SUPV3L1

Summary

SUPV3L1 (Suv3 like RNA helicase, HGNC:11471) is a protein-coding gene on chromosome 10q22.1, encoding ATP-dependent RNA helicase SUPV3L1, mitochondrial (Q8IYB8). Major helicase player in mitochondrial RNA metabolism. It is a common-essential gene (DepMap: required in 91.7% of cancer cell lines).

Enables several functions, including double-stranded RNA binding activity; helicase activity; and protein homodimerization activity. Involved in several processes, including mitochondrial RNA 3’-end processing; mitochondrial RNA surveillance; and positive regulation of mitochondrial RNA catabolic process. Located in mitochondrial nucleoid and nucleus. Part of mitochondrial degradosome.

Source: NCBI Gene 6832 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 122 total
• Druggable target: yes
• Cancer dependency (DepMap): dependent in 91.7% of screened cell lines (common-essential)
• MANE Select transcript: NM_003171

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11471
Approved symbol	SUPV3L1
Name	Suv3 like RNA helicase
Location	10q22.1
Locus type	gene with protein product
Status	Approved
Aliases	SUV3
Ensembl gene	ENSG00000156502
Ensembl biotype	protein_coding
OMIM	605122
Entrez	6832

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 13 protein_coding, 4 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000359655, ENST00000422378, ENST00000471069, ENST00000478227, ENST00000483572, ENST00000486661, ENST00000497254, ENST00000854044, ENST00000854045, ENST00000854046, ENST00000854047, ENST00000917552, ENST00000917553, ENST00000917554, ENST00000917555, ENST00000956079, ENST00000956080, ENST00000956081

RefSeq mRNA: 7 — MANE Select: NM_003171 NM_001301683, NM_001323584, NM_001323585, NM_001323586, NM_001323587, NM_001323588, NM_003171

CCDS: CCDS7287

Canonical transcript exons

ENST00000359655 — 15 exons

Exon	Start	End
ENSE00001026860	69196992	69197083
ENSE00001026862	69198372	69198552
ENSE00001026864	69199104	69199197
ENSE00001647342	69207793	69207941
ENSE00001674720	69202867	69203043
ENSE00001724551	69202439	69202519
ENSE00001864569	69180234	69180562
ENSE00001925122	69208600	69209093
ENSE00002243009	69200280	69200499
ENSE00003465434	69185987	69186064
ENSE00003538135	69189267	69189435
ENSE00003541049	69186443	69186550
ENSE00003557080	69187642	69187756
ENSE00003626775	69191655	69191766
ENSE00003646809	69195188	69195265

Expression profiles

Bgee: expression breadth ubiquitous, 284 present calls, max score 94.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 31.3842 / max 238.3430, expressed in 1818 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
105327	30.1375	1817
105328	0.5281	285
105325	0.4231	42
105324	0.2750	36
105326	0.0205	11

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	94.37	gold quality
secondary oocyte	CL:0000655	94.29	gold quality
apex of heart	UBERON:0002098	93.45	gold quality
mucosa of transverse colon	UBERON:0004991	93.22	gold quality
cerebellar hemisphere	UBERON:0002245	93.11	gold quality
gastrocnemius	UBERON:0001388	93.05	gold quality
cerebellar cortex	UBERON:0002129	93.01	gold quality
muscle of leg	UBERON:0001383	92.88	gold quality
right testis	UBERON:0004534	92.58	gold quality
left testis	UBERON:0004533	92.56	gold quality
right hemisphere of cerebellum	UBERON:0014890	92.43	gold quality
right lobe of liver	UBERON:0001114	92.32	gold quality
right frontal lobe	UBERON:0002810	91.87	gold quality
skin of abdomen	UBERON:0001416	91.85	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	91.84	gold quality
right atrium auricular region	UBERON:0006631	91.81	gold quality
hindlimb stylopod muscle	UBERON:0004252	91.80	gold quality
skin of leg	UBERON:0001511	91.79	gold quality
right adrenal gland cortex	UBERON:0035827	91.73	gold quality
heart left ventricle	UBERON:0002084	91.63	gold quality
calcaneal tendon	UBERON:0003701	91.61	gold quality
nucleus accumbens	UBERON:0001882	91.59	gold quality
putamen	UBERON:0001874	91.47	gold quality
cerebellum	UBERON:0002037	91.38	gold quality
cardiac ventricle	UBERON:0002082	91.35	gold quality
caudate nucleus	UBERON:0001873	91.34	gold quality
Brodmann (1909) area 9	UBERON:0013540	91.33	gold quality
cingulate cortex	UBERON:0003027	91.32	gold quality
adenohypophysis	UBERON:0002196	91.31	gold quality
testis	UBERON:0000473	91.29	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.49

Regulation

Is transcription factor: no

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 91.7% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 17)

• Localisation of hSuv3p helicase in the mitochondrial matrix and its preferential unwinding of dsDNA. (PMID:12466530)
• Human SUV3 is an ATP-dependent multiple-substrate helicase; in addition to dsRNA and dsDNA unwinding activity, SUV3-70 and SUV3-83 can unwind heteroduplexes of RNA and DNA. (PMID:15096047)
• data suggest that hSUV3 is a housekeeping gene with an enhancer region & regulatory elements in basal promoter (PMID:15919122)
• Suv3 protein interacts with HBXIP, previously identified as a cofactor of survivin in suppression of apoptosis (PMID:16176273)
• Down-regulation of hSUV3 results in cell cycle perturbations and in apoptosis, which is both AIF- and caspase-dependent, and proceeds with the induction of p53. (PMID:17352692)
• Human SUV3 protein interacts with human WRN and BLM helicases. Silencing of the SUV3 gene in the human cell line HeLa resulted in elevation of homologous recombination as measured by the frequency of sister chromatid exchange during mitotic cell division. (PMID:17961633)
• SUV3 is essential for maintaining proper mitochondrial function, likely through a conserved role in mitochondrial RNA regulation. (PMID:18678873)
• The complex of hSUV3-hPNPase is an integral entity for efficient degradation of structured RNA and may be the long sought RNA-degrading complex in the mammalian mitochondria. (PMID:19509288)
• The hSuv3p activity was found to be necessary in the regulation of stability of mature, properly formed mRNAs and for removal of the noncoding processing intermediates transcribed from both H and L-strands. (PMID:19864255)
• Interaction between PNPase and hSuv3 is essential for efficient mitochondrial RNA degradation. (PMID:23221631)
• SUV3 bridges PNPase and mtPAP to form a transient complex in modulating mt-mRNA poly(A) tail length depending on the mitochondrial matrix Pi level. (PMID:24770417)
• the capacity of hSuv3 DNA unwinding activity might be sensitive to the local availability of specific inorganic cofactors (PMID:25446650)
• the nucleolar- associated human SUV3 protein is an important factor in regulation of the cell cycle. (PMID:28291845)
• Identification of immune cells and mRNA associated with prognosis of gastric cancer. (PMID:32164594)
• Mitochondrial RNA processing defect caused by a SUPV3L1 mutation in two siblings with a novel neurodegenerative syndrome. (PMID:35023579)
• Dimeric assembly of human Suv3 helicase promotes its RNA unwinding function in mitochondrial RNA degradosome for RNA decay. (PMID:35481630)
• [SUV3 knockdown inhibits proliferation, migration, and invasion of hepatocellular carcinoma cells and induces PD-L1 expression]. (PMID:39267568)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	supv3l1	ENSDARG00000077728
mus_musculus	Supv3l1	ENSMUSG00000020079
rattus_norvegicus	Supv3l1	ENSRNOG00000000392
drosophila_melanogaster	Suv3	FBGN0037232
caenorhabditis_elegans		WBGENE00007444

Protein

Protein identifiers

ATP-dependent RNA helicase SUPV3L1, mitochondrial — Q8IYB8 (reviewed: Q8IYB8)

Alternative names: Suppressor of var1 3-like protein 1

All UniProt accessions (2): Q8IYB8, B1AR60

UniProt curated annotations — full annotation on UniProt →

Function. Major helicase player in mitochondrial RNA metabolism. Component of the mitochondrial degradosome (mtEXO) complex, that degrades 3’ overhang double-stranded RNA with a 3’-to-5’ directionality in an ATP-dependent manner. Involved in the degradation of non-coding mitochondrial transcripts (MT-ncRNA) and tRNA-like molecules. ATPase and ATP-dependent multisubstrate helicase, able to unwind double-stranded (ds) DNA and RNA, and RNA/DNA heteroduplexes in the 5’-to-3’ direction. Plays a role in the RNA surveillance system in mitochondria; regulates the stability of mature mRNAs, the removal of aberrantly formed mRNAs and the rapid degradation of non coding processing intermediates. Also implicated in recombination and chromatin maintenance pathways. May protect cells from apoptosis. Associates with mitochondrial DNA.

Subunit / interactions. Homodimer; in free form. Component of the mitochondrial degradosome (mtEXO) complex which is a heteropentamer containing 2 copies of SUPV3L1 and 3 copies of PNPT1. As part of mitochondrial degradosome complex, interacts with GRSF1 in a RNA-dependent manner; the interaction enhances the activity of the complex. Interacts with LAMTOR5/HBXIP, WRN and BLM.

Subcellular location. Nucleus. Mitochondrion matrix. Mitochondrion nucleoid.

Tissue specificity. Broadly expressed.

Activity regulation. Helicase activity toward DNA substrate is inhibited by micromolar concentrations of 5,6-dichloro-1-(beta-D-ribofuranosyl)benzotriazole (DRBT) and 4,5,6,7-tetrabromobenzotriazole (TBBT). Helicase activity toward RNA substrate is inhibited by elevated concentrations of TBBT. Inhibited by some ring-expanded nucleoside analogs.

Similarity. Belongs to the helicase family.

RefSeq proteins (7): NP_001288612, NP_001310513, NP_001310514, NP_001310515, NP_001310516, NP_001310517, NP_003162* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001650	Helicase_C-like	Domain
IPR022192	SUV3_C	Domain
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR041082	Suv3_C_1	Domain
IPR041453	Suv3_N	Domain
IPR044774	Suv3_DEXQc	Domain
IPR050699	SUPV3-like	Family
IPR055206	DEXQc_SUV3	Domain

Pfam: PF00271, PF12513, PF18114, PF18147, PF22527

Catalyzed reactions (Rhea), 1 shown:

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

UniProt features (75 total): helix 33, strand 18, turn 4, modified residue 3, mutagenesis site 3, region of interest 3, sequence variant 2, sequence conflict 2, domain 2, compositionally biased region 2, transit peptide 1, chain 1, binding site 1

Structure

Experimental structures (PDB)

11 structures.

PDB	Method	Resolution (Å)
3RC3	X-RAY DIFFRACTION	2.08
3RC8	X-RAY DIFFRACTION	2.9
7W1R	X-RAY DIFFRACTION	3.2
9VCT	ELECTRON MICROSCOPY	3.47
9VCV	ELECTRON MICROSCOPY	3.63
9VCW	ELECTRON MICROSCOPY	3.75
9VCU	ELECTRON MICROSCOPY	3.84
9VCC	ELECTRON MICROSCOPY	3.92
9VC8	ELECTRON MICROSCOPY	4.04
9VD1	ELECTRON MICROSCOPY	4.16
9VD0	ELECTRON MICROSCOPY	4.42

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IYB8-F1	83.87	0.70

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): 207–214

Post-translational modifications (3): 99, 220, 725

Mutagenesis-validated functional residues (3):

Position	Phenotype
207	abolishes atpase and dsdna and dsrna helicase activities.
213	abolishes atpase activity. abolishes helicase activity and reduces double-stranded rna degradation. does not abolish for
576–581	does not abolish atpase activity. shows a loss of double-stranded rna-binding, helicase and degrading activities.

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-9836573	Mitochondrial RNA degradation
R-HSA-8953854	Metabolism of RNA

MSigDB gene sets: 203 (showing top): GOMF_RNA_NUCLEASE_ACTIVITY, GOMF_NUCLEASE_ACTIVITY, GOBP_GROWTH, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_RNA_SURVEILLANCE, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CELL_GROWTH, GOBP_MITOCHONDRIAL_RNA_PROCESSING, GOBP_MITOCHONDRIAL_RNA_METABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_GROWTH, DODD_NASOPHARYNGEAL_CARCINOMA_UP, USF_02

GO Biological Process (12): mitochondrial RNA catabolic process (GO:0000957), mitochondrial mRNA catabolic process (GO:0000958), positive regulation of mitochondrial RNA catabolic process (GO:0000962), mitochondrial RNA 3’-end processing (GO:0000965), DNA recombination (GO:0006310), RNA catabolic process (GO:0006401), mitochondrion organization (GO:0007005), positive regulation of cell growth (GO:0030307), mitochondrial ncRNA surveillance (GO:0035945), mitochondrial mRNA surveillance (GO:0035946), negative regulation of apoptotic process (GO:0043066), mitochondrial RNA surveillance (GO:2000827)

GO Molecular Function (14): DNA binding (GO:0003677), DNA helicase activity (GO:0003678), RNA binding (GO:0003723), RNA helicase activity (GO:0003724), double-stranded RNA binding (GO:0003725), helicase activity (GO:0004386), ATP binding (GO:0005524), ATP hydrolysis activity (GO:0016887), 3’-5’ RNA helicase activity (GO:0034458), identical protein binding (GO:0042802), protein homodimerization activity (GO:0042803), nucleotide binding (GO:0000166), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (5): nucleus (GO:0005634), mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759), mitochondrial nucleoid (GO:0042645), mitochondrial degradosome (GO:0045025)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Metabolism of RNA	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
mitochondrion	6
mitochondrial RNA catabolic process	3
mitochondrial RNA surveillance	2
nucleic acid binding	2
helicase activity	2
ATP-dependent activity	2
intracellular membrane-bounded organelle	2
mitochondrial RNA metabolic process	1
RNA catabolic process	1
mRNA catabolic process	1
regulation of mitochondrial RNA catabolic process	1
positive regulation of catabolic process	1
positive regulation of RNA metabolic process	1
mitochondrial RNA processing	1
RNA 3’-end processing	1
DNA metabolic process	1
RNA metabolic process	1
nucleic acid catabolic process	1
organelle organization	1
regulation of cell growth	1
cell growth	1
positive regulation of growth	1
positive regulation of cellular process	1
mitochondrial mRNA catabolic process	1
apoptotic process	1
regulation of apoptotic process	1
negative regulation of programmed cell death	1
cytoplasmic RNA surveillance	1
ATP-dependent activity, acting on DNA	1
ATP-dependent activity, acting on RNA	1
catalytic activity, acting on RNA	1
RNA binding	1
nucleic acid conformation isomerase activity	1
catalytic activity, acting on a nucleic acid	1
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
ribonucleoside triphosphate phosphatase activity	1
RNA helicase activity	1
protein binding	1
identical protein binding	1

Protein interactions and networks

STRING

1398 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SUPV3L1	PNPT1	Q8TCS8	997
SUPV3L1	SEM1	Q6ZVN7	945
SUPV3L1	MTPAP	Q9NVV4	824
SUPV3L1	GRSF1	Q12849	748
SUPV3L1	EIF4A3	P38919	739
SUPV3L1	PDE12	Q6L8Q7	663
SUPV3L1	ELAC2	Q9BQ52	660
SUPV3L1	SKIC2	Q15477	644
SUPV3L1	LACTB2	Q53H82	637
SUPV3L1	SLIRP	Q9GZT3	634
SUPV3L1	POLRMT	O00411	632
SUPV3L1	MRM1	Q6IN84	609
SUPV3L1	LRPPRC	P42704	608
SUPV3L1	FASTKD2	Q9NYY8	605
SUPV3L1	REXO2	Q9Y3B8	603

IntAct

92 interactions, top by confidence:

A	B	Type	Score
SUPV3L1	PNPT1	psi-mi:“MI:0407”(direct interaction)	0.860
PNPT1	SUPV3L1	psi-mi:“MI:0407”(direct interaction)	0.860
PNPT1	SUPV3L1	psi-mi:“MI:0915”(physical association)	0.860
SUPV3L1	SUPV3L1	psi-mi:“MI:0407”(direct interaction)	0.660
LIN28A	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
LZTS2	SUPV3L1	psi-mi:“MI:0915”(physical association)	0.560
SUPV3L1	LZTS2	psi-mi:“MI:0915”(physical association)	0.560
SUPV3L1	MAGEB6	psi-mi:“MI:0915”(physical association)	0.560
BHLHA15	RPLP0	psi-mi:“MI:0914”(association)	0.530
WASF3	HOXB9	psi-mi:“MI:0914”(association)	0.530
ZMAT3	ACTA2	psi-mi:“MI:0914”(association)	0.530
MRPL2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
ELAVL2	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
MRPS34	ZZEF1	psi-mi:“MI:0914”(association)	0.530
MRPS18C	MRPS14	psi-mi:“MI:0914”(association)	0.530
IGF2BP3	PTCD1	psi-mi:“MI:0914”(association)	0.530
ILF2	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
RBM3	PRMT5	psi-mi:“MI:0914”(association)	0.530
CDKN2AIP	MAGEB2	psi-mi:“MI:0914”(association)	0.530
SUPV3L1	HNRNPDL	psi-mi:“MI:0914”(association)	0.480
CUL3	PXDNL	psi-mi:“MI:0914”(association)	0.350
LRRK2		psi-mi:“MI:0914”(association)	0.350
MRPS34	CIBAR1	psi-mi:“MI:0914”(association)	0.350
ELAVL2	IGF2BP3	psi-mi:“MI:0914”(association)	0.350

BioGRID (171): LZTS2 (Two-hybrid), SUPV3L1 (Affinity Capture-MS), SUPV3L1 (Affinity Capture-MS), SUPV3L1 (Affinity Capture-MS), SUPV3L1 (Affinity Capture-MS), SUPV3L1 (Affinity Capture-MS), PNPT1 (Affinity Capture-MS), SUPV3L1 (Affinity Capture-MS), SUPV3L1 (Affinity Capture-MS), HNRNPDL (Affinity Capture-MS), RBM3 (Affinity Capture-MS), SUPV3L1 (Affinity Capture-MS), USP9X (Affinity Capture-MS), SUPV3L1 (Affinity Capture-MS), SUPV3L1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0P0V4R0, A0A1D5PRR9, A4IG62, A9UMG5, B4JNS2, F1R345, F4HQE2, F4KFV7, O75417, P0C928, P42285, Q14527, Q16X92, Q28E61, Q2VPA6, Q43093, Q56YN3, Q5JK52, Q5U2U7, Q5W9E7, Q5ZJT0, Q5ZLV4, Q60446, Q642J4, Q6PCL9, Q6PCN7, Q6PFE3, Q7XT07, Q8CGS6, Q8H2D5, Q8IYB8, Q8IYD8, Q8K394, Q94BR5, Q95216, Q9BWT3, Q9CZU3, Q9DG67, Q9FF61, Q9FT73

Diamond homologs: A4IG62, F4KFV7, O74727, O94445, P32580, Q01IJ3, Q10D00, Q17828, Q295E6, Q59TB2, Q5EBA1, Q5ZJT0, Q61SU7, Q7X745, Q80YD1, Q8IYB8, Q9SMX1, Q9VN03, P35207, Q9XIF2, Q9ZVW2, Q9CZU3, A6UN73, P9WMR0, P9WMR1, Q9ZBD8, P0DMI1, Q15477, Q23223, Q6NZR5, O14232, O59801

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 109 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
Mitochondrial translation initiation	15	27.6×	4e-16
Mitochondrial translation elongation	15	27.6×	4e-16
Mitochondrial ribosome-associated quality control	15	26.7×	4e-16
Mitochondrial translation	13	25.9×	8e-14
Mitochondrial translation termination	15	23.9×	2e-15
Translation	14	12.6×	1e-10
Processing of Capped Intron-Containing Pre-mRNA	7	8.3×	7e-04
Mitochondrial protein degradation	5	8.3×	7e-03

GO biological processes:

GO term	Partners	Fold	FDR
mitochondrial translation	17	29.8×	5e-18
RNA processing	7	15.5×	1e-04
translation	9	9.3×	1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	93
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2469 predictions. Top by Δscore:

Variant	Effect	Δscore
10:69180561:GA:G	donor_gain	1.0000
10:69180563:G:GG	donor_gain	1.0000
10:69187640:A:AG	acceptor_gain	1.0000
10:69187641:G:GG	acceptor_gain	1.0000
10:69187641:GCTC:G	acceptor_gain	1.0000
10:69189423:GA:G	donor_gain	1.0000
10:69189425:G:GG	donor_gain	1.0000
10:69189433:GCT:G	donor_gain	1.0000
10:69189436:G:GG	donor_gain	1.0000
10:69189440:G:GG	donor_gain	1.0000
10:69191767:G:GG	donor_gain	1.0000
10:69197075:G:GT	donor_gain	1.0000
10:69198489:G:GG	donor_gain	1.0000
10:69199096:T:TA	acceptor_gain	1.0000
10:69199098:TTTTA:T	acceptor_loss	1.0000
10:69199099:TTTAG:T	acceptor_loss	1.0000
10:69199100:TTAGG:T	acceptor_loss	1.0000
10:69199101:TAG:T	acceptor_loss	1.0000
10:69199102:A:AG	acceptor_gain	1.0000
10:69199102:A:T	acceptor_loss	1.0000
10:69199102:AG:A	acceptor_gain	1.0000
10:69199102:AGG:A	acceptor_gain	1.0000
10:69199103:G:GG	acceptor_gain	1.0000
10:69199103:GG:G	acceptor_gain	1.0000
10:69199103:GGG:G	acceptor_gain	1.0000
10:69199103:GGGAC:G	acceptor_gain	1.0000
10:69199194:ATTT:A	donor_gain	1.0000
10:69199195:TTT:T	donor_gain	1.0000
10:69199195:TTTG:T	donor_loss	1.0000
10:69199196:TT:T	donor_gain	1.0000

AlphaMissense

5169 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:69195247:T:A	W305R	1.000
10:69195247:T:C	W305R	1.000
10:69198454:G:A	C369Y	1.000
10:69198455:C:G	C369W	1.000
10:69198460:T:A	V371D	1.000
10:69198532:T:A	I395K	1.000
10:69198544:T:C	L399P	1.000
10:69199166:G:C	A423P	1.000
10:69199170:C:T	T424I	1.000
10:69199187:G:A	G430R	1.000
10:69199187:G:C	G430R	1.000
10:69187680:G:C	A166P	0.999
10:69189324:C:A	N210K	0.999
10:69189324:C:G	N210K	0.999
10:69189392:T:C	L233P	0.999
10:69191666:T:G	C251W	0.999
10:69191680:G:A	G256D	0.999
10:69191740:T:A	V276D	0.999
10:69191742:G:A	E277K	0.999
10:69191743:A:T	E277V	0.999
10:69195197:C:A	A288D	0.999
10:69195205:G:C	D291H	0.999
10:69195206:A:C	D291A	0.999
10:69195206:A:T	D291V	0.999
10:69195209:A:C	E292A	0.999
10:69195209:A:T	E292V	0.999
10:69195236:G:T	R301I	0.999
10:69195238:G:A	G302R	0.999
10:69195238:G:C	G302R	0.999
10:69195239:G:A	G302E	0.999

dbSNP variants (sampled 300 via entrez): RS1000257126 (10:69188785 C>A), RS1000284022 (10:69178999 T>C,G), RS1000310878 (10:69189070 C>A,G), RS1000329348 (10:69185314 G>A,C), RS1000543102 (10:69191159 G>A), RS1000804785 (10:69205540 T>G), RS1000837744 (10:69194722 G>A), RS1000878214 (10:69203438 T>C,G), RS1000893273 (10:69191400 T>C), RS1001224487 (10:69188353 T>A,G), RS1001226952 (10:69193637 C>T), RS1001257217 (10:69182712 T>C), RS1001274824 (10:69194839 A>T), RS1001325611 (10:69194512 C>A,T), RS1001369524 (10:69188506 T>TGTTTGTTA)

Disease associations

OMIM: gene MIM:605122 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001533_13	Immune reponse to smallpox (secreted IL-1beta)	1.000000e-09
GCST002110_3	Glycemic traits (pregnancy)	1.000000e-22
GCST009464_14	Facial morphology	3.000000e-08

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004645	response to vaccine
EFO:0004873	cytokine measurement
EFO:0004307	glucose tolerance test

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3642 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, increases expression, affects cotreatment	3
Cyclosporine	increases expression	2
FR900359	increases phosphorylation	1
bisphenol F	increases expression	1
alpha phellandrene	decreases expression	1
perfluoro-n-nonanoic acid	increases expression	1
deguelin	increases expression	1
bisphenol B	increases expression	1
abrine	increases expression	1
picoxystrobin	increases expression	1
Acetaminophen	decreases expression	1
Atrazine	decreases expression	1
Dexamethasone	decreases expression, affects cotreatment	1
Doxorubicin	decreases expression	1
Fluorouracil	decreases expression	1
Indomethacin	decreases expression, affects cotreatment	1
Ivermectin	decreases expression	1
Phenobarbital	affects expression	1
Ribonucleotides	affects binding	1
Rotenone	increases expression	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Valproic Acid	affects expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Copper Sulfate	increases expression	1

ChEMBL screening assays

3 unique, capped per target: 3 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL810793	Binding	Inhibitory activity determined against human Suv3 helicase using DNA as substrate	Potent inhibition of NTPase/helicase of the West Nile Virus by ring-expanded (“fat”) nucleoside analogues. — J Med Chem

Clinical trials (associated diseases)

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