EXOSC7

Summary

EXOSC7 (exosome component 7, HGNC:28112) is a protein-coding gene on chromosome 3p21.31, encoding Exosome complex component RRP42 (Q15024). Non-catalytic component of the RNA exosome complex which has 3’->5’ exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. It is a common-essential gene (DepMap: required in 94.3% of cancer cell lines).

Predicted to enable mRNA 3’-UTR AU-rich region binding activity. Involved in RNA catabolic process and RNA processing. Located in cytosol and nucleolus. Part of exosome (RNase complex).

Source: NCBI Gene 23016 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 57 total
• Cancer dependency (DepMap): dependent in 94.3% of screened cell lines (common-essential)
• MANE Select transcript: NM_015004

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28112
Approved symbol	EXOSC7
Name	exosome component 7
Location	3p21.31
Locus type	gene with protein product
Status	Approved
Aliases	hRrp42p, Rrp42p, RRP42, EAP1, KIAA0116, p8
Ensembl gene	ENSG00000075914
Ensembl biotype	protein_coding
OMIM	606488
Entrez	23016

Gene structure

Transcript identifiers

Ensembl transcripts: 23 — 13 protein_coding, 8 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000265564, ENST00000459856, ENST00000461361, ENST00000467846, ENST00000468667, ENST00000477865, ENST00000481405, ENST00000482004, ENST00000486727, ENST00000491476, ENST00000498168, ENST00000864641, ENST00000864642, ENST00000864643, ENST00000921130, ENST00000921131, ENST00000921132, ENST00000921133, ENST00000921134, ENST00000921135, ENST00000921136, ENST00000921137, ENST00000921138

RefSeq mRNA: 1 — MANE Select: NM_015004 NM_015004

CCDS: CCDS2725

Canonical transcript exons

ENST00000265564 — 8 exons

Exon	Start	End
ENSE00001912576	44976244	44976334
ENSE00003479292	44989550	44989644
ENSE00003483972	45011235	45011471
ENSE00003498333	45001538	45001608
ENSE00003504873	45005291	45005414
ENSE00003597591	44997087	44997252
ENSE00003641489	45007420	45007575
ENSE00003674606	44989140	44989241

Expression profiles

Bgee: expression breadth ubiquitous, 297 present calls, max score 98.81.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 31.8339 / max 230.9802, expressed in 1823 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
36353	31.0210	1822
36354	0.4579	208
36352	0.3550	192

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	98.81	gold quality
secondary oocyte	CL:0000655	98.05	gold quality
diaphragm	UBERON:0001103	97.42	gold quality
skin of leg	UBERON:0001511	96.65	gold quality
right adrenal gland	UBERON:0001233	96.45	gold quality
left adrenal gland	UBERON:0001234	96.45	gold quality
skin of abdomen	UBERON:0001416	96.43	gold quality
left adrenal gland cortex	UBERON:0035825	96.36	gold quality
right adrenal gland cortex	UBERON:0035827	96.24	gold quality
adrenal cortex	UBERON:0001235	96.20	gold quality
body of tongue	UBERON:0011876	96.05	gold quality
zone of skin	UBERON:0000014	95.89	gold quality
gingival epithelium	UBERON:0001949	95.88	gold quality
adrenal gland	UBERON:0002369	95.63	gold quality
nipple	UBERON:0002030	95.18	gold quality
gingiva	UBERON:0001828	94.78	gold quality
triceps brachii	UBERON:0001509	94.72	gold quality
tongue	UBERON:0001723	94.25	gold quality
pharyngeal mucosa	UBERON:0000355	94.19	gold quality
tongue squamous epithelium	UBERON:0006919	94.19	gold quality
gastrocnemius	UBERON:0001388	94.14	gold quality
muscle of leg	UBERON:0001383	93.82	gold quality
ectocervix	UBERON:0012249	93.79	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	93.70	gold quality
palpebral conjunctiva	UBERON:0001812	93.59	gold quality
biceps brachii	UBERON:0001507	93.54	gold quality
penis	UBERON:0000989	93.46	gold quality
muscle organ	UBERON:0001630	93.37	gold quality
skeletal muscle organ	UBERON:0014892	93.37	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	93.36	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-10553	yes	43.10
E-GEOD-135922	yes	37.54
E-CURD-46	yes	28.14
E-HCAD-9	yes	21.91
E-HCAD-1	yes	18.11
E-ANND-3	yes	10.52

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

37 targeting EXOSC7, 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-5011-5P	100.00	83.46	5820
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-590-3P	99.96	74.34	6478
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-651-3P	99.94	73.48	5177
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-548AQ-5P	99.94	71.34	3426
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
HSA-MIR-548H-5P	99.94	71.24	3488
HSA-MIR-548I	99.94	71.25	3481
HSA-MIR-548J-5P	99.94	71.14	3489
HSA-MIR-548O-5P	99.94	71.24	3488
HSA-MIR-548W	99.94	71.24	3488
HSA-MIR-548Y	99.94	71.28	3514

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 94.3% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 3)

• The association of hCsl4p with the exosome is mediated by protein-protein interactions with hRrp42p and hRrp46p. (PMID:11812149)
• Protein-protein interactions between human exosome components support the assembly of RNase PH-type subunits into a six-membered PNPase-like ring. (PMID:12419256)
• EXOSC7 gene expression is decreased in both classic and follicular variants of papillary thyroid carcinoma. (PMID:21509594)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	exosc7	ENSDARG00000100060
mus_musculus	Exosc7	ENSMUSG00000025785
rattus_norvegicus	Exosc7	ENSRNOG00000060337
drosophila_melanogaster	Rrp42	FBGN0034065
caenorhabditis_elegans		WBGENE00009289

Paralogs (2): EXOSC8 (ENSG00000120699), EXOSC9 (ENSG00000123737)

Protein

Protein identifiers

Exosome complex component RRP42 — Q15024 (reviewed: Q15024)

Alternative names: Exosome component 7, Ribosomal RNA-processing protein 42, p8

All UniProt accessions (1): Q15024

UniProt curated annotations — full annotation on UniProt →

Function. Non-catalytic component of the RNA exosome complex which has 3’->5’ exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding ‘pervasive’ transcripts, such as antisense RNA species and promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3’ untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes.

Subunit / interactions. Component of the RNA exosome core complex (Exo-9), composed of EXOSC1, EXOSC2, EXOSC3, EXOSC4, EXOSC5, EXOSC6, EXOSC7, EXOSC8 and EXOSC9; within the complex interacts with EXOSC2 and EXOSC4. The catalytically inactive RNA exosome core complex (Exo-9) associates with the catalytic subunit EXOSC10/RRP6. Exo-9 may associate with DIS3 to form the nucleolar exosome complex, or DIS3L to form the cytoplasmic exosome complex. Exo-9 is formed by a hexameric base ring consisting of the heterodimers EXOSC4-EXOSC9, EXOSC5-EXOSC8 and EXOSC6-EXOSC7, and a cap ring consisting of EXOSC1, EXOSC2 and EXOSC3. The RNA exosome complex associates with cofactors C1D/RRP47, MPHOSPH6/MPP6 and MTREX/MTR4. Interacts with ZC3HAV1. Interacts with DIS3; the interaction is direct.

Subcellular location. Nucleus. Nucleolus. Cytoplasm.

Similarity. Belongs to the RNase PH family.

RefSeq proteins (1): NP_055819* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001247	ExoRNase_PH_dom1	Domain
IPR015847	ExoRNase_PH_dom2	Domain
IPR020568	Ribosomal_Su5_D2-typ_SF	Homologous_superfamily
IPR027408	PNPase/RNase_PH_dom_sf	Homologous_superfamily
IPR036345	ExoRNase_PH_dom2_sf	Homologous_superfamily
IPR050590	Exosome_comp_Rrp42_subfam	Family

Pfam: PF01138, PF03725

UniProt features (35 total): strand 17, helix 6, turn 5, modified residue 3, sequence variant 2, initiator methionine 1, chain 1

Structure

Experimental structures (PDB)

8 structures.

PDB	Method	Resolution (Å)
9G8M	ELECTRON MICROSCOPY	3.3
2NN6	X-RAY DIFFRACTION	3.35
9G8O	ELECTRON MICROSCOPY	3.4
6D6Q	ELECTRON MICROSCOPY	3.45
6D6R	ELECTRON MICROSCOPY	3.45
9G8N	ELECTRON MICROSCOPY	3.7
6H25	ELECTRON MICROSCOPY	3.8
9G8P	ELECTRON MICROSCOPY	7

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q15024-F1	84.39	0.34

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 (3): 2, 116, 177

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

ID	Pathway
R-HSA-380994	ATF4 activates genes in response to endoplasmic reticulum stress
R-HSA-429958	mRNA decay by 3’ to 5’ exoribonuclease
R-HSA-450385	Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA
R-HSA-450513	Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA
R-HSA-450604	KSRP (KHSRP) binds and destabilizes mRNA
R-HSA-6791226	Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-9930044	Nuclear RNA decay

MSigDB gene sets: 187 (showing top): GOBP_RIBOSOME_BIOGENESIS, MULLIGHAN_NPM1_SIGNATURE_3_UP, REACTOME_UNFOLDED_PROTEIN_RESPONSE_UPR, GOMF_RNA_NUCLEASE_ACTIVITY, SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_UP, GOMF_NUCLEASE_ACTIVITY, MODULE_151, GOBP_TRNA_METABOLIC_PROCESS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, COUP_01, SCHUHMACHER_MYC_TARGETS_UP, MUELLER_PLURINET, GOBP_RNA_SURVEILLANCE

GO Biological Process (11): exonucleolytic trimming to generate mature 3’-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000467), rRNA processing (GO:0006364), RNA processing (GO:0006396), RNA catabolic process (GO:0006401), rRNA catabolic process (GO:0016075), U1 snRNA 3’-end processing (GO:0034473), U4 snRNA 3’-end processing (GO:0034475), U5 snRNA 3’-end processing (GO:0034476), nuclear mRNA surveillance (GO:0071028), nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035), TRAMP-dependent tRNA surveillance pathway (GO:0071038)

GO Molecular Function (4): 3’-5’-RNA exonuclease activity (GO:0000175), RNA binding (GO:0003723), mRNA 3’-UTR AU-rich region binding (GO:0035925), protein binding (GO:0005515)

GO Cellular Component (10): nuclear exosome (RNase complex) (GO:0000176), cytoplasmic exosome (RNase complex) (GO:0000177), exosome (RNase complex) (GO:0000178), nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytosol (GO:0005829), nucleolar exosome (RNase complex) (GO:0101019), cytoplasm (GO:0005737), exoribonuclease complex (GO:1905354)

Reactome top-level categories

Rollup of top-5 pathways:

Category	Pathways
Regulation of mRNA stability by proteins that bind AU-rich elements	3
PERK regulates gene expression	1
Deadenylation-dependent mRNA decay	1
rRNA processing in the nucleus and cytosol	1
Metabolism of RNA	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
snRNA 3’-end processing	3
nuclear RNA surveillance	3
nuclear lumen	3
cellular anatomical structure	3
rRNA metabolic process	2
exosome (RNase complex)	2
cytoplasm	2
intracellular anatomical structure	2
maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	1
rRNA 3’-end processing	1
RNA processing	1
ribosome biogenesis	1
gene expression	1
RNA biosynthetic process	1
primary metabolic process	1
RNA metabolic process	1
nucleic acid catabolic process	1
RNA catabolic process	1
nuclear-transcribed mRNA catabolic process	1
tRNA surveillance	1
3’-5’ exonuclease activity	1
RNA exonuclease activity, producing 5’-phosphomonoesters	1
nucleic acid binding	1
mRNA 3’-UTR binding	1
binding	1
nucleus	1
nuclear protein-containing complex	1
exoribonuclease complex	1
intracellular membrane-bounded organelle	1
intracellular membraneless organelle	1
nuclear exosome (RNase complex)	1
nucleolus	1
catalytic complex	1

Protein interactions and networks

STRING

1968 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
EXOSC7	EXOSC5	Q9NQT4	999
EXOSC7	EXOSC6	Q5RKV6	999
EXOSC7	EXOSC4	Q9NPD3	999
EXOSC7	EXOSC3	Q9NQT5	999
EXOSC7	EXOSC1	Q9Y3B2	999
EXOSC7	EXOSC9	Q06265	991
EXOSC7	EXOSC2	Q13868	991
EXOSC7	EXOSC8	Q96B26	991
EXOSC7	DIS3	Q9Y2L1	935
EXOSC7	EXOSC10	Q01780	915
EXOSC7	SKIC2	Q15477	855
EXOSC7	ZC3HAV1	Q7Z2W4	815
EXOSC7	DIS3L	Q8TF46	801
EXOSC7	MTREX	P42285	758
EXOSC7	MPHOSPH6	Q99547	758

IntAct

120 interactions, top by confidence:

A	B	Type	Score
EXOSC1	EXOSC7	psi-mi:“MI:0915”(physical association)	0.910
EXOSC1	EXOSC7	psi-mi:“MI:0407”(direct interaction)	0.910
EXOSC7	EXOSC1	psi-mi:“MI:0915”(physical association)	0.910
EXOSC4	EXOSC7	psi-mi:“MI:0915”(physical association)	0.900
EXOSC7	EXOSC4	psi-mi:“MI:0915”(physical association)	0.900
EXOSC7	EXOSC2	psi-mi:“MI:0915”(physical association)	0.890
EXOSC2	EXOSC7	psi-mi:“MI:0915”(physical association)	0.890
EXOSC1	EXOSC2	psi-mi:“MI:0914”(association)	0.850
EXOSC4	EXOSC10	psi-mi:“MI:0914”(association)	0.840
GDI1	RAB4A	psi-mi:“MI:0914”(association)	0.820
EXOSC1	EXOSC10	psi-mi:“MI:0915”(physical association)	0.810
EXOSC1	EXOSC10	psi-mi:“MI:0914”(association)	0.810
EXOSC3	EXOSC10	psi-mi:“MI:0914”(association)	0.790
EXOSC10	EXOSC7	psi-mi:“MI:0915”(physical association)	0.750
EXOSC7	EXOSC10	psi-mi:“MI:0914”(association)	0.750
DIS3	EXOSC10	psi-mi:“MI:0914”(association)	0.740
RBM7	MTREX	psi-mi:“MI:0914”(association)	0.730
DIS3L	EXOSC2	psi-mi:“MI:0914”(association)	0.690
MPHOSPH6	MTREX	psi-mi:“MI:0914”(association)	0.690
EXOSC7	IP6K1	psi-mi:“MI:0915”(physical association)	0.670
IP6K1	EXOSC7	psi-mi:“MI:0915”(physical association)	0.670
C1D	ZFC3H1	psi-mi:“MI:0914”(association)	0.640
EXOSC3	MTREX	psi-mi:“MI:0914”(association)	0.640
EXOSC5	ZFC3H1	psi-mi:“MI:0914”(association)	0.640
EXOSC9	EXOSC10	psi-mi:“MI:0914”(association)	0.640

BioGRID (275): EXOSC7 (Affinity Capture-MS), EXOSC7 (Affinity Capture-MS), EXOSC10 (Affinity Capture-MS), MPHOSPH6 (Affinity Capture-MS), EXOSC8 (Affinity Capture-MS), SKIV2L2 (Affinity Capture-MS), EXOSC4 (Affinity Capture-MS), HBS1L (Affinity Capture-MS), EXOSC9 (Affinity Capture-MS), DIS3L (Affinity Capture-MS), EXOSC5 (Affinity Capture-MS), ZCCHC8 (Affinity Capture-MS), EXOSC2 (Affinity Capture-MS), EXOSC1 (Affinity Capture-MS), ZFC3H1 (Affinity Capture-MS)

ESM2 similar proteins: A7M6E7, B8BJ39, B8BM17, B9I2J6, B9N1F9, O09171, O22216, O22718, O35490, O80526, O89000, P11029, P11497, P28173, P35433, Q01217, Q06203, Q12882, Q13085, Q15024, Q28007, Q28559, Q28943, Q2QNG7, Q2QXR8, Q2QZ86, Q2RAK2, Q3T0V9, Q5I597, Q5M8Z0, Q5R895, Q5RFG2, Q5SWU9, Q5XGM3, Q5XGS8, Q6NYG8, Q8CHR6, Q8CIH9, Q8IX04, Q8S0G4

Diamond homologs: A2C412, A4QEY2, A4YJR3, A5E8I9, A6Q4N2, B2V890, B3EH06, B3EMN6, B5YFY8, B6YSE7, B8I2R5, C1DTW6, C3MQ47, C3MVG5, C3N5R4, C3NED0, C3NHC2, C3PH09, C4KHE3, C4LJ74, C5A2B8, O26778, O29756, O59224, O74918, Q05636, Q06265, Q0W2Y7, Q10205, Q15024, Q2GGA4, Q2KHU3, Q3SW80, Q3SWZ4, Q3YSC4, Q47RU5, Q4QR75, Q54VM4, Q5FHK5, Q5HBH6

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
EXOSC7	“form complex”	Exosome_Complex	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 90 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 decay by 3’ to 5’ exoribonuclease	7	74.6×	3e-10
Nuclear RNA decay	15	69.1×	2e-22
Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA	7	66.3×	4e-10
Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA	7	66.3×	4e-10
KSRP (KHSRP) binds and destabilizes mRNA	7	66.3×	4e-10
ATF4 activates genes in response to endoplasmic reticulum stress	7	42.6×	1e-08
rRNA processing in the nucleus and cytosol	7	16.8×	9e-06
Major pathway of rRNA processing in the nucleolus and cytosol	17	15.7×	6e-14

GO biological processes:

GO term	Partners	Fold	FDR
maturation of 5.8S rRNA	5	65.0×	6e-07
rRNA catabolic process	5	61.2×	7e-07
nuclear-transcribed mRNA catabolic process	6	56.7×	5e-08
RNA catabolic process	10	56.2×	6e-13
mRNA catabolic process	5	30.6×	2e-05
RNA processing	10	27.0×	6e-10
rRNA processing	13	22.7×	4e-12
ribosomal small subunit biogenesis	6	16.9×	5e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	43
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1981 predictions. Top by Δscore:

Variant	Effect	Δscore
3:44989548:AG:A	acceptor_gain	1.0000
3:44989549:GG:G	acceptor_gain	1.0000
3:44997084:T:G	acceptor_gain	1.0000
3:44997085:A:AG	acceptor_gain	1.0000
3:44997086:G:GA	acceptor_gain	1.0000
3:44997086:GTTC:G	acceptor_gain	1.0000
3:44997086:GTTCA:G	acceptor_gain	1.0000
3:44997249:GCTG:G	donor_gain	1.0000
3:44997251:TGGT:T	donor_loss	1.0000
3:44997253:G:GG	donor_gain	1.0000
3:44997253:GT:G	donor_loss	1.0000
3:44997254:TGA:T	donor_loss	1.0000
3:44997255:GAGTA:G	donor_loss	1.0000
3:44997256:AGTAT:A	donor_loss	1.0000
3:45001520:A:AG	acceptor_gain	1.0000
3:45001521:A:G	acceptor_gain	1.0000
3:45001536:A:AG	acceptor_gain	1.0000
3:45001537:G:GG	acceptor_gain	1.0000
3:45007504:G:GT	donor_gain	1.0000
3:45007525:A:T	donor_gain	1.0000
3:45007575:GGTGA:G	donor_loss	1.0000
3:45007576:GTGA:G	donor_loss	1.0000
3:45007577:T:G	donor_loss	1.0000
3:45026467:GAAAG:G	donor_gain	1.0000
3:45026469:AAGG:A	donor_loss	1.0000
3:45026471:GGTA:G	donor_loss	1.0000
3:45026472:G:C	donor_loss	1.0000
3:45035522:A:AG	acceptor_gain	1.0000
3:45035523:G:GA	acceptor_gain	1.0000
3:45035523:GTCT:G	acceptor_gain	1.0000

AlphaMissense

1900 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:44989149:C:A	R23S	0.995
3:44989227:G:C	A49P	0.994
3:44997229:T:A	W133R	0.994
3:44997229:T:C	W133R	0.994
3:44989161:C:A	R27S	0.993
3:44989222:G:A	G47E	0.993
3:44989228:C:A	A49D	0.993
3:44989162:G:C	R27P	0.992
3:44989619:G:C	G77R	0.992
3:44989638:T:A	V83D	0.992
3:45001593:C:A	A159D	0.991
3:44989224:T:C	S48P	0.990
3:44997231:G:C	W133C	0.990
3:44997231:G:T	W133C	0.990
3:45001592:G:C	A159P	0.990
3:45001596:T:C	L160P	0.990
3:44989221:G:T	G47W	0.989
3:45007441:G:C	D213H	0.989
3:45011239:G:A	G259D	0.988
3:44989234:T:A	V51D	0.987
3:44989620:G:A	G77D	0.987
3:45005401:T:A	V201D	0.987
3:45011251:G:A	G263D	0.987
3:44989569:T:A	V60E	0.986
3:45011328:T:C	F289L	0.986
3:45011330:C:A	F289L	0.986
3:45011330:C:G	F289L	0.986
3:44976326:G:C	G17R	0.985
3:44997109:T:C	F93L	0.985
3:44997111:T:A	F93L	0.985

dbSNP variants (sampled 300 via entrez): RS1000054948 (3:44987043 C>T), RS1000081123 (3:44994214 CTAAGAGTGG>C), RS1000117594 (3:45008204 C>T), RS1000183681 (3:44989057 T>G), RS1000226129 (3:44974522 C>T), RS1000290621 (3:44982615 G>C), RS1000352085 (3:44975945 G>A,C), RS1000431447 (3:44994665 C>T), RS1000487909 (3:44976114 C>G), RS1000557129 (3:44976017 C>A,T), RS1000600229 (3:44982270 G>A), RS1000694426 (3:44975673 G>A,C), RS1000832990 (3:44981051 G>A), RS1000874067 (3:45000707 A>T), RS1000942220 (3:44993465 A>G,T)

Disease associations

OMIM: gene MIM:606488 | 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
GCST002481_7	Acne (severe)	3.000000e-06
GCST007130_1	Cerebrospinal fluid t-tau:AB1-42 ratio	5.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007708	t-tau:beta-amyloid 1-42 ratio measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects methylation, decreases expression, increases abundance	3
FR900359	increases phosphorylation	1
dicrotophos	decreases expression	1
bis(tri-n-butyltin)oxide	decreases expression	1
bisphenol A	decreases expression	1
deoxynivalenol	increases expression	1
glycidyl methacrylate	increases expression	1
CGP 52608	increases reaction, affects binding	1
(+)-JQ1 compound	decreases expression	1
Arsenic	decreases expression, increases abundance	1
Atrazine	increases expression	1
Benzo(a)pyrene	affects methylation	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Ivermectin	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Plant Extracts	decreases expression	1
Silicon Dioxide	increases expression	1
Thiram	decreases expression	1
Tretinoin	decreases expression	1
Valproic Acid	decreases expression	1
Thapsigargin	affects expression	1
Zinc Sulfate	decreases expression	1
Particulate Matter	decreases expression	1

Clinical trials (associated diseases)

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