DDX56

Summary

DDX56 (DEAD-box helicase 56, HGNC:18193) is a protein-coding gene on chromosome 7p13, encoding Probable ATP-dependent RNA helicase DDX56 (Q9NY93). Nucleolar RNA helicase that plays a role in various biological processes including innate immunity, ribosome biogenesis or nucleolus organization. It is a common-essential gene (DepMap: required in 100.0% of cancer 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 shows ATPase activity in the presence of polynucleotides and associates with nucleoplasmic 65S preribosomal particles. This gene may be involved in ribosome synthesis, most likely during assembly of the large 60S ribosomal subunit. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 54606 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 109 total
• Cancer dependency (DepMap): dependent in 100.0% of screened cell lines (common-essential)
• MANE Select transcript: NM_019082

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18193
Approved symbol	DDX56
Name	DEAD-box helicase 56
Location	7p13
Locus type	gene with protein product
Status	Approved
Aliases	NOH61
Ensembl gene	ENSG00000136271
Ensembl biotype	protein_coding
OMIM	608023
Entrez	54606

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 11 protein_coding, 4 nonsense_mediated_decay, 3 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000258772, ENST00000415758, ENST00000421223, ENST00000431640, ENST00000433257, ENST00000446987, ENST00000448192, ENST00000467318, ENST00000473924, ENST00000479440, ENST00000479602, ENST00000485367, ENST00000875707, ENST00000875708, ENST00000875709, ENST00000875710, ENST00000875711, ENST00000921591, ENST00000960131, ENST00000960132

RefSeq mRNA: 2 — MANE Select: NM_019082 NM_001257189, NM_019082

CCDS: CCDS5492, CCDS59053

Canonical transcript exons

ENST00000258772 — 14 exons

Exon	Start	End
ENSE00000924210	44573583	44573744
ENSE00001724731	44573836	44573908
ENSE00001813604	44565804	44566079
ENSE00003462534	44571492	44571736
ENSE00003478004	44568903	44568992
ENSE00003490025	44569809	44569903
ENSE00003515068	44570015	44570128
ENSE00003524268	44568118	44568223
ENSE00003524634	44572347	44572437
ENSE00003525659	44569130	44569203
ENSE00003560432	44570758	44570877
ENSE00003561063	44572890	44573050
ENSE00003568265	44566448	44566524
ENSE00003583263	44572574	44572744

Expression profiles

Bgee: expression breadth ubiquitous, 279 present calls, max score 96.92.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 49.3359 / max 368.6408, expressed in 1821 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
83885	47.9225	1820
83886	1.4133	743

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lower esophagus mucosa	UBERON:0035834	96.92	gold quality
cerebellar hemisphere	UBERON:0002245	96.91	gold quality
cerebellar cortex	UBERON:0002129	96.83	gold quality
right hemisphere of cerebellum	UBERON:0014890	96.83	gold quality
right lobe of thyroid gland	UBERON:0001119	96.82	gold quality
left lobe of thyroid gland	UBERON:0001120	96.69	gold quality
mucosa of transverse colon	UBERON:0004991	96.30	gold quality
metanephros cortex	UBERON:0010533	96.00	gold quality
adenohypophysis	UBERON:0002196	95.94	gold quality
right ovary	UBERON:0002118	95.83	gold quality
left ovary	UBERON:0002119	95.82	gold quality
granulocyte	CL:0000094	95.80	gold quality
right lobe of liver	UBERON:0001114	95.70	gold quality
thyroid gland	UBERON:0002046	95.69	gold quality
apex of heart	UBERON:0002098	95.67	gold quality
skin of leg	UBERON:0001511	95.62	gold quality
left uterine tube	UBERON:0001303	95.59	gold quality
right adrenal gland cortex	UBERON:0035827	95.52	gold quality
skin of abdomen	UBERON:0001416	95.45	gold quality
right adrenal gland	UBERON:0001233	95.42	gold quality
endocervix	UBERON:0000458	95.41	gold quality
small intestine Peyer’s patch	UBERON:0003454	95.40	gold quality
right uterine tube	UBERON:0001302	95.39	gold quality
left adrenal gland cortex	UBERON:0035825	95.38	gold quality
cerebellum	UBERON:0002037	95.33	gold quality
left adrenal gland	UBERON:0001234	95.23	gold quality
body of stomach	UBERON:0001161	95.04	gold quality
body of pancreas	UBERON:0001150	94.88	gold quality
pituitary gland	UBERON:0000007	94.82	gold quality
nerve	UBERON:0001021	94.78	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)

15 targeting DDX56, 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-3120-5P	100.00	65.56	965
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-6857-5P	99.87	65.32	985
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-421	98.90	67.04	1883
HSA-MIR-6755-3P	98.61	66.90	834
HSA-MIR-4709-5P	98.51	67.25	1335
HSA-MIR-4450	98.26	68.35	725
HSA-MIR-450A-2-3P	97.91	67.56	1459
HSA-MIR-4521	97.73	67.64	684
HSA-MIR-1202	97.19	66.43	827
HSA-MIR-3972	97.19	66.46	808
HSA-MIR-6736-3P	96.98	65.22	1342
HSA-MIR-4540	96.90	67.46	473
HSA-MIR-6889-5P	90.26	64.13	291

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 100.0% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 11)

• DDX26 maps to7p12, a region of frequent chromosome amplifications in glioblastoma involving the EGFR gene. (PMID:11593297)
• Coimmunoprecipitation confirmed that capsid protein binds to human DDX56 in infected cells and that this interaction is required for assembly of infectious West Nile virus particles. (PMID:21411523)
• The helicase activity of DDX56 is required for its role in assembly of infectious West Nile virus particles. (PMID:22925334)
• West Nile virus infection results in relocalization of DDX56 from nucleoli to virus assembly sites on the endoplasmic reticululm (ER), an observation that is consistent with a role for DDX56 in WNV virion assembly. (PMID:27821284)
• DDX56 inhibits type I interferon by disrupting assembly of IRF3-IPO5 to inhibit IRF3 nucleus import. (PMID:31340999)
• Study identified DDX56 as a novel oncogene on chromosome 7p and a prognostic biomarker of colorectal cancer (CRC). DDX56 can induce oncogenic splicing abnormalities of the G2-M cell cycle checkpoint gene WEE1 which contributes to the inhibition of proliferation and cell cycle progression. (PMID:31390121)
• DDX56 Binds to Chikungunya Virus RNA To Control Infection. (PMID:33109765)
• The DEAD-box helicase DDX56 is a conserved stemness regulator in normal and cancer stem cells. (PMID:33789112)
• DDX56 modulates post-transcriptional Wnt signaling through miRNAs and is associated with early recurrence in squamous cell lung carcinoma. (PMID:34446021)
• DEAD-box helicase 56 functions as an oncogene promote cell proliferation and invasion in gastric cancer via the FOXO1/p21 Cip1/c-Myc signaling pathway. (PMID:35723050)
• DDX56 transcriptionally activates MIST1 to facilitate tumorigenesis of HCC through PTEN-AKT signaling. (PMID:36168636)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ddx56	ENSDARG00000020913
mus_musculus	Ddx56	ENSMUSG00000004393
rattus_norvegicus	Ddx56	ENSRNOG00000004670
drosophila_melanogaster	Ddx56	FBGN0001565
caenorhabditis_elegans		WBGENE00016073

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), EIF4A3 (ENSG00000141543), DDX46 (ENSG00000145833), 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 DDX56 — Q9NY93 (reviewed: Q9NY93)

Alternative names: ATP-dependent 61 kDa nucleolar RNA helicase, DEAD box protein 21, DEAD box protein 56

All UniProt accessions (6): Q9NY93, F8WDT8, F8WEI3, G3V0G3, H7BZN7, H7C3E9

UniProt curated annotations — full annotation on UniProt →

Function. Nucleolar RNA helicase that plays a role in various biological processes including innate immunity, ribosome biogenesis or nucleolus organization. Plays an essential role in maintaining nucleolar integrity in planarian stem cells. Maintains embryonic stem cells proliferation by conventional regulation of ribosome assembly and interaction with OCT4 and POU5F1 complex. Regulates antiviral innate immunity by inhibiting the virus-triggered signaling nuclear translocation of IRF3. Mechanistically, acts by disrupting the interaction between IRF3 and importin IPO5. May play a role in later stages of the processing of the pre-ribosomal particles leading to mature 60S ribosomal subunits. Has intrinsic ATPase activity. (Microbial infection) Helicase activity is important for packaging viral RNA into virions during West Nile virus infection. (Microbial infection) Plays a positive role in foot-and-mouth disease virus replication by inhibiting the phosphorylation of IRF3 leading to inhibition of type I interferon. (Microbial infection) Plays a positive role in EMCV replication by interrupting IRF3 phosphorylation and its nucleus translocation.

Subunit / interactions. May form homooligomeric complexes. Interacts with IRF3. Interacts with OCT4 and POU5F1. (Microbial infection) Interacts with West Nile virus capsid protein C. (Microbial infection) Interacts with foot-and-mouth disease virus protein 3A; this interaction leads to inhibition of type I interferon production. (Microbial infection) Interacts with EMCV protein 3C; this interaction leads to inhibition of type I interferon production.

Subcellular location. Nucleus. Nucleolus.

Tissue specificity. Detected in heart, brain, liver, pancreas, placenta and lung.

Similarity. Belongs to the DEAD box helicase family. DDX56/DBP9 subfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NY93-1	1	yes
Q9NY93-2	2

RefSeq proteins (2): NP_001244118, NP_061955* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
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
IPR050079	DEAD_box_RNA_helicase	Family

Pfam: PF00270, PF00271

Catalyzed reactions (Rhea), 1 shown:

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

UniProt features (19 total): sequence conflict 4, modified residue 3, domain 2, mutagenesis site 2, short sequence motif 2, compositionally biased region 2, chain 1, splice variant 1, region of interest 1, binding site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NY93-F1	80.08	0.36

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): 51–58

Post-translational modifications (3): 141, 532, 126

Mutagenesis-validated functional residues (2):

Position	Phenotype
166	complete loss of interaction with irf3. about 3-4 times less genomic rna in west nile virus particles.
167	complete loss of interaction with irf3. about 3-4 times less genomic rna in west nile virus particles.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 124 (showing top): GOBP_RIBOSOME_BIOGENESIS, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOBP_MODULATION_OF_PROCESS_OF_ANOTHER_ORGANISM, GOBP_NEUROGENESIS, GOBP_NEGATIVE_REGULATION_OF_TYPE_I_INTERFERON_PRODUCTION, GOBP_HOST_MEDIATED_PERTURBATION_OF_VIRAL_PROCESS, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GOBP_CYTOKINE_PRODUCTION, GOBP_VIRAL_GENOME_REPLICATION, GOBP_VIRAL_LIFE_CYCLE, WEST_ADRENOCORTICAL_CARCINOMA_VS_ADENOMA_UP, GOBP_DEFENSE_RESPONSE_TO_VIRUS, GOBP_REGULATION_OF_NEURON_PROJECTION_DEVELOPMENT, chr7p13

GO Biological Process (8): rRNA processing (GO:0006364), positive regulation of neuron projection development (GO:0010976), negative regulation of type I interferon production (GO:0032480), host-mediated perturbation of viral RNA genome replication (GO:0044830), defense response to virus (GO:0051607), cytoplasmic pattern recognition receptor signaling pathway (GO:0002753), protein import into nucleus (GO:0006606), ribosome biogenesis (GO:0042254)

GO Molecular Function (11): RNA binding (GO:0003723), RNA helicase activity (GO:0003724), ATP binding (GO:0005524), ATP hydrolysis activity (GO:0016887), RNA stem-loop binding (GO:0035613), protein sequestering activity (GO:0140311), nucleotide binding (GO:0000166), nucleic acid binding (GO:0003676), helicase activity (GO:0004386), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (4): nucleus (GO:0005634), nucleolus (GO:0005730), cytosol (GO:0005829), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
ATP-dependent activity	2
binding	2
cellular anatomical structure	2
RNA processing	1
rRNA metabolic process	1
ribosome biogenesis	1
regulation of neuron projection development	1
neuron projection development	1
positive regulation of cell projection organization	1
negative regulation of cytokine production	1
regulation of type I interferon production	1
type I interferon production	1
viral RNA genome replication	1
host-mediated perturbation of viral process	1
defense response	1
response to virus	1
positive regulation of cytokine production	1
pattern recognition receptor signaling pathway	1
intracellular receptor signaling pathway	1
intracellular protein transport	1
protein localization to nucleus	1
import into nucleus	1
establishment of protein localization to organelle	1
ribonucleoprotein complex biogenesis	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
RNA binding	1
protein binding	1
molecular sequestering 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
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

4516 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DDX56	DHX36	Q9H2U1	996
DDX56	DDX1	Q92499	989
DDX56	DHX8	Q14562	818
DDX56	EBNA1BP2	Q99848	767
DDX56	WDR46	O15213	764
DDX56	SIRT7	Q9NRC8	720
DDX56	TLE5	Q08117	705
DDX56	RIGI	O95786	701
DDX56	DHX15	O43143	684
DDX56	YBX1	P16990	682
DDX56	DHX9	Q08211	677
DDX56	FBL	P22087	663
DDX56	MYBBP1A	Q9BQG0	647
DDX56	DHX33	Q9H6R0	633
DDX56	GNL3	Q9BVP2	615

IntAct

243 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
NEUROG3	GXYLT2	psi-mi:“MI:0914”(association)	0.640
RPL14	RRP8	psi-mi:“MI:0914”(association)	0.640
NPM1	NVL	psi-mi:“MI:0914”(association)	0.610
EIF4A3	DDX56	psi-mi:“MI:0915”(physical association)	0.560
MECP2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
MAGEB10	GTPBP10	psi-mi:“MI:0914”(association)	0.530
H1-6	ZNF724	psi-mi:“MI:0914”(association)	0.530
RBM34	NVL	psi-mi:“MI:0914”(association)	0.530
RPL37A	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
RPL18	NOP56	psi-mi:“MI:0914”(association)	0.530
RPL30	RRP8	psi-mi:“MI:0914”(association)	0.530
RPL18A	RRP8	psi-mi:“MI:0914”(association)	0.530
PPAN	PPM1G	psi-mi:“MI:0914”(association)	0.530
MAGEB2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
HNRNPK	DDX56	psi-mi:“MI:0915”(physical association)	0.400
DDX56	PPP2R5E	psi-mi:“MI:0915”(physical association)	0.400
DDX56	NS	psi-mi:“MI:0915”(physical association)	0.370
NS1	DDX56	psi-mi:“MI:0915”(physical association)	0.370
DDX56	NS1	psi-mi:“MI:0915”(physical association)	0.370
NS	DDX56	psi-mi:“MI:0915”(physical association)	0.370
DDX56	E2	psi-mi:“MI:0915”(physical association)	0.370
SOX30	DDX56	psi-mi:“MI:0915”(physical association)	0.370
DDX56	EHD2	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (361): DDX56 (Affinity Capture-MS), DDX56 (Affinity Capture-MS), DDX56 (Affinity Capture-MS), DDX56 (Affinity Capture-MS), DDX56 (Affinity Capture-MS), DDX56 (Affinity Capture-MS), AATF (Co-fractionation), CEBPZ (Co-fractionation), DDX10 (Co-fractionation), DDX56 (Co-fractionation), DDX56 (Co-fractionation), DDX56 (Co-fractionation), DDX56 (Co-fractionation), DDX56 (Co-fractionation), DDX56 (Co-fractionation)

ESM2 similar proteins: A0A061IR73, A0A7N9VSG0, A7YSY2, D4A2B7, O14325, O15381, O43542, O60058, P32794, P40694, P46465, P54776, P54777, Q0VA52, Q13608, Q1HG60, Q21222, Q2NKY8, Q2TAF8, Q3EBD3, Q3SX23, Q3ULF4, Q3UMC0, Q5AWS6, Q5BJS0, Q5BL07, Q5PQY6, Q5R607, Q5R6M5, Q5ZI74, Q6H795, Q7L2E3, Q7TT47, Q7XL03, Q80SX8, Q86WA8, Q8NB90, Q8R2Q4, Q8SSJ5, Q99LC9

Diamond homologs: A1C7F7, A1CNV8, A1D1R8, A1DHV3, A2QCW6, A3LV40, A3LZT3, A4QTR1, A4R5B8, A5DC85, A5DLR3, A5DZT7, A5E572, A5E6W6, A6R2L6, A6R918, A6SFW7, A6SNX1, A6ZXU0, A7A1G0, A7E449, A7EM78, A7TPC9, O34750, O49289, O60080, P0A9P6, P0A9P7, P0A9P8, P0C2N7, P0CQ92, P0CQ93, P0CR10, P0CR11, P33906, P57453, Q06218, Q0CY48, Q0INC5, Q0UMB6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 204 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	26	25.4×	7e-28
Viral mRNA Translation	26	25.4×	7e-28
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	26	25.1×	8e-28
Selenocysteine synthesis	26	24.0×	2e-27
Eukaryotic Translation Termination	26	24.0×	2e-27
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	26	23.6×	2e-27
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA	26	23.6×	2e-27
Formation of a pool of free 40S subunits	26	22.4×	9e-27

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	26	26.8×	2e-27
maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	5	26.0×	2e-04
ribosome biogenesis	7	24.3×	2e-06
translation	30	17.1×	6e-26
ribosomal small subunit biogenesis	12	15.2×	7e-09
ribosomal large subunit biogenesis	6	14.8×	4e-04
intrinsic apoptotic signaling pathway	6	11.9×	1e-03
rRNA processing	12	9.4×	1e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	86
Likely benign	3
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

1790 predictions. Top by Δscore:

Variant	Effect	Δscore
7:44566442:CCGTA:C	donor_loss	1.0000
7:44566443:CGTA:C	donor_loss	1.0000
7:44566444:GTAC:G	donor_loss	1.0000
7:44566447:CCT:C	donor_loss	1.0000
7:44566525:C:CC	acceptor_gain	1.0000
7:44568111:CACT:C	donor_loss	1.0000
7:44568112:ACTC:A	donor_loss	1.0000
7:44568113:CTCA:C	donor_loss	1.0000
7:44568114:T:TC	donor_loss	1.0000
7:44568115:CACCC:C	donor_loss	1.0000
7:44568116:A:AC	donor_gain	1.0000
7:44568116:AC:A	donor_gain	1.0000
7:44568116:ACC:A	donor_gain	1.0000
7:44568117:C:A	donor_loss	1.0000
7:44568117:C:CC	donor_gain	1.0000
7:44568117:CC:C	donor_gain	1.0000
7:44568117:CCC:C	donor_gain	1.0000
7:44568117:CCCA:C	donor_gain	1.0000
7:44568219:TATGT:T	acceptor_gain	1.0000
7:44568220:ATGT:A	acceptor_gain	1.0000
7:44568221:TGT:T	acceptor_gain	1.0000
7:44568221:TGTCT:T	acceptor_loss	1.0000
7:44568222:GT:G	acceptor_gain	1.0000
7:44568222:GTCTG:G	acceptor_loss	1.0000
7:44568223:TC:T	acceptor_loss	1.0000
7:44568224:C:CC	acceptor_gain	1.0000
7:44568228:C:CT	acceptor_gain	1.0000
7:44568229:G:T	acceptor_gain	1.0000
7:44568898:CTCA:C	donor_loss	1.0000
7:44568900:CA:C	donor_loss	1.0000

AlphaMissense

3522 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:44572399:G:T	A198D	0.999
7:44572628:T:A	E167V	0.999
7:44573634:C:A	K57N	0.999
7:44573634:C:G	K57N	0.999
7:44573636:T:G	K57Q	0.999
7:44573638:C:T	G56E	0.999
7:44568953:C:G	A445P	0.998
7:44569903:C:A	R375S	0.998
7:44569903:C:G	R375S	0.998
7:44570015:C:A	R375M	0.998
7:44570015:C:G	R375T	0.998
7:44571492:C:A	R297M	0.998
7:44572619:A:G	L170P	0.998
7:44572622:T:C	D169G	0.998
7:44572628:T:G	E167A	0.998
7:44572709:C:T	G140E	0.998
7:44572710:C:G	G140R	0.998
7:44572710:C:T	G140R	0.998
7:44573626:G:T	A60D	0.998
7:44573629:G:T	A59D	0.998
7:44573635:T:A	K57M	0.998
7:44573638:C:A	G56V	0.998
7:44573639:C:A	G56W	0.998
7:44573644:C:T	G54D	0.998
7:44570024:C:G	R372P	0.997
7:44570830:A:T	I313K	0.997
7:44570856:G:C	F304L	0.997
7:44570856:G:T	F304L	0.997
7:44570858:A:G	F304L	0.997
7:44572621:G:C	D169E	0.997

dbSNP variants (sampled 300 via entrez): RS1000250141 (7:44572266 A>C), RS1000873245 (7:44573524 G>A), RS1000953468 (7:44566935 G>A), RS1001288224 (7:44571277 G>A,C), RS1001317809 (7:44566051 C>G,T), RS1001386134 (7:44567212 C>T), RS1001403736 (7:44571000 T>A,C), RS1001430797 (7:44571641 C>G), RS1001685830 (7:44565748 G>A,C), RS1001757694 (7:44571908 A>G), RS1001880722 (7:44567828 C>T), RS1001913297 (7:44567648 C>A,T), RS1002357407 (7:44573282 G>A), RS1002369554 (7:44575371 C>T), RS1002963182 (7:44570168 C>T)

Disease associations

OMIM: gene MIM:608023 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST008077_83	LDL cholesterol levels	1.000000e-06
GCST008078_152	LDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	7.000000e-27
GCST008078_60	LDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	3.000000e-29
GCST008079_3	LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	1.000000e-35
GCST008079_44	LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	2.000000e-38
GCST008086_44	LDL cholesterol levels in current drinkers	3.000000e-09
GCST008086_72	LDL cholesterol levels in current drinkers	8.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:0004329	alcohol drinking

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression, decreases expression, affects cotreatment, increases abundance	2
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	2
Acetaminophen	decreases expression, affects response to substance	2
Acrolein	affects cotreatment, increases oxidation, increases abundance	2
Ozone	affects cotreatment, increases oxidation, increases abundance	2
Valproic Acid	affects expression, decreases expression, decreases methylation	2
Aflatoxin B1	affects cotreatment, decreases expression, increases expression	2
aristolochic acid I	increases expression	1
TAK-243	increases sumoylation	1
bufotalin	decreases expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
deoxynivalenol	increases expression	1
cobaltous chloride	decreases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
nivalenol	increases expression	1
abrine	increases expression	1
Sunitinib	increases expression	1
Fulvestrant	increases methylation	1
Air Pollutants	affects cotreatment, increases abundance, increases oxidation	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation	1
Chelating Agents	affects binding, decreases expression	1
Copper	affects binding, decreases expression	1
Coumestrol	increases expression	1
Dimethyl Sulfoxide	increases expression	1
Dinitrochlorobenzene	affects binding	1
Hydrogen Peroxide	affects expression	1
Ivermectin	decreases expression	1
Manganese	increases expression, affects cotreatment, increases abundance	1
Ribonucleotides	affects binding	1

Clinical trials (associated diseases)

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