NOB1

Summary

NOB1 (NIN1 (RPN12) binding protein 1 homolog, HGNC:29540) is a protein-coding gene on chromosome 16q22.1, encoding RNA-binding protein NOB1 (Q9ULX3). May play a role in mRNA degradation. It is a common-essential gene (DepMap: required in 97.1% of cancer cell lines).

In yeast, over 200 protein and RNA cofactors are required for ribosome assembly, and these are generally conserved in eukaryotes. These factors orchestrate modification and cleavage of the initial 35S precursor rRNA transcript into the mature 18S, 5.8S, and 25S rRNAs, folding of the rRNA, and binding of ribosomal proteins and 5S RNA. Nob1 is involved in pre-rRNA processing. In a late cytoplasmic processing step, Nob1 cleaves a 20S rRNA intermediate at cleavage site D to produce the mature 18S rRNA (Lamanna and Karbstein, 2009 [PubMed 19706509]).

Source: NCBI Gene 28987 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 100 total
• Cancer dependency (DepMap): dependent in 97.1% of screened cell lines (common-essential)
• MANE Select transcript: NM_014062

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29540
Approved symbol	NOB1
Name	NIN1 (RPN12) binding protein 1 homolog
Location	16q22.1
Locus type	gene with protein product
Status	Approved
Aliases	NOB1P, ART-4, MST158
Ensembl gene	ENSG00000141101
Ensembl biotype	protein_coding
OMIM	613586
Entrez	28987

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 3 protein_coding, 3 retained_intron, 2 nonsense_mediated_decay

ENST00000268802, ENST00000561677, ENST00000562416, ENST00000563055, ENST00000564620, ENST00000569871, ENST00000899343, ENST00000920840

RefSeq mRNA: 1 — MANE Select: NM_014062 NM_014062

CCDS: CCDS10884

Canonical transcript exons

ENST00000268802 — 9 exons

Exon	Start	End
ENSE00000946648	69741871	69742601
ENSE00001382694	69754594	69754726
ENSE00002594411	69754848	69754926
ENSE00003534992	69749559	69749630
ENSE00003605575	69748918	69749118
ENSE00003623363	69752241	69752371
ENSE00003625917	69748232	69748329
ENSE00003626117	69744873	69745017
ENSE00003668642	69749213	69749338

Expression profiles

Bgee: expression breadth ubiquitous, 142 present calls, max score 96.19.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 80.0335 / max 413.9087, expressed in 1823 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
157917	80.0335	1823

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
body of pancreas	UBERON:0001150	96.19	gold quality
right adrenal gland	UBERON:0001233	94.39	gold quality
right adrenal gland cortex	UBERON:0035827	94.33	gold quality
left adrenal gland	UBERON:0001234	94.32	gold quality
left adrenal gland cortex	UBERON:0035825	94.09	gold quality
pancreas	UBERON:0001264	93.71	gold quality
left ovary	UBERON:0002119	93.66	gold quality
ovary	UBERON:0000992	93.51	gold quality
stromal cell of endometrium	CL:0002255	93.41	gold quality
adrenal gland	UBERON:0002369	93.22	gold quality
fallopian tube	UBERON:0003889	92.59	gold quality
right ovary	UBERON:0002118	92.45	gold quality
esophagus mucosa	UBERON:0002469	92.34	gold quality
lymph node	UBERON:0000029	92.20	gold quality
skin of abdomen	UBERON:0001416	92.12	gold quality
zone of skin	UBERON:0000014	92.04	gold quality
skin of leg	UBERON:0001511	92.02	gold quality
body of stomach	UBERON:0001161	91.87	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	91.64	gold quality
fundus of stomach	UBERON:0001160	91.43	gold quality
right uterine tube	UBERON:0001302	91.14	gold quality
duodenum	UBERON:0002114	91.07	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	90.99	gold quality
lower esophagus mucosa	UBERON:0035834	90.78	gold quality
vagina	UBERON:0000996	90.77	gold quality
omental fat pad	UBERON:0010414	90.76	gold quality
gall bladder	UBERON:0002110	90.73	gold quality
thoracic mammary gland	UBERON:0005200	90.73	gold quality
stomach	UBERON:0000945	90.71	gold quality
placenta	UBERON:0001987	90.71	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-112	yes	8.60
E-MTAB-6142	no	177.84
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

20 targeting NOB1, 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-497-5P	99.92	71.83	2674
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-4677-5P	99.70	70.09	1940
HSA-MIR-3128	99.50	67.85	1258
HSA-MIR-4652-3P	99.33	70.02	2742
HSA-MIR-190B-3P	99.33	68.29	1382
HSA-MIR-5584-3P	99.23	68.79	1351
HSA-MIR-6868-5P	99.06	65.69	1284
HSA-MIR-491-3P	98.88	68.86	1224
HSA-MIR-4635	98.74	67.63	1339
HSA-MIR-4799-3P	97.78	65.97	893
HSA-MIR-4720-5P	97.46	65.67	893
HSA-MIR-5588-5P	97.46	65.70	913
HSA-MIR-139-3P	95.24	63.10	316

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 97.1% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 36)

• Cloning, expression and characterization of the human NOB1 gene and its products. (PMID:16172919)
• These results suggested that NOB1 may act as an oncogenic factor in ovarian cancer (PMID:21287298)
• Nob1 is an important regulator of the tumorigenic properties of human hepatocellular carcinoma and could be used as a candidate therapeutic target. (PMID:21573803)
• NOB1 expression is higher in colorectal cancer than in normal colorectal tissues. Expression was not correlated to such tumor characteristics as gender, age, histological differentiation grade, depth of invasion and lymph node metastasis. (PMID:22445998)
• The expression level of the NOB1 gene in the thyroid may play a key role in the occurrence and development of papillary thyroid carcinoma. (PMID:23685895)
• NOB1 promotes glioma cell growth and migration and could be a candidate for molecular targeting during gene therapy treatments of glioma. (PMID:23911301)
• aberrant expression of NOB1 in breast infiltrating ductal carcinoma is possibly involved with tumorigenesis and development, and the NOB1 protein could act as a potential biomarker for prognosis assessment of breast infiltrating ductal carcinoma. (PMID:24133592)
• NOB1 expression status was closely correlated with important histopathologic characteristics and the recurrence and metastasis of prostate carcinomas. (PMID:24228091)
• Enhanced expression of NOB1 gene plays an important role in the occurrence and development of NSCLC. (PMID:24272676)
• These findings provide evidence that Nob1 is an indicator of poor prognosis in prostate carcinoma. (PMID:24493285)
• NOB1 depletion may inhibit osteosarcoma development by increasing E-cadherin and beta-catenin expression. (PMID:24714960)
• NOB1 is involved in the malignant transformation and tumorigenecity of human prostate cancer cells. (PMID:25169742)
• Downregulation of NOB1 was able to significantly activate constitutive phosphorylation of p38 MAPK, which might contribute to the inhibition of papillary thyroid carcinoma cell growth. (PMID:25231838)
• NOB1 expression was associated with poor prognosis in ccRCC patients. (PMID:25420906)
• Enhanced expression of NOB1 is related to poor overall survival and progression-free survival in patients with resected non-small cell lung cancer. (PMID:25450647)
• These findings suggest that NOB1 may be a potential prognostic indicator for PCa. (PMID:25503472)
• NOB1 gene silencing by lentivirus-mediated RNA interference can inhibit tumor growth by inducing apoptosis of cancerous human colorectal cells. (PMID:25624720)
• Downregulation of miR-326 inhibited tumor proliferation and tumor metastasis by directly targeting NOB1 in colorectal carcinoma. Upregulation of miR-326 in CRC cells was revealed to be associated with a feedback loop involving downregulation of the NOB1. (PMID:25760058)
• CONCLUSION: Our results suggest that enhanced expression of NOB1 related with poor early response to cisplatin-based chemotherapy in patients with advanced non-small cell lung cancer (PMID:25971309)
• NOB1 protein in gastric cancer tissue and adjacent normal tissue was diffusely expressed in the cytoplasm and nucleus. NOB1 protein and mRNA expression was higher than normal in gastric cancer tissue and was directly related to tumor size. (PMID:26122232)
• These results suggest that NOB1 may act as an important regulator in non-small cell lung cancer growth and could be a therapeutic target of nonsmall cell lung cancer. (PMID:26178254)
• The results suggested that NOB1 is important in OSCC development and serves as a candidate indicator of aggressiveness and a therapeutic target of oral squamous cell carcinoma. (PMID:26370469)
• we suggest that targeting miR-192 and NOB1 is a novel strategy which will assist in the development of new therapeutics that will be used in the future to prevent and treat prostate cancer. (PMID:26743688)
• NOB1 plays an oncogenic role in laryngeal cancer cells through the regulation of JNK signaling pathway. (PMID:27035645)
• The expression of NOB1 was also found to be higher in multidrug-resistant gastric cancer cells than that of sensitive cells. This novel MAb will be valuable for investigating the role of NOB1 in carcinogenesis and multidrug resistance of gastric cancer. (PMID:27097067)
• miR-139-3p may act as a tumor suppressor that can inhibitcervical cancer cell proliferation, migration and invasion and induce cell apoptosis through down-regulation of NOB1 expression. (PMID:27505862)
• The proto-oncogene NOB1 as a direct target of miR-326 in gastric cancer. (PMID:27733214)
• our results indicate that miR-330-5p inhibits non-small-cell lung cancer (NSCLC) cell growth through downregulation of NOB1 expression. Our study suggests that miR-330-5p may serve as a potential therapeutic target for the treatment of NSCLC (PMID:28849232)
• Authors identified that SNHG1 increased human nin one binding protein (NOB1), an oncogene, through sponging miR-326 as competing endogenous RNA (ceRNA), finally prompting cell growth, migration and invasion in OS. (PMID:29115574)
• These results suggested that RIOK2 and NOB1 may be potential targets in the treatment of Non-small cell lung cancer (NSCLC), and miR145 may be considered a therapeutic inhibitor of both genes. (PMID:29749434)
• A detailed characterization of Nob1 organization and its interaction with Pno1. (PMID:30176151)
• NOB1 was correlated with clinical outcomes and prognosis of gastric cancer patients and was an independent risk factor for 5-year mortality of GC patients. (PMID:30274015)
• NOB1: A Potential Biomarker or Target in Cancer. (PMID:30854959)
• Silencing NOB1 Can Affect Cell Proliferation and Apoptosis Via the C-Jun N-Terminal Kinase Pathway in Colorectal Cancer. (PMID:31906747)
• MiR-363 suppresses cell migration, invasion, and epithelial-mesenchymal transition of osteosarcoma by binding to NOB1. (PMID:32357945)
• LncRNA FEZF1-AS1 aggravates cell proliferation and migration in glioblastoma. (PMID:34530115)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	nob1	ENSDARG00000016080
mus_musculus	Nob1	ENSMUSG00000003848
rattus_norvegicus	Nob1	ENSRNOG00000021890
drosophila_melanogaster	CG2972	FBGN0030177
caenorhabditis_elegans	nobh-1	WBGENE00021843

Protein

Protein identifiers

RNA-binding protein NOB1 — Q9ULX3 (reviewed: Q9ULX3)

Alternative names: Phosphorylation regulatory protein HP-10, Protein ART-4

All UniProt accessions (2): Q9ULX3, H3BUR4

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in mRNA degradation. Endonuclease required for processing of 20S pre-rRNA precursor and biogenesis of 40S ribosomal subunits.

Subunit / interactions. Interacts with UPF2. Component of the small ribosomal subunit, ribosomal RNA processing complex (SSU RRP complex).

Subcellular location. Nucleus.

Tissue specificity. Detected in liver, lung, placenta, endothelial cells and spleen.

Similarity. Belongs to the NOB1 family.

RefSeq proteins (1): NP_054781* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002716	PIN_dom	Domain
IPR014881	NOB1_Zn-bd	Domain
IPR017117	Nob1_euk	Family
IPR033411	Ribonuclease_PIN	Domain
IPR033461	WRNPLPNID	Domain
IPR036283	NOB1_Zf-like_sf	Homologous_superfamily
IPR039907	NOB1	Family

Pfam: PF08772, PF15017, PF17146

UniProt features (53 total): strand 16, helix 12, turn 8, modified residue 4, binding site 4, sequence variant 2, initiator methionine 1, chain 1, sequence conflict 1, domain 1, zinc finger region 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

14 structures.

PDB	Method	Resolution (Å)
6ZXE	ELECTRON MICROSCOPY	3
7WTZ	ELECTRON MICROSCOPY	3
6ZUO	ELECTRON MICROSCOPY	3.1
7WTX	ELECTRON MICROSCOPY	3.1
6ZXD	ELECTRON MICROSCOPY	3.2
7WTW	ELECTRON MICROSCOPY	3.2
7WU0	ELECTRON MICROSCOPY	3.3
6G5I	ELECTRON MICROSCOPY	3.5
6G18	ELECTRON MICROSCOPY	3.6
6ZXF	ELECTRON MICROSCOPY	3.7
8ZDC	ELECTRON MICROSCOPY	3.8
6G4S	ELECTRON MICROSCOPY	4
6G51	ELECTRON MICROSCOPY	4.1
6G53	ELECTRON MICROSCOPY	4.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9ULX3-F1	72.53	0.29

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 (4): 270; 273; 285; 288

Post-translational modifications (4): 184, 201, 325, 352

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-6791226	Major pathway of rRNA processing in the nucleolus and cytosol

MSigDB gene sets: 128 (showing top): GOBP_RIBOSOME_BIOGENESIS, GOMF_ENDONUCLEASE_ACTIVITY, YAATNRNNNYNATT_UNKNOWN, GOMF_RNA_NUCLEASE_ACTIVITY, chr16q22, PAX4_01, GOMF_NUCLEASE_ACTIVITY, GOBP_MATURATION_OF_SSU_RRNA, NFKB_Q6, SRF_Q5_01, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, GOMF_RNA_ENDONUCLEASE_ACTIVITY, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, GOBP_SENSORY_PERCEPTION_OF_LIGHT_STIMULUS, CCCNNNNNNAAGWT_UNKNOWN

GO Biological Process (4): rRNA processing (GO:0006364), visual perception (GO:0007601), maturation of SSU-rRNA (GO:0030490), ribosomal small subunit biogenesis (GO:0042274)

GO Molecular Function (7): RNA endonuclease activity (GO:0004521), zinc ion binding (GO:0008270), hydrolase activity (GO:0016787), nuclease activity (GO:0004518), endonuclease activity (GO:0004519), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (4): nucleoplasm (GO:0005654), cytosol (GO:0005829), preribosome, small subunit precursor (GO:0030688), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
rRNA processing in the nucleus and cytosol	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
ribosome biogenesis	2
cellular anatomical structure	2
RNA processing	1
rRNA metabolic process	1
sensory perception of light stimulus	1
rRNA processing	1
ribosomal small subunit biogenesis	1
ribonucleoprotein complex biogenesis	1
endonuclease activity	1
RNA nuclease activity	1
transition metal ion binding	1
catalytic activity	1
catalytic activity, acting on a nucleic acid	1
nuclease activity	1
binding	1
cation binding	1
nuclear lumen	1
cytoplasm	1
preribosome	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1976 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NOB1	NINJ1	Q92982	968
NOB1	PSMD8	P48556	966
NOB1	PNO1	Q9NRX1	946
NOB1	BYSL	Q13895	902
NOB1	RIOK2	Q9BVS4	894
NOB1	LTV1	Q96GA3	889
NOB1	TSR1	Q2NL82	877
NOB1	RIOK1	Q9BRS2	875
NOB1	TXNL4B	Q9NX01	806
NOB1	BMS1	Q14692	747
NOB1	FCF1	Q9Y324	727
NOB1	DHX15	O43143	711
NOB1	PDCD11	Q14690	690
NOB1	RRP12	Q5JTH9	675
NOB1	RPS3	P23396	649
NOB1	RCL1	Q9Y2P8	649

IntAct

79 interactions, top by confidence:

A	B	Type	Score
PNO1	NOB1	psi-mi:“MI:0915”(physical association)	0.740
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
RIOK1	PRMT5	psi-mi:“MI:0914”(association)	0.710
BYSL	PARN	psi-mi:“MI:0914”(association)	0.640
NOB1	KLHL22	psi-mi:“MI:0914”(association)	0.640
KSR2	POLR3A	psi-mi:“MI:0914”(association)	0.530
LRRC4C	DVL2	psi-mi:“MI:0914”(association)	0.530
RPS2	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
RIOK2	BYSL	psi-mi:“MI:0914”(association)	0.530
HLA-DPA1	TYW5	psi-mi:“MI:0914”(association)	0.530
DNA2	CIAO1	psi-mi:“MI:0914”(association)	0.530
Cep152	SH3PXD2B	psi-mi:“MI:0914”(association)	0.350
Racgap1	DDX3X	psi-mi:“MI:0914”(association)	0.350
RPL10	RPS6	psi-mi:“MI:0914”(association)	0.350
Ncstn	DERL1	psi-mi:“MI:0914”(association)	0.350
Rrbp1	PIPSL	psi-mi:“MI:0914”(association)	0.350
NPM1	RPSA	psi-mi:“MI:0914”(association)	0.350
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
RIPK4	VWA8	psi-mi:“MI:0914”(association)	0.350
HSCB	RBP5	psi-mi:“MI:0914”(association)	0.350
Mecom	ESYT2	psi-mi:“MI:0914”(association)	0.350
MAP3K14	IKBKG	psi-mi:“MI:0914”(association)	0.350
HLA-DPA1	GXYLT2	psi-mi:“MI:0914”(association)	0.350
DNA2	TARSL2	psi-mi:“MI:0914”(association)	0.350
NOB1	ANKHD1	psi-mi:“MI:0914”(association)	0.350

BioGRID (159): NOB1 (Affinity Capture-MS), NOB1 (Affinity Capture-MS), NOB1 (Affinity Capture-MS), NOB1 (Affinity Capture-MS), NOB1 (Affinity Capture-MS), GNL2 (Co-fractionation), NOB1 (Co-fractionation), NOB1 (Co-fractionation), NOB1 (Co-fractionation), NOB1 (Co-fractionation), NOB1 (Co-fractionation), NOB1 (Co-fractionation), NOB1 (Co-fractionation), NOB1 (Co-fractionation), TSR1 (Co-fractionation)

ESM2 similar proteins: A0A1W2PQ27, A0A1W2PQ64, A0A1W2PQC6, A0A1W2PQD8, A0A1W2PQJ5, A0A1W2PR75, A2AV36, A4QN59, A6QQV6, D4A1F2, F1RA39, G5E8F4, J9SQF3, O00142, O42868, O55239, O95050, O95932, O97972, P0CR76, P0CR77, P40261, P40936, P53538, Q01841, Q22453, Q32LP9, Q4R7D0, Q566Y1, Q5M9G7, Q5RFR7, Q5U4E8, Q5XG58, Q62160, Q6C195, Q6CQ61, Q6DE00, Q6FMU7, Q6PCI6, Q810S1

Diamond homologs: O27890, O29862, O58440, P57674, Q3T042, Q4R537, Q58869, Q5RBB3, Q6VEU1, Q8BW10, Q9ULX3, Q9UZ20, Q9YD10, Q9FLL1, Q9UTK0, Q08444

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 102 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
Eukaryotic Translation Initiation	7	29.6×	1e-07
Cap-dependent Translation Initiation	7	29.6×	1e-07
SARS-CoV-1 modulates host translation machinery	7	29.6×	1e-07
Eukaryotic Translation Elongation	7	26.7×	2e-07
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S	7	26.1×	2e-07
rRNA processing in the nucleus and cytosol	11	24.2×	1e-10
Influenza Viral RNA Transcription and Replication	8	23.6×	1e-07
Nonsense-Mediated Decay (NMD)	7	22.4×	5e-07

GO biological processes:

GO term	Partners	Fold	FDR
maturation of SSU-rRNA	6	52.2×	2e-07
maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	6	46.0×	4e-07
ribosomal small subunit biogenesis	13	33.6×	4e-14
cytoplasmic translation	11	23.1×	4e-10
rRNA processing	6	9.7×	3e-03
translation	8	9.3×	2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	80
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

854 predictions. Top by Δscore:

Variant	Effect	Δscore
16:69742597:GAGTA:G	acceptor_gain	1.0000
16:69742599:GTA:G	acceptor_gain	1.0000
16:69742600:TA:T	acceptor_gain	1.0000
16:69742600:TACTG:T	acceptor_loss	1.0000
16:69742602:C:CC	acceptor_gain	1.0000
16:69742603:T:A	acceptor_loss	1.0000
16:69744868:CTCA:C	donor_loss	1.0000
16:69744869:TCA:T	donor_loss	1.0000
16:69744871:A:AC	donor_gain	1.0000
16:69744871:A:AG	donor_loss	1.0000
16:69744871:AC:A	donor_gain	1.0000
16:69744872:C:CC	donor_gain	1.0000
16:69744872:C:CG	donor_loss	1.0000
16:69744872:CC:C	donor_gain	1.0000
16:69745013:TTGTC:T	acceptor_gain	1.0000
16:69745016:TC:T	acceptor_gain	1.0000
16:69745016:TCC:T	acceptor_loss	1.0000
16:69745017:CC:C	acceptor_gain	1.0000
16:69745018:C:CC	acceptor_gain	1.0000
16:69745019:T:C	acceptor_loss	1.0000
16:69748227:CAT:C	donor_loss	1.0000
16:69748227:CATA:C	donor_gain	1.0000
16:69748228:ATA:A	donor_loss	1.0000
16:69748229:TACTT:T	donor_loss	1.0000
16:69748230:A:AC	donor_gain	1.0000
16:69748230:A:T	donor_loss	1.0000
16:69748231:C:A	donor_loss	1.0000
16:69748231:C:CA	donor_gain	1.0000
16:69748233:TGAA:T	donor_gain	1.0000
16:69748325:ACATT:A	acceptor_gain	1.0000

AlphaMissense

2697 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:69748248:A:G	C270R	0.998
16:69748247:C:G	C270S	0.997
16:69748248:A:T	C270S	0.997
16:69744989:A:G	C285R	0.994
16:69748239:A:G	C273R	0.994
16:69748246:G:C	C270W	0.994
16:69748247:C:T	C270Y	0.994
16:69748250:C:G	R269P	0.994
16:69744990:G:C	F284L	0.992
16:69744990:G:T	F284L	0.992
16:69744992:A:G	F284L	0.992
16:69748247:C:A	C270F	0.992
16:69744979:C:G	C288S	0.991
16:69744980:A:T	C288S	0.991
16:69748238:C:G	C273S	0.991
16:69748239:A:T	C273S	0.991
16:69748944:A:G	C234R	0.991
16:69744964:A:G	L293P	0.990
16:69748918:C:A	Q242H	0.990
16:69748918:C:G	Q242H	0.990
16:69744980:A:G	C288R	0.989
16:69748930:G:C	D238E	0.989
16:69748930:G:T	D238E	0.989
16:69748937:G:A	T236I	0.989
16:69752302:A:G	L89P	0.989
16:69744979:C:T	C288Y	0.988
16:69748238:C:T	C273Y	0.988
16:69748237:A:C	C273W	0.987
16:69748927:G:C	F239L	0.987
16:69748927:G:T	F239L	0.987

dbSNP variants (sampled 300 via entrez): RS1000322230 (16:69751420 A>C,G), RS1000341411 (16:69754933 G>A), RS1000528374 (16:69746048 A>G), RS1000795085 (16:69741475 C>G,T), RS1000859047 (16:69754668 G>A,C), RS1000957886 (16:69743607 C>A), RS1001267750 (16:69744551 C>T), RS1001685025 (16:69753964 C>A,T), RS1001859808 (16:69742005 A>G), RS1001906043 (16:69754291 G>A), RS1001961963 (16:69751828 G>A), RS1002263367 (16:69743547 C>G,T), RS1002387761 (16:69756292 A>G), RS1002895686 (16:69746850 T>C), RS1003227122 (16:69752965 C>T)

Disease associations

OMIM: gene MIM:613586 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

10 associations (top):

Study	Trait	p-value
GCST004267_1	Blood osmolality (transformed sodium)	6.000000e-12
GCST004267_7	Blood osmolality (transformed sodium)	6.000000e-10
GCST005951_13	Body mass index	5.000000e-11
GCST007267_229	Systolic blood pressure	4.000000e-11
GCST007293_28	Body fat distribution (arm fat ratio)	3.000000e-12
GCST007293_6	Body fat distribution (arm fat ratio)	5.000000e-06
GCST007293_62	Body fat distribution (arm fat ratio)	2.000000e-17
GCST007295_15	Body fat distribution (leg fat ratio)	3.000000e-06
GCST007295_99	Body fat distribution (leg fat ratio)	5.000000e-06
GCST007327_186	Smoking status (ever vs never smokers)	6.000000e-12

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0006335	systolic blood pressure
EFO:0004341	body fat distribution
EFO:0004318	smoking behavior

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects cotreatment, increases abundance, increases expression, decreases expression	3
Valproic Acid	affects expression, decreases expression	2
aristolochic acid I	increases expression	1
FR900359	increases phosphorylation	1
sodium arsenate	decreases expression	1
beta-lapachone	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
potassium chromate(VI)	affects cotreatment, increases expression	1
coumarin	increases phosphorylation	1
epigallocatechin gallate	affects cotreatment, increases expression	1
di-n-butylphosphoric acid	affects expression	1
cylindrospermopsin	increases expression	1
perfluoro-n-nonanoic acid	increases expression	1
abrine	decreases expression	1
Sunitinib	increases expression	1
Arsenic	increases abundance, increases expression, affects cotreatment	1
Benzo(a)pyrene	decreases methylation	1
Caffeine	affects phosphorylation	1
Ivermectin	decreases expression	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Phenobarbital	affects expression	1
Ribonucleotides	affects binding	1
Rotenone	decreases expression	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Cyclosporine	increases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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