UBERON:0006920	94.18	gold quality
epithelium of nasopharynx	UBERON:0001951	93.88	gold quality
endometrium epithelium	UBERON:0004811	93.88	gold quality
paraflocculus	UBERON:0005351	93.82	gold quality
mucosa of sigmoid colon	UBERON:0004993	93.81	gold quality
pleura	UBERON:0000977	93.74	gold quality
germinal epithelium of ovary	UBERON:0001304	93.73	gold quality
buccal mucosa cell	CL:0002336	93.71	silver quality
ventricular zone	UBERON:0003053	93.60	gold quality
rectum	UBERON:0001052	93.57	gold quality
parietal pleura	UBERON:0002400	93.56	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	93.42	gold quality
embryo	UBERON:0000922	93.33	gold quality
epithelium of esophagus	UBERON:0001976	93.30	gold quality
biceps brachii	UBERON:0001507	93.24	gold quality
skin of hip	UBERON:0001554	93.23	gold quality
cortical plate	UBERON:0005343	93.20	gold quality
vermiform appendix	UBERON:0001154	93.09	gold quality
colonic epithelium	UBERON:0000397	92.95	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	11.23

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

122 targeting DDX46, 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-1252-5P	100.00	69.80	2774
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-8087	99.90	69.55	1351
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-4302	99.89	67.94	1187
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-519D-3P	99.88	73.97	2607
HSA-MIR-106B-5P	99.88	74.72	2795

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 88.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 11)

• characterization of protein associated with the human 17S U2 snRNP and one of its stable subunits, SF3b; results indicate that Prp5 plays an important role in pre-mRNA splicing, acting during or prior to prespliceosome assembly (PMID:12234937)
• Prp5 forms a bridge between U1 and U2 Small Nuclear Ribonucleoproteins at the time of pre-spliceosome formation (PMID:14713954)
• Short-term exercise resulted in a significant increase of mRNA expression of genes encoding proteins involved in the formation of precatalytic splisosome: DDX46. (PMID:19902070)
• DDX46 is critical for colorectal cancer (CRC) cell proliferation and is a potential therapeutic target for CRC treatment. (PMID:25680556)
• DDX46 is critical for ESCC cells proliferation. (PMID:27176873)
• Knockdown of DDX46 inhibited osteosarcoma cell proliferation. (PMID:27697093)
• DDX46 silencing inhibits cell proliferation by activating apoptosis and autophagy in cutaneous squamous cell carcinoma. (PMID:33000271)
• Knockdown of DDX46 suppresses the proliferation and invasion of gastric cancer through inactivating Akt/GSK-3beta/beta-catenin pathway. (PMID:33347858)
• The role of DDX46 in breast cancer proliferation and invasiveness: A potential therapeutic target. (PMID:36200534)
• Mechanisms of the RNA helicases DDX42 and DDX46 in human U2 snRNP assembly. (PMID:36797247)
• Oncogenic DDX46 promotes pancreatic cancer development and gemcitabine resistance by facilitating the JMJD6/CDK4 signaling pathway. (PMID:38764294)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ddx46	ENSDARG00000099458
mus_musculus	Ddx46	ENSMUSG00000021500
rattus_norvegicus	Ddx46	ENSRNOG00000021637

Paralogs (38): DDX20 (ENSG00000064703), DDX3Y (ENSG00000067048), DDX1 (ENSG00000079785), DDX43 (ENSG00000080007), DDX18 (ENSG00000088205), DDX24 (ENSG00000089737), DDX17 (ENSG00000100201), DDX49 (ENSG00000105671), DDX50 (ENSG00000107625), DDX5 (ENSG00000108654), DDX25 (ENSG00000109832), DDX6 (ENSG00000110367), DDX55 (ENSG00000111364), DDX59 (ENSG00000118197), DDX54 (ENSG00000123064), DDX39A (ENSG00000123136), DDX27 (ENSG00000124228), DDX31 (ENSG00000125485), DDX56 (ENSG00000136271), EIF4A3 (ENSG00000141543), DDX4 (ENSG00000152670), EIF4A2 (ENSG00000156976), DDX19B (ENSG00000157349), EIF4A1 (ENSG00000161960), DDX21 (ENSG00000165732), DDX19A (ENSG00000168872), TDRD12 (ENSG00000173809), DDX23 (ENSG00000174243), DDX10 (ENSG00000178105), DDX28 (ENSG00000182810), DDX41 (ENSG00000183258), DDX53 (ENSG00000184735), DDX51 (ENSG00000185163), DDX42 (ENSG00000198231), DDX39B (ENSG00000198563), DDX47 (ENSG00000213782), DDX3X (ENSG00000215301), DDX52 (ENSG00000278053)

Protein

Protein identifiers

Probable ATP-dependent RNA helicase DDX46 — Q7L014 (reviewed: Q7L014)

Alternative names: DEAD box protein 46, PRP5 homolog

All UniProt accessions (4): A0A0C4DG89, D6RJA6, Q7L014, H0YAD5

UniProt curated annotations — full annotation on UniProt →

Function. Component of the 17S U2 SnRNP complex of the spliceosome, a large ribonucleoprotein complex that removes introns from transcribed pre-mRNAs. The 17S U2 SnRNP complex (1) directly participates in early spliceosome assembly and (2) mediates recognition of the intron branch site during pre-mRNA splicing by promoting the selection of the pre-mRNA branch-site adenosine, the nucleophile for the first step of splicing. Within the 17S U2 SnRNP complex, DDX46 plays essential roles during assembly of pre-spliceosome and proofreading of the branch site.

Subunit / interactions. Component of the 17S U2 SnRNP complex, a ribonucleoprotein complex that contains small nuclear RNA (snRNA) U2 and a number of specific proteins. Within the 17S U2 SnRNP complex, DDX46 is part of the SF3B subcomplex, which is required for ‘A’ complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence in pre-mRNA. Recruited to the 17S U2 SnRNP complex following release of DDX42; DDX42 and DDX46 bind the SF3B subcomplex in a competitive manner.

Subcellular location. Nucleus speckle. Nucleus. Cajal body.

Similarity. Belongs to the DEAD box helicase family. DDX46/PRP5 subfamily.

RefSeq proteins (2): NP_001287789, NP_055644 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000629	RNA-helicase_DEAD-box_CS	Conserved_site
IPR001650	Helicase_C-like	Domain
IPR011545	DEAD/DEAH_box_helicase_dom	Domain
IPR014001	Helicase_ATP-bd	Domain
IPR014014	RNA_helicase_DEAD_Q_motif	Domain
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR056149	PRP5/DDX46/KHDC4_KH	Domain

Pfam: PF00270, PF00271, PF23469

Catalyzed reactions (Rhea), 1 shown:

• ATP + H2O = ADP + phosphate + H(+) (RHEA:13065)

UniProt features (80 total): helix 18, strand 18, modified residue 10, sequence conflict 9, compositionally biased region 7, cross-link 5, domain 2, turn 2, short sequence motif 2, initiator methionine 1, chain 1, binding site 1, lipid moiety-binding region 1, sequence variant 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

6 structures.

PDB	Method	Resolution (Å)
7Q3L	ELECTRON MICROSCOPY	2.21
7EVO	ELECTRON MICROSCOPY	2.5
7VPX	ELECTRON MICROSCOPY	3
6Y50	ELECTRON MICROSCOPY	4.1
6Y53	ELECTRON MICROSCOPY	7.1
6Y5Q	ELECTRON MICROSCOPY	7.1

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7L014-F1	69.22	0.31

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 (1): 416–423

Post-translational modifications (16): 199, 263, 294, 295, 296, 346, 776, 804, 903, 928, 2, 186, 325, 779, 907, 915

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-72163	mRNA Splicing - Major Pathway
R-HSA-9770562	mRNA Polyadenylation
R-HSA-9918481	Dengue Virus-Host Interactions
R-HSA-9943411	CHD1 and CHD2 subfamily

MSigDB gene sets: 215 (showing top): MITSIADES_RESPONSE_TO_APLIDIN_DN, MORF_HDAC2, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, PUJANA_CHEK2_PCC_NETWORK, WEI_MYCN_TARGETS_WITH_E_BOX, WANG_LMO4_TARGETS_DN, REACTOME_MRNA_3_END_PROCESSING, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_RNA_SPLICING, MORF_PRKDC, GARY_CD5_TARGETS_DN, REACTOME_MRNA_SPLICING, SCHLOSSER_SERUM_RESPONSE_DN, MORF_RAP1A

GO Biological Process (4): mRNA splicing, via spliceosome (GO:0000398), U2-type prespliceosome assembly (GO:1903241), mRNA processing (GO:0006397), RNA splicing (GO:0008380)

GO Molecular Function (9): RNA binding (GO:0003723), RNA helicase activity (GO:0003724), ATP binding (GO:0005524), ATP hydrolysis activity (GO:0016887), nucleotide binding (GO:0000166), nucleic acid binding (GO:0003676), helicase activity (GO:0004386), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (8): fibrillar center (GO:0001650), nucleus (GO:0005634), nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), U2-type spliceosomal complex (GO:0005684), U2 snRNP (GO:0005686), Cajal body (GO:0015030), nuclear speck (GO:0016607)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
mRNA Splicing	1
mRNA 3’-end processing	1
Dengue Virus Infection	1
CHD chromatin remodelers	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
ATP-dependent activity	2
binding	2
cellular anatomical structure	2
nuclear ribonucleoprotein granule	2
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
spliceosomal complex assembly	1
mRNA metabolic process	1
nucleic acid binding	1
helicase activity	1
ATP-dependent activity, acting on RNA	1
catalytic activity, acting on RNA	1
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
ribonucleoside triphosphate phosphatase activity	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
nucleic acid conformation isomerase activity	1
catalytic activity, acting on a nucleic acid	1
catalytic activity	1
nucleolus	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
nuclear protein-containing complex	1
ribonucleoprotein complex	1
spliceosomal complex	1
spliceosomal snRNP complex	1

Protein interactions and networks

STRING

3570 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DDX46	ALKBH5	Q6P6C2	981
DDX46	DHX38	Q92620	976
DDX46	SNRNP200	O75643	862
DDX46	SF3A2	Q15428	835
DDX46	SF3B1	O75533	828
DDX46	MAVS	Q7Z434	816
DDX46	TRAF3	Q13114	809
DDX46	SF3A3	Q12874	797
DDX46	SF3A1	Q15459	788
DDX46	DHX15	O43143	760
DDX46	TRAF6	Q9Y4K3	748
DDX46	PRPF8	Q6P2Q9	728
DDX46	XAB2	Q9HCS7	693
DDX46	DHX16	O60231	668
DDX46	PHF5A	Q7RTV0	667
DDX46	HTATSF1	O43719	667

IntAct

135 interactions, top by confidence:

A	B	Type	Score
SNRPF	GEMIN2	psi-mi:“MI:0914”(association)	0.910
CSNK1A1	FAM83G	psi-mi:“MI:0914”(association)	0.900
MED21	MED19	psi-mi:“MI:0914”(association)	0.880
HIF1AN	APBA3	psi-mi:“MI:0914”(association)	0.850
DDX46	SRPK2	psi-mi:“MI:0915”(physical association)	0.800
SNRPE	GEMIN2	psi-mi:“MI:0914”(association)	0.770
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
NCBP2	KPNA3	psi-mi:“MI:0914”(association)	0.640
SNRPA1	U2SURP	psi-mi:“MI:0914”(association)	0.640
SNRPB	SART1	psi-mi:“MI:0914”(association)	0.640
SUMO1	CBX4	psi-mi:“MI:0914”(association)	0.600
SNRNP27	UBA6	psi-mi:“MI:0914”(association)	0.530
SNRPE	PRMT5	psi-mi:“MI:0914”(association)	0.530
HSD3B2	NARS1	psi-mi:“MI:0914”(association)	0.530
SNRPE	SNRPGP15	psi-mi:“MI:0914”(association)	0.530
SRPK2	RRP9	psi-mi:“MI:0914”(association)	0.530
EZH1	EPOP	psi-mi:“MI:0914”(association)	0.530
ZNF181	DDX46	psi-mi:“MI:0915”(physical association)	0.400
CCDC77	DDX46	psi-mi:“MI:0915”(physical association)	0.400
Sf3a1	U2SURP	psi-mi:“MI:0915”(physical association)	0.400
DDX46	SF3A2	psi-mi:“MI:0915”(physical association)	0.400
JUN		psi-mi:“MI:0914”(association)	0.350
JUN	TPM3	psi-mi:“MI:0914”(association)	0.350
RRP1B	ZNF785	psi-mi:“MI:0914”(association)	0.350
METTL14	HMGB1P1	psi-mi:“MI:0914”(association)	0.350
MAB21L2	PTBP1	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (301): DDX46 (Affinity Capture-MS), DDX46 (Affinity Capture-MS), DDX46 (Affinity Capture-MS), DDX46 (Affinity Capture-MS), DDX46 (Affinity Capture-MS), DDX46 (Affinity Capture-MS), DDX46 (Affinity Capture-MS), DDX46 (Affinity Capture-MS), DDX46 (Co-fractionation), DDX46 (Co-fractionation), DDX46 (Co-fractionation), DDX46 (Co-fractionation), DDX46 (Co-fractionation), DDX46 (Co-fractionation), DDX46 (Co-fractionation)

ESM2 similar proteins: A1Z9L3, A2A4P0, A3KFM7, A3KMI0, B2RR83, D3ZA12, D4A2Z8, E9PZM4, F4IJV4, F4JY24, O14647, O42643, O45244, O60231, O60264, P28370, P34498, P40201, P41877, P93008, Q05B79, Q09530, Q10752, Q14562, Q17R09, Q24368, Q38953, Q4TVV3, Q53RK8, Q54F05, Q569Z5, Q5R6D8, Q5R746, Q62780, Q6PGB8, Q767K6, Q7G8Y3, Q7L014, Q7YR39, Q7ZU90

Diamond homologs: A0A1D6GDY8, A0A1D6LAB7, A0R8U6, A1C5V3, A1DG51, A1DGZ7, A5DL80, A5DS77, A6ZRX0, A6ZUA1, B9XXL6, O25029, P0A4D7, P0A4D8, P0A9P6, P0A9P7, P0A9P8, P20447, P24783, P25888, P33906, P42305, P44586, P46942, P57453, P96614, P9WH04, P9WH05, Q0CL13, Q0D8N0, Q0DM51, Q0ILZ4, Q10202, Q1DP69, Q2FF45, Q2FWH5, Q2U070, Q2YUH3, Q39189, Q3B8Q1

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
DDX46	“form complex”	“U2 snRNP complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 189 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
Metabolism of non-coding RNA	5	24.0×	1e-04
mRNA Splicing	22	18.3×	9e-20
Processing of Capped Intron-Containing Pre-mRNA	26	16.2×	5e-22
mRNA Splicing - Minor Pathway	9	15.3×	5e-07
Transport of Mature Transcript to Cytoplasm	5	14.4×	8e-04
mRNA Polyadenylation	20	13.3×	4e-15
RNA Polymerase II Transcription Termination	8	13.3×	1e-05
mRNA Splicing - Major Pathway	30	12.4×	5e-22

GO biological processes:

GO term	Partners	Fold	FDR
U2-type prespliceosome assembly	9	33.8×	1e-09
negative regulation of mRNA splicing, via spliceosome	6	27.7×	1e-05
spliceosomal complex assembly	6	21.8×	5e-05
spliceosomal snRNP assembly	6	21.0×	5e-05
RNA splicing, via transesterification reactions	5	18.8×	7e-04
mRNA splicing, via spliceosome	23	12.7×	5e-16
regulation of alternative mRNA splicing, via spliceosome	8	11.8×	5e-05
RNA splicing	22	11.7×	8e-15

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	29
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3937 predictions. Top by Δscore:

Variant	Effect	Δscore
5:134763978:G:GT	donor_gain	1.0000
5:134766916:GAC:G	acceptor_gain	1.0000
5:134767043:C:T	donor_gain	1.0000
5:134768206:TTC:T	donor_gain	1.0000
5:134770897:T:A	acceptor_gain	1.0000
5:134770973:G:GT	donor_gain	1.0000
5:134770976:G:GT	donor_gain	1.0000
5:134770992:A:G	donor_gain	1.0000
5:134770997:G:GT	donor_gain	1.0000
5:134770998:GC:G	donor_gain	1.0000
5:134771000:G:GG	donor_gain	1.0000
5:134773685:A:AG	acceptor_gain	1.0000
5:134773686:T:G	acceptor_gain	1.0000
5:134773693:A:AG	acceptor_gain	1.0000
5:134773694:A:G	acceptor_gain	1.0000
5:134773695:G:GC	acceptor_gain	1.0000
5:134773695:GA:G	acceptor_gain	1.0000
5:134773695:GAA:G	acceptor_gain	1.0000
5:134773695:GAAC:G	acceptor_gain	1.0000
5:134773695:GAACT:G	acceptor_gain	1.0000
5:134773697:A:AG	acceptor_gain	1.0000
5:134773810:G:GT	donor_gain	1.0000
5:134773811:A:T	donor_gain	1.0000
5:134773833:G:T	donor_gain	1.0000
5:134773840:TG:T	donor_gain	1.0000
5:134773841:GG:G	donor_gain	1.0000
5:134773852:G:GT	donor_gain	1.0000
5:134773858:GATGG:G	donor_loss	1.0000
5:134773859:ATGGT:A	donor_loss	1.0000
5:134773860:TGGTA:T	donor_loss	1.0000

AlphaMissense

6793 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:134773736:G:C	R163P	1.000
5:134773758:G:C	W170C	1.000
5:134773758:G:T	W170C	1.000
5:134773760:G:C	R171P	1.000
5:134773840:T:A	W198R	1.000
5:134773840:T:C	W198R	1.000
5:134773842:G:C	W198C	1.000
5:134773842:G:T	W198C	1.000
5:134782960:G:C	R354P	1.000
5:134783019:T:A	W374R	1.000
5:134783019:T:C	W374R	1.000
5:134783032:G:A	G378E	1.000
5:134784392:T:A	I398N	1.000
5:134784403:G:C	A402P	1.000
5:134784425:G:T	G409V	1.000
5:134784428:G:C	R410P	1.000
5:134784437:T:A	I413N	1.000
5:134784439:G:C	G414R	1.000
5:134784440:G:A	G414D	1.000
5:134784445:G:C	A416P	1.000
5:134784446:C:A	A416D	1.000
5:134784452:C:T	T418I	1.000
5:134784454:G:A	G419R	1.000
5:134784454:G:C	G419R	1.000
5:134784455:G:A	G419E	1.000
5:134784455:G:T	G419V	1.000
5:134784457:A:C	S420R	1.000
5:134784459:T:A	S420R	1.000
5:134784459:T:G	S420R	1.000
5:134784460:G:A	G421R	1.000

dbSNP variants (sampled 300 via entrez): RS1000000691 (5:134816818 A>G), RS1000019324 (5:134817147 T>C,G), RS1000060014 (5:134813093 C>T), RS1000072917 (5:134780050 T>C,G), RS1000112139 (5:134765823 T>A), RS1000115823 (5:134831235 C>A,G,T), RS1000175901 (5:134819830 C>T), RS1000182409 (5:134777310 A>G,T), RS1000187975 (5:134780269 G>A), RS1000307450 (5:134807432 T>C), RS1000307565 (5:134757169 C>T), RS1000333639 (5:134759959 G>A,C), RS1000384701 (5:134792948 A>T), RS1000396314 (5:134830173 A>G), RS1000418357 (5:134773383 G>A,C)

Disease associations

OMIM: gene MIM:617848 | 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
GCST000175_35	Height	8.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, decreases expression, decreases methylation	3
Valproic Acid	affects cotreatment, increases expression, affects expression	3
Cadmium Chloride	decreases expression, increases expression	3
sodium arsenite	affects binding, increases reaction, decreases expression	2
Air Pollutants	affects cotreatment, increases abundance, increases oxidation, decreases expression	2
aristolochic acid I	decreases expression	1
TAK-243	decreases sumoylation	1
2,4,6-tribromophenol	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
deoxynivalenol	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
butyraldehyde	decreases expression	1
coumarin	increases phosphorylation	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
cylindrospermopsin	decreases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
ICG 001	increases expression	1
abrine	decreases expression	1
LDN 193189	affects cotreatment, decreases expression	1
NSC 689534	affects binding, decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Decitabine	affects expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Allergens	increases expression	1
Arbutin	increases expression	1
Atrazine	decreases expression	1
Caffeine	affects phosphorylation	1

Clinical trials (associated diseases)

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