SLU7

Summary

SLU7 (spliceosome associated SLU7, HGNC:16939) is a protein-coding gene on chromosome 5q33.3, encoding Pre-mRNA-splicing factor SLU7 (O95391). Required for pre-mRNA splicing as component of the spliceosome. It is a common-essential gene (DepMap: required in 99.0% of cancer cell lines).

Pre-mRNA splicing occurs in two sequential transesterification steps. The protein encoded by this gene is a splicing factor that has been found to be essential during the second catalytic step in the pre-mRNA splicing process. It associates with the spliceosome and contains a zinc knuckle motif that is found in other splicing factors and is involved in protein-nucleic acid and protein-protein interactions.

Source: NCBI Gene 10569 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 73 total
• Cancer dependency (DepMap): dependent in 99.0% of screened cell lines (common-essential)
• MANE Select transcript: NM_006425

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16939
Approved symbol	SLU7
Name	spliceosome associated SLU7
Location	5q33.3
Locus type	gene with protein product
Status	Approved
Aliases	9G8
Ensembl gene	ENSG00000164609
Ensembl biotype	protein_coding
OMIM	605974
Entrez	10569

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 9 protein_coding, 5 retained_intron

ENST00000297151, ENST00000518268, ENST00000519349, ENST00000520664, ENST00000520841, ENST00000521190, ENST00000521320, ENST00000521826, ENST00000523219, ENST00000855629, ENST00000938507, ENST00000938508, ENST00000938509, ENST00000960560

RefSeq mRNA: 7 — MANE Select: NM_006425 NM_001364517, NM_001364518, NM_001364520, NM_001364521, NM_001364522, NM_001364523, NM_006425

CCDS: CCDS4352

Canonical transcript exons

ENST00000297151 — 16 exons

Exon	Start	End
ENSE00001085832	160404809	160404880
ENSE00001085835	160408650	160408697
ENSE00001085836	160405031	160405135
ENSE00001085837	160413899	160413979
ENSE00001085838	160401641	160403464
ENSE00001085842	160413456	160413620
ENSE00001085843	160408329	160408460
ENSE00001085844	160406468	160406629
ENSE00001085845	160412451	160412519
ENSE00001085846	160404440	160404556
ENSE00002120240	160419023	160419081
ENSE00003576847	160407746	160407813
ENSE00003650401	160407971	160408068
ENSE00003665631	160407476	160407615
ENSE00003682530	160414319	160414472
ENSE00003682859	160415125	160415310

Expression profiles

Bgee: expression breadth ubiquitous, 263 present calls, max score 96.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.7476 / max 1909.0307, expressed in 1786 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
64633	26.9424	1785
64635	0.6544	320
64634	0.6339	331
64631	0.4267	187
64636	0.0903	39

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
epithelial cell of pancreas	CL:0000083	96.37	gold quality
amniotic fluid	UBERON:0000173	96.35	gold quality
bone marrow cell	CL:0002092	96.21	gold quality
calcaneal tendon	UBERON:0003701	96.07	gold quality
colonic epithelium	UBERON:0000397	96.02	gold quality
islet of Langerhans	UBERON:0000006	95.79	gold quality
monocyte	CL:0000576	95.70	gold quality
leukocyte	CL:0000738	95.64	gold quality
prefrontal cortex	UBERON:0000451	95.32	gold quality
primary visual cortex	UBERON:0002436	95.25	gold quality
tendon	UBERON:0000043	95.18	gold quality
tendon of biceps brachii	UBERON:0008188	95.18	gold quality
Brodmann (1909) area 23	UBERON:0013554	94.74	gold quality
cardiac muscle of right atrium	UBERON:0003379	94.69	gold quality
stromal cell of endometrium	CL:0002255	94.67	gold quality
endothelial cell	CL:0000115	94.66	gold quality
upper arm skin	UBERON:0004263	94.56	gold quality
sural nerve	UBERON:0015488	94.51	gold quality
left ventricle myocardium	UBERON:0006566	94.46	gold quality
occipital lobe	UBERON:0002021	94.18	gold quality
embryo	UBERON:0000922	94.16	gold quality
ganglionic eminence	UBERON:0004023	94.16	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	93.93	gold quality
frontal cortex	UBERON:0001870	93.86	gold quality
frontal lobe	UBERON:0016525	93.86	gold quality
sperm	CL:0000019	93.72	gold quality
myocardium	UBERON:0002349	93.56	gold quality
bone marrow	UBERON:0002371	93.56	gold quality
deltoid	UBERON:0001476	93.54	gold quality
neocortex	UBERON:0001950	93.52	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-7303	no	267.53
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AP1, AR, ARID1A, ASCL1, ATF2, ATF3, BCL3, BHLHE41, CLOCK, CREB1, CREM, DLX4, EGR1, ELF4, ELK1, ERF, ESR1, ESR2, ESRRA, EVX1, FOS, FOSB, FOXM1, GFI1, GLI3, GTF2I, HES1, HES7, HESX1, HHEX, HNF1A, HNF4A, HSF1, HSF2, IRF2, IRF3, IRF6, IRF9, JUN, JUNB

miRNA regulators (miRDB)

95 targeting SLU7, 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-3924	100.00	72.09	2394
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.0% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 12)

• The zinc-knuckle motif of hSlu7 determines the cellular localization of the protein through a nucleocytoplasmic-sensitive shuttling balance. (PMID:15181151)
• hSlu7 has a broad effect on alternative splicing (PMID:15728250)
• Regulation of transcription of the RNA splicing factor hSlu7 by Elk-1 and Sp1 affects alternative splicing (PMID:17804646)
• RBM22 and hSlu7 differ significantly in their subcellular distributions under stress conditions, and RBM22 enhances the cytoplasmic translocation of hSlu7 under stress. (PMID:21122810)
• These observations together point to an altered recruitment and dependence on SLU7, suggesting its role in facilitating transitions that promote catalysis, and highlight the diversity in spliceosome assembly. (PMID:23754748)
• SLU7 knockdown in liver cells resulted in profound changes in pre-mRNA splicing and gene expression, leading to impaired glucose and lipid metabolism, refractoriness to key metabolic hormones, and reversion to a fetal-like gene expression pattern. (PMID:24865429)
• these findings indicate that SLU7 is co-opted by hepatocellular carcinoma (HCC) cells and other tumor cell types to maintain survival, and identify this splicing regulator as a new determinant for the expression of the oncogenic miR-17-92 cluster. This novel mechanism may be exploited for the development of antitumoral strategies in cancers displaying such SLU7-miR-17-92 crosstalk (PMID:26804174)
• High SLU7 expression is associated with alcoholic steatohepatitis. (PMID:29870742)
• We define a molecular pathway through which SLU7 keeps in check the generation of truncated forms of the splicing factor SRSF3 (SRp20) (SRSF3-TR). Behaving as dominant negative, or by gain-of-function, SRSF3-TR impair the correct splicing and expression of the splicing regulator SRSF1 (ASF/SF2) and the crucial SCC protein sororin. (PMID:30657957)
• Splicing Factor SLU7 Prevents Oxidative Stress-Mediated Hepatocyte Nuclear Factor 4alpha Degradation, Preserving Hepatic Differentiation and Protecting From Liver Damage. (PMID:34170569)
• The splicing regulator SLU7 is required to preserve DNMT1 protein stability and DNA methylation. (PMID:34331453)
• SLU7: A New Hub of Gene Expression Regulation-From Epigenetics to Protein Stability in Health and Disease. (PMID:36362191)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	slu7	ENSDARG00000038870
mus_musculus	Slu7	ENSMUSG00000020409
rattus_norvegicus	Slu7	ENSRNOG00000003822
drosophila_melanogaster	Slu7	FBGN0039626
caenorhabditis_elegans		WBGENE00010629

Protein

Protein identifiers

Pre-mRNA-splicing factor SLU7 — O95391 (reviewed: O95391)

All UniProt accessions (4): A0A0C4DGD2, E5RGM7, E5RK41, O95391

UniProt curated annotations — full annotation on UniProt →

Function. Required for pre-mRNA splicing as component of the spliceosome. Participates in the second catalytic step of pre-mRNA splicing, when the free hydroxyl group of exon I attacks the 3’-splice site to generate spliced mRNA and the excised lariat intron. Required for holding exon 1 properly in the spliceosome and for correct AG identification when more than one possible AG exists in 3’-splicing site region. May be involved in the activation of proximal AG. Probably also involved in alternative splicing regulation.

Subunit / interactions. Component of pre-catalytic, catalytic and post-catalytic spliceosomes. Associates with the spliceosome prior to recognition of the 3’-splice site for step II, probably during catalysis of step I.

Subcellular location. Nucleus. Nucleus speckle. Cytoplasm.

Domain organisation. The CCHC-type zinc finger is required to retain the protein within the nucleus and prevent its shuttle back to the cytoplasm via the CRM1 pathway.

Similarity. Belongs to the SLU7 family.

RefSeq proteins (7): NP_001351446, NP_001351447, NP_001351449, NP_001351450, NP_001351451, NP_001351452, NP_006416* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR021715	Slu7_dom	Domain
IPR039974	Splicing_factor_SLU7	Family

Pfam: PF11708

UniProt features (50 total): mutagenesis site 10, turn 8, helix 7, compositionally biased region 5, modified residue 4, region of interest 4, strand 4, cross-link 2, sequence variant 2, initiator methionine 1, chain 1, zinc finger region 1, short sequence motif 1

Structure

Experimental structures (PDB)

7 structures.

PDB	Method	Resolution (Å)
8C6J	ELECTRON MICROSCOPY	2.8
6ICZ	ELECTRON MICROSCOPY	3
6QDV	ELECTRON MICROSCOPY	3.3
9FMD	ELECTRON MICROSCOPY	3.3
5XJC	ELECTRON MICROSCOPY	3.6
7W5A	ELECTRON MICROSCOPY	3.6
7W5B	ELECTRON MICROSCOPY	4.3

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O95391-F1	75.72	0.15

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 (6): 2, 215, 227, 235, 349, 408

Mutagenesis-validated functional residues (10):

Position	Phenotype
116	abolishes nuclear localization.
117	abolishes nuclear localization.
120	induces a cytoplasmic localization; when associated with s-123; g-128 and s-133.
123	induces a cytoplasmic localization; when associated with s-120; g-128 and s-133.
125–126	does not affect nuclear localization.
128	induces a cytoplasmic localization; when associated with s-120; s-123 and s-133.
129	abolishes nuclear localization.
133	induces a cytoplasmic localization; when associated with s-120; s-123 and g-128.
136	abolishes nuclear localization.
166	abolishes nuclear localization.

Function

Pathways and Gene Ontology

Reactome pathways

10 pathways

ID	Pathway
R-HSA-159236	Transport of Mature mRNA derived from an Intron-Containing Transcript
R-HSA-72163	mRNA Splicing - Major Pathway
R-HSA-72187	mRNA 3’-end processing
R-HSA-73856	RNA Polymerase II Transcription Termination
R-HSA-72172	mRNA Splicing
R-HSA-72202	Transport of Mature Transcript to Cytoplasm
R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA
R-HSA-73857	RNA Polymerase II Transcription
R-HSA-74160	Gene expression (Transcription)
R-HSA-8953854	Metabolism of RNA

MSigDB gene sets: 154 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_DN, TGCGCANK_UNKNOWN, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_ALTERNATIVE_MRNA_SPLICING_VIA_SPLICEOSOME, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, REACTOME_MRNA_3_END_PROCESSING, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_RNA_SPLICING, GOBP_CELLULAR_RESPONSE_TO_HEAT, REACTOME_MRNA_SPLICING, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS, HFH1_01, GOBP_MRNA_SPLICE_SITE_RECOGNITION, MODULE_98

GO Biological Process (8): RNA splicing, via transesterification reactions (GO:0000375), alternative mRNA splicing, via spliceosome (GO:0000380), mRNA 3’-splice site recognition (GO:0000389), mRNA splicing, via spliceosome (GO:0000398), intracellular protein transport (GO:0006886), RNA splicing (GO:0008380), cellular response to heat (GO:0034605), mRNA processing (GO:0006397)

GO Molecular Function (5): second spliceosomal transesterification activity (GO:0000386), zinc ion binding (GO:0008270), pre-mRNA 3’-splice site binding (GO:0030628), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (9): nucleus (GO:0005634), nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), cytoplasm (GO:0005737), cytosol (GO:0005829), membrane (GO:0016020), nuclear speck (GO:0016607), small nuclear ribonucleoprotein complex (GO:0030532), catalytic step 2 spliceosome (GO:0071013)

Reactome top-level categories

Rollup of top-6 pathways:

Category	Pathways
Processing of Capped Intron-Containing Pre-mRNA	3
Transport of Mature Transcript to Cytoplasm	1
mRNA Splicing	1
RNA Polymerase II Transcription	1
Metabolism of RNA	1
Gene expression (Transcription)	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
RNA processing	2
nuclear protein-containing complex	2
ribonucleoprotein complex	2
RNA splicing	1
mRNA splicing, via spliceosome	1
mRNA splice site recognition	1
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
intracellular protein localization	1
protein transport	1
intracellular transport	1
response to heat	1
cellular response to stress	1
mRNA metabolic process	1
RNA splicing, via transesterification reactions	1
catalytic activity, acting on RNA	1
transition metal ion binding	1
pre-mRNA binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular anatomical structure	1
cytoplasm	1
nuclear ribonucleoprotein granule	1
Sm-like protein family complex	1
Prp19 complex	1
spliceosomal complex	1
U5 snRNP	1
catalytic complex	1

Protein interactions and networks

STRING

1618 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLU7	PRPF18	Q99633	995
SLU7	DHX8	Q14562	971
SLU7	DHX38	Q92620	921
SLU7	CWC25	Q9NXE8	893
SLU7	YJU2	Q9BW85	853
SLU7	SNRNP200	O75643	834
SLU7	CDC40	O60508	811
SLU7	DHX15	O43143	791
SLU7	EFTUD2	Q15029	756
SLU7	COL4A3	Q01955	719
SLU7	DHX16	O60231	718
SLU7	CWC22	Q9HCG8	717
SLU7	TFIP11	Q9UBB9	708
SLU7	SRSF5	Q13243	693
SLU7	CWC27	Q6UX04	691

IntAct

139 interactions, top by confidence:

A	B	Type	Score
SLU7	PPIL3	psi-mi:“MI:0915”(physical association)	0.850
PPIL3	SLU7	psi-mi:“MI:0915”(physical association)	0.850
PPIL3	SLU7	psi-mi:“MI:0914”(association)	0.850
SLU7	GOLGA2	psi-mi:“MI:0915”(physical association)	0.720
GOLGA2	SLU7	psi-mi:“MI:0915”(physical association)	0.720
KRT40	SLU7	psi-mi:“MI:0915”(physical association)	0.560
SLU7	CEP70	psi-mi:“MI:0915”(physical association)	0.560
LZTS2	SLU7	psi-mi:“MI:0915”(physical association)	0.560
THAP1	SLU7	psi-mi:“MI:0915”(physical association)	0.560
SLU7	KRT40	psi-mi:“MI:0915”(physical association)	0.560
CEP70	SLU7	psi-mi:“MI:0915”(physical association)	0.560
SLU7	THAP1	psi-mi:“MI:0915”(physical association)	0.560
SLU7	LZTS2	psi-mi:“MI:0915”(physical association)	0.560
SLU7	TEPSIN	psi-mi:“MI:0915”(physical association)	0.560
SLU7	AIMP2	psi-mi:“MI:0915”(physical association)	0.560
SLU7	FHL3	psi-mi:“MI:0915”(physical association)	0.560
SLU7	MCC	psi-mi:“MI:0915”(physical association)	0.560
SLU7	PIBF1	psi-mi:“MI:0915”(physical association)	0.560
SLU7	NFKBID	psi-mi:“MI:0915”(physical association)	0.560
SLU7	DEF6	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (195): SLU7 (Two-hybrid), PPIL3 (Two-hybrid), THAP1 (Two-hybrid), CEP70 (Two-hybrid), LZTS2 (Two-hybrid), KRT40 (Two-hybrid), SLU7 (Affinity Capture-RNA), CCDC85B (Two-hybrid), PPIL3 (Two-hybrid), SLU7 (Affinity Capture-MS), SLU7 (Affinity Capture-MS), SLU7 (Affinity Capture-MS), SLU7 (Affinity Capture-MS), SLU7 (Affinity Capture-MS), SLU7 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GVH7, A0A4X1TZW7, A0A5F8MPE6, E1B836, E1C760, E7EXT2, F7AEX0, O74370, O95391, P21374, P51950, Q20716, Q24276, Q24740, Q28E45, Q2F5J3, Q2KI00, Q3B820, Q3KQD1, Q3TGF2, Q3ZBE5, Q45GW3, Q4R4P2, Q502W7, Q569B9, Q5EAW4, Q5RHY1, Q5U4F3, Q5XI37, Q5XIN9, Q5ZIG2, Q69ZQ2, Q6SP97, Q7L590, Q80ZG5, Q8BHJ9, Q8BRC6, Q8CDN8, Q8NCR3, Q8TC29

Diamond homologs: A2YQU8, O23174, O95391, P0CR52, P0CR53, Q21278, Q3KQD1, Q3ZBE5, Q4R4P2, Q4WWR2, Q51LA6, Q54TA0, Q5B3U2, Q5U3F2, Q5ZIG2, Q6C9T0, Q6ZK48, Q7SDY6, Q80ZG5, Q8BHJ9, Q9SHY8, Q9VAQ7, Q9Y7Y2, Q74ZN9, Q5ADL4, Q6BMK7, Q6FRY5, Q02775

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
mRNA Splicing - Minor Pathway	6	20.1×	4e-05
mRNA Splicing - Major Pathway	22	17.9×	1e-19
mRNA 3’-end processing	6	17.6×	7e-05
mRNA Polyadenylation	13	17.0×	8e-11
mRNA Splicing	9	14.8×	9e-07
Processing of Capped Intron-Containing Pre-mRNA	12	14.7×	3e-09
Transport of Mature mRNA derived from an Intron-Containing Transcript	6	13.6×	3e-04
Dengue Virus-Host Interactions	18	12.3×	7e-13

GO biological processes:

GO term	Partners	Fold	FDR
mRNA stabilization	5	20.8×	7e-04
mRNA splicing, via spliceosome	15	15.6×	2e-11
RNA splicing	11	11.0×	1e-06
mRNA processing	12	10.7×	4e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	45
Likely benign	4
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1623 predictions. Top by Δscore:

Variant	Effect	Δscore
5:160403460:AGTGC:A	acceptor_gain	1.0000
5:160403461:GTGC:G	acceptor_gain	1.0000
5:160403462:TGC:T	acceptor_gain	1.0000
5:160403463:GC:G	acceptor_gain	1.0000
5:160403464:CC:C	acceptor_gain	1.0000
5:160403465:C:CA	acceptor_loss	1.0000
5:160403465:C:CC	acceptor_gain	1.0000
5:160403470:G:C	acceptor_gain	1.0000
5:160403470:G:GC	acceptor_gain	1.0000
5:160404436:TTACC:T	donor_loss	1.0000
5:160404437:TACCT:T	donor_loss	1.0000
5:160404438:A:AC	donor_gain	1.0000
5:160404438:A:AT	donor_loss	1.0000
5:160404439:C:CC	donor_gain	1.0000
5:160404439:C:CT	donor_loss	1.0000
5:160404552:TGCAG:T	acceptor_gain	1.0000
5:160404553:GCAG:G	acceptor_gain	1.0000
5:160404554:CAG:C	acceptor_gain	1.0000
5:160404554:CAGC:C	acceptor_gain	1.0000
5:160404555:AG:A	acceptor_gain	1.0000
5:160404557:C:CC	acceptor_gain	1.0000
5:160404558:T:G	acceptor_loss	1.0000
5:160404644:TGA:T	donor_gain	1.0000
5:160404804:CTTA:C	donor_loss	1.0000
5:160404805:TTACC:T	donor_loss	1.0000
5:160404806:TAC:T	donor_loss	1.0000
5:160404807:A:AC	donor_gain	1.0000
5:160404807:ACCT:A	donor_gain	1.0000
5:160404808:C:CC	donor_gain	1.0000
5:160404808:CCT:C	donor_gain	1.0000

AlphaMissense

3905 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:160405102:A:G	W441R	1.000
5:160405102:A:T	W441R	1.000
5:160405125:C:T	G433E	1.000
5:160407601:C:G	A334P	1.000
5:160407611:A:C	F330L	1.000
5:160407611:A:T	F330L	1.000
5:160407613:A:G	F330L	1.000
5:160407792:G:C	N313K	1.000
5:160407792:G:T	N313K	1.000
5:160407799:C:T	G311E	1.000
5:160407800:C:G	G311R	1.000
5:160407800:C:T	G311R	1.000
5:160408001:G:T	P296H	1.000
5:160408009:T:A	R293S	1.000
5:160408009:T:G	R293S	1.000
5:160408010:C:A	R293I	1.000
5:160408010:C:G	R293T	1.000
5:160408013:A:C	M292R	1.000
5:160408013:A:G	M292T	1.000
5:160408013:A:T	M292K	1.000
5:160408017:C:G	A291P	1.000
5:160408018:T:A	R290S	1.000
5:160408018:T:G	R290S	1.000
5:160408019:C:A	R290I	1.000
5:160408019:C:G	R290T	1.000
5:160408022:G:A	T289I	1.000
5:160408024:T:A	K288N	1.000
5:160408024:T:G	K288N	1.000
5:160408025:T:A	K288I	1.000
5:160408026:T:C	K288E	1.000

dbSNP variants (sampled 300 via entrez): RS1000199380 (5:160404955 A>C,G,T), RS1000234097 (5:160401617 A>G), RS1000419052 (5:160406810 G>A,C), RS1000465140 (5:160402005 A>T), RS1000652121 (5:160415346 G>A), RS1000734217 (5:160408532 C>G,T), RS1001034010 (5:160418384 A>G), RS1001063626 (5:160418689 G>A,C), RS1001358371 (5:160411606 G>A), RS1001389279 (5:160408373 G>A,T), RS1001413728 (5:160408825 A>G), RS1001594565 (5:160414505 G>A), RS1001599701 (5:160414778 G>C), RS1002036041 (5:160419754 C>T), RS1002312177 (5:160413930 G>A)

Disease associations

OMIM: gene MIM:605974 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST005183_4	Common carotid intima-media thickness	1.000000e-06
GCST010043_132	Asthma	1.000000e-12

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases abundance, increases expression	2
Benzo(a)pyrene	increases expression, increases methylation	2
Tobacco Smoke Pollution	increases expression	2
Valproic Acid	affects expression, decreases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression, decreases expression	2
FR900359	decreases phosphorylation	1
TAK-243	increases sumoylation	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	affects binding, increases activity, increases expression	1
trichostatin A	affects expression	1
cobaltous chloride	increases expression	1
cupric oxide	increases expression	1
di-n-butylphosphoric acid	affects expression	1
4-phenylbutyric acid	decreases expression	1
CGP 52608	increases reaction, affects binding	1
ICG 001	decreases expression	1
abrine	increases expression	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	increases expression	1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine	increases expression, increases response to substance	1
jinfukang	decreases expression	1
MT19c compound	increases expression	1
PCI 5002	affects cotreatment, increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	increases abundance, increases expression	1
Copper	affects binding, decreases expression	1
Dimethyl Sulfoxide	increases expression	1
Disulfiram	affects binding, decreases expression	1
Ethyl Methanesulfonate	increases expression	1

Clinical trials (associated diseases)

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