RPRD1B

Summary

RPRD1B (regulation of nuclear pre-mRNA domain containing 1B, HGNC:16209) is a protein-coding gene on chromosome 20q11.23, encoding Regulation of nuclear pre-mRNA domain-containing protein 1B (Q9NQG5). Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD by RPAP2. It is a selective cancer dependency (DepMap: 45.4% of cell lines).

Enables RNA polymerase II complex binding activity and identical protein binding activity. Involved in several processes, including RNA polymerase II promoter clearance; positive regulation of cell population proliferation; and positive regulation of transcription by RNA polymerase II. Located in nucleoplasm. Part of transcription preinitiation complex.

Source: NCBI Gene 58490 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 19 total
• Cancer dependency (DepMap): dependent in 45.4% of screened cell lines
• MANE Select transcript: NM_021215

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16209
Approved symbol	RPRD1B
Name	regulation of nuclear pre-mRNA domain containing 1B
Location	20q11.23
Locus type	gene with protein product
Status	Approved
Aliases	dJ1057B20.2, DKFZp434P0735, CREPT, FLJ44520, NET60, Kub5-Hera, K-H
Ensembl gene	ENSG00000101413
Ensembl biotype	protein_coding
OMIM	614694
Entrez	58490

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 9 protein_coding, 3 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000373433, ENST00000449186, ENST00000462548, ENST00000471511, ENST00000484683, ENST00000495457, ENST00000614670, ENST00000618318, ENST00000622494, ENST00000881433, ENST00000881434, ENST00000881435, ENST00000881436, ENST00000881437

RefSeq mRNA: 1 — MANE Select: NM_021215 NM_021215

CCDS: CCDS13301

Canonical transcript exons

ENST00000373433 — 7 exons

Exon	Start	End
ENSE00000661915	38040435	38040564
ENSE00001460564	38089726	38092364
ENSE00001460570	38033746	38034098
ENSE00003547852	38066081	38066256
ENSE00003630027	38057532	38057644
ENSE00003685845	38059394	38059520
ENSE00003690036	38048348	38048481

Expression profiles

Bgee: expression breadth ubiquitous, 243 present calls, max score 95.27.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.2505 / max 454.6364, expressed in 1814 samples.

FANTOM5 promoters (20 alternative TSS)

Promoter ID	TPM avg	Samples expressed
184538	9.8194	1782
184536	7.2997	1744
184537	2.0190	1196
184540	0.8373	414
184539	0.7275	469
184535	0.3739	189
184554	0.3181	141
184546	0.1932	8
184553	0.1359	59
184547	0.1250	8

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ileal mucosa	UBERON:0000331	95.27	gold quality
tibialis anterior	UBERON:0001385	94.92	gold quality
cardiac muscle of right atrium	UBERON:0003379	94.77	gold quality
left ventricle myocardium	UBERON:0006566	92.79	gold quality
cardiac atrium	UBERON:0002081	92.51	gold quality
right atrium auricular region	UBERON:0006631	92.43	gold quality
gastrocnemius	UBERON:0001388	92.34	gold quality
right lobe of liver	UBERON:0001114	92.31	gold quality
calcaneal tendon	UBERON:0003701	92.30	gold quality
muscle of leg	UBERON:0001383	92.18	gold quality
deltoid	UBERON:0001476	91.44	silver quality
bone marrow cell	CL:0002092	91.25	gold quality
sural nerve	UBERON:0015488	91.03	gold quality
colonic epithelium	UBERON:0000397	90.98	gold quality
right uterine tube	UBERON:0001302	90.88	gold quality
body of uterus	UBERON:0009853	90.73	gold quality
heart left ventricle	UBERON:0002084	90.56	gold quality
heart	UBERON:0000948	90.42	gold quality
cardiac ventricle	UBERON:0002082	90.35	gold quality
smooth muscle tissue	UBERON:0001135	90.09	gold quality
upper arm skin	UBERON:0004263	89.89	silver quality
liver	UBERON:0002107	89.77	gold quality
lower esophagus	UBERON:0013473	89.70	gold quality
lower esophagus muscularis layer	UBERON:0035833	89.69	gold quality
myocardium	UBERON:0002349	89.67	gold quality
tonsil	UBERON:0002372	89.34	gold quality
hindlimb stylopod muscle	UBERON:0004252	89.34	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	89.25	gold quality
muscle tissue	UBERON:0002385	89.07	gold quality
adrenal tissue	UBERON:0018303	89.06	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.18
E-MTAB-7303	no	254.21

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
CCNB1	Activation

miRNA regulators (miRDB)

172 targeting RPRD1B, 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-1277-5P	100.00	73.95	5056
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 45.4% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 27)

• CREPT increases cyclin D1 transcription during tumorigenesis. (PMID:22264791)
• RPRD1B overexpression promotes tumor growth and accelerates cell cycle progression. (PMID:24452636)
• This study reports that K-H functions in RNAPII regulation, and aids in stabilizing interactions between transcription termination factors, localizing Xrn2 to the 3’-end of genes and ultimately suppressing R-loop formation. (PMID:24589584)
• study suggests that CREPT acts as an activator to promote transcriptional activity of the beta-catenin.TCF4 complex in response to Wnt signaling. (PMID:24982424)
• RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and coordinate the dephosphorylation of RNAPII phospho-S5 by RPAP2. (PMID:24997600)
• CREPT displays unique immunostaining for retroperitoneal leiomyosarcoma tissue and can be used to supplement other currently available markers. (PMID:25400738)
• a detailed description of proteins associating with K-H/RPRD1B in higher-order protein complexes is required to further elucidate its role in various cellular processes (PMID:26819409)
• In addition, CREPT overexpression significantly promoted tumor growth in vivo. Mechanism study showed that CREPT may regulate cell proliferation and cell cycle through the regulation on cyclin D3, CDK4 and CDK6. (PMID:27773816)
• Consistently, samples from oral squamous cell carcinoma (OSCC) patients exhibited a noticeably stronger CREPT expression than noncancerous samples. In contrast, knocking down of CREPT in OSCC cell lines significantly reduced proliferation, colony formation and migration as well as the expression of cyclin D1 and c-Myc, but promoted apoptosis. (PMID:28369091)
• Ccisplatin-induced peripheral neuropathy(isIPN) is associated with age, modifiable risk factors, and genetically determined expression level of RPRD1B Further study of implicated genes could elucidate the pathophysiologic underpinnings of CisIPN. (PMID:28611204)
• Mechanistically, CREPT regulated beta-catenin/TCF4/cyclin D1 pathway in BC. In conclusion, the data suggested that miR-138/CREPT involved BC progression, providing potential therapeutic targets for BC. (PMID:28893536)
• CREPT is closely relevant to the proliferation of NSCLC cells. (PMID:29397041)
• Aberrant overexpression of CREPT contributes to tumorigenesis of colorectal cancer by promoting cell proliferation and accelerating the cell cycle, and confers sensitivity to 5-fluorouracil. (PMID:29398868)
• Altogether, our results provided a novel insight into CREPT in regulating gastric cancer progression through apoptosis regulated by ROS/p53 pathways. (PMID:29402413)
• CREPT plays a pivotal oncogenic role in colorectal carcinogenesis through promoting Wnt/beta-catenin pathway via cooperating with p300. CREPT may serve as a prognostic biomarker of patients with colorectal cancer. (PMID:29563608)
• Data show that miR-383 targeted the 3’ untranslated regions (3’-UTR) of CREPT mRNA directly. (PMID:29938829)
• The study provides a mechanism by which gastric tumor cells maintain their high proliferation rate via coordination of AURKB and CREPT on the expression of CCNB1. (PMID:30518842)
• these results demonstrate that CREPT exerts an oncogenic role in glioma and its expression is regulated by miR-596. (PMID:30995540)
• Crosstalk between RNA Pol II C-terminal domain acetylation and phosphorylation via RPRD1B protein and its isoforms has been reported. (PMID:31054975)
• Overexpression of cell-cycle related and expression-elevated protein in tumor (CREPT) in malignant cervical cancer. (PMID:31939329)
• MiR-139-5p inhibits the proliferation of gastric cancer cells by targeting Regulation of Nuclear Pre-mRNA Domain Containing 1B. (PMID:32327260)
• RPRD1B is a potentially molecular target for diagnosis and prevention of human papillomavirus E6/E7 infection-induced cervical cancer: A case-control study. (PMID:32866332)
• CREPT serves as a biomarker of poor survival in pancreatic ductal adenocarcinoma. (PMID:33125631)
• CREPT is required for murine stem cell maintenance during intestinal regeneration. (PMID:33431892)
• CREPT/RPRD1B promotes tumorigenesis through STAT3-driven gene transcription in a p300-dependent manner. (PMID:33531691)
• Immunohistochemical expression levels of cyclin D1 and CREPT reflect the course and prognosis in oral precancerous lesions and squamous cell carcinoma. (PMID:33838964)
• Long non-coding RNA NEAT1 mediated RPRD1B stability facilitates fatty acid metabolism and lymph node metastasis via c-Jun/c-Fos/SREBP1 axis in gastric cancer. (PMID:36171622)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	rprd1b	ENSDARG00000038113
mus_musculus	Rprd1b	ENSMUSG00000027651
rattus_norvegicus	Rprd1b	ENSRNOG00000012923
drosophila_melanogaster	CG9018	FBGN0035318
caenorhabditis_elegans		WBGENE00015347

Paralogs (2): RPRD1A (ENSG00000141425), RPRD2 (ENSG00000163125)

Protein

Protein identifiers

Regulation of nuclear pre-mRNA domain-containing protein 1B — Q9NQG5 (reviewed: Q9NQG5)

Alternative names: Cell cycle-related and expression-elevated protein in tumor

All UniProt accessions (6): Q9NQG5, A0A087WUK3, A0A087X2D2, A2A2M0, E9PIQ9, E9PQF3

UniProt curated annotations — full annotation on UniProt →

Function. Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD by RPAP2. Transcriptional regulator which enhances expression of CCND1. Promotes binding of RNA polymerase II to the CCDN1 promoter and to the termination region before the poly-A site but decreases its binding after the poly-A site. Prevents RNA polymerase II from reading through the 3’ end termination site and may allow it to be recruited back to the promoter through promotion of the formation of a chromatin loop. Also enhances the transcription of a number of other cell cycle-related genes including CDK2, CDK4, CDK6 and cyclin-E but not CDKN1A, CDKN1B or cyclin-A. Promotes cell proliferation.

Subunit / interactions. Homodimer. May form a heterodimer with RPRD1A. Associates with RPAP2. Associates with the RNA polymerase II complex.

Subcellular location. Nucleus.

Tissue specificity. Preferentially expressed in a range of tumor tissues including colon, lung, liver, breast, prostate, stomach, uterine endometrium and cervical cancers with higher levels in tumors than in adjacent non-tumor tissue (at protein level).

Similarity. Belongs to the UPF0400 (RTT103) family.

RefSeq proteins (1): NP_067038* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006569	CID_dom	Domain
IPR008942	ENTH_VHS	Homologous_superfamily
IPR032337	RPRD1A/B_C	Domain
IPR047882	RPRD1B_CID	Domain

Pfam: PF04818, PF16566

UniProt features (27 total): helix 13, modified residue 6, initiator methionine 1, chain 1, mutagenesis site 1, sequence conflict 1, turn 1, domain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

7 structures.

PDB	Method	Resolution (Å)
4Q94	X-RAY DIFFRACTION	1.85
4Q96	X-RAY DIFFRACTION	1.85
4FU3	X-RAY DIFFRACTION	1.9
4HFG	X-RAY DIFFRACTION	2
4FLA	X-RAY DIFFRACTION	2.2
9B9L	X-RAY DIFFRACTION	2.5
4NAD	X-RAY DIFFRACTION	2.8

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NQG5-F1	83.22	0.65

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): 299, 2, 132, 134, 161, 166

Mutagenesis-validated functional residues (1):

Position	Phenotype
114	complete loss of binding to polr2a ctd in vivo.

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-6807505	RNA polymerase II transcribes snRNA genes
R-HSA-73857	RNA Polymerase II Transcription
R-HSA-74160	Gene expression (Transcription)

MSigDB gene sets: 158 (showing top): KONG_E2F3_TARGETS, YY1_Q6, COUP_01, CCANNAGRKGGC_UNKNOWN, GOBP_REGULATION_OF_CELL_CYCLE, GOBP_MRNA_3_END_PROCESSING, HNF4_DR1_Q3, HNF4_01, PPAR_DR1_Q2, DOUGLAS_BMI1_TARGETS_DN, chr20q11, GOBP_REGULATION_OF_CELL_CYCLE_PROCESS, BERENJENO_TRANSFORMED_BY_RHOA_UP, GCCATNTTG_YY1_Q6, PPARG_01

GO Biological Process (6): RNA polymerase II promoter clearance (GO:0001111), positive regulation of cell population proliferation (GO:0008284), regulation of cell cycle process (GO:0010564), mRNA 3’-end processing (GO:0031124), positive regulation of transcription by RNA polymerase II (GO:0045944), regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (5): RNA polymerase II complex binding (GO:0000993), identical protein binding (GO:0042802), RNA polymerase II C-terminal domain binding (GO:0099122), protein binding (GO:0005515), RNA polymerase II CTD heptapeptide repeat phosphatase activity (GO:0008420)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), transcription preinitiation complex (GO:0097550)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
RNA Polymerase II Transcription	1
Gene expression (Transcription)	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transcription by RNA polymerase II	3
promoter clearance during DNA-templated transcription	1
cell population proliferation	1
regulation of cell population proliferation	1
positive regulation of cellular process	1
cell cycle process	1
regulation of cell cycle	1
mRNA processing	1
RNA 3’-end processing	1
regulation of transcription by RNA polymerase II	1
positive regulation of DNA-templated transcription	1
regulation of DNA-templated transcription	1
RNA polymerase core enzyme binding	1
protein binding	1
RNA polymerase II complex binding	1
binding	1
protein serine/threonine phosphatase activity	1
RNA polymerase II CTD heptapeptide repeat modifying activity	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1
protein-DNA complex	1

Protein interactions and networks

STRING

1336 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RPRD1B	RPAP2	Q8IXW5	808
RPRD1B	RECQL5	O94762	580
RPRD1B	POLR2A	P24928	580
RPRD1B	SCAF8	Q9UPN6	554
RPRD1B	PCF11	O94913	488
RPRD1B	GPN1	Q9HCN4	483
RPRD1B	SCAF4	O95104	467
RPRD1B	XRN2	Q9H0D6	463
RPRD1B	JAG2	Q9Y219	449
RPRD1B	MRPS27	Q92552	439
RPRD1B	RPRD1A	Q96P16	435
RPRD1B	COPS2	P61201	412
RPRD1B	ARHGAP21	Q5T5U3	410
RPRD1B	INTS14	Q96SY0	410
RPRD1B	MCM7	P33993	402

IntAct

203 interactions, top by confidence:

A	B	Type	Score
RPRD1B	POLR2A	psi-mi:“MI:0914”(association)	0.920
RPRD1B	POLR2A	psi-mi:“MI:0915”(physical association)	0.920
POLR2A	RPRD1B	psi-mi:“MI:0915”(physical association)	0.920
POLR2J	POLR1C	psi-mi:“MI:0914”(association)	0.830
RPRD1B	RPRD1A	psi-mi:“MI:0915”(physical association)	0.820
RPAP2	RPRD1B	psi-mi:“MI:0407”(direct interaction)	0.810
RPRD1B	RPAP2	psi-mi:“MI:0915”(physical association)	0.810
RPRD1B	RPRD1B	psi-mi:“MI:0407”(direct interaction)	0.770
RPRD1B	RPRD1B	psi-mi:“MI:0915”(physical association)	0.770
RPRD1B	RECQL5	psi-mi:“MI:0914”(association)	0.730
DPF2	ARID1A	psi-mi:“MI:0914”(association)	0.730
POLR2E	MED19	psi-mi:“MI:0914”(association)	0.730
RPRD1B	POLR2D	psi-mi:“MI:0914”(association)	0.730
POLR2J	POLR2D	psi-mi:“MI:0914”(association)	0.730
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710

BioGRID (344): RPRD1B (Affinity Capture-MS), RPRD1B (Affinity Capture-MS), RPRD1B (Affinity Capture-MS), POLR2E (Affinity Capture-MS), POLR2G (Affinity Capture-MS), CTDP1 (Affinity Capture-MS), RPAP2 (Affinity Capture-MS), POLR2A (Affinity Capture-MS), POLR2M (Affinity Capture-MS), RPRD1A (Affinity Capture-MS), POLR2D (Affinity Capture-MS), RPRD2 (Affinity Capture-MS), RECQL5 (Affinity Capture-MS), POLR2B (Affinity Capture-MS), POLR2J (Affinity Capture-MS)

ESM2 similar proteins: A1A5Z3, A4QND0, A5WVX1, A6QLY4, A9UMP7, B5X5B4, B5X9S9, B5XFI8, C0HAV3, C1BGZ8, C1BHN7, C1BXU5, C3KHF2, O00329, O02741, O35904, O88512, P05161, P54729, Q0D261, Q14AI0, Q19KS6, Q28DG7, Q4R720, Q5E951, Q5FW14, Q5R8F5, Q5U378, Q5XIR9, Q5ZJI9, Q64339, Q66HA5, Q66I84, Q6I7R3, Q6NTR1, Q6NU25, Q6PBQ2, Q7T0X5, Q7ZWB2, Q8K1A6

Diamond homologs: Q0P5J9, Q5R8Y3, Q5ZM30, Q8VDS4, Q96P16, Q9CSU0, Q9NQG5, Q5VT52, Q6NXI6, Q05543

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
RPRD1B	“up-regulates quantity by expression”	CCNB1	“transcriptional regulation”
AURKB	“up-regulates activity”	RPRD1B	phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 156 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
FGFR2 mutant receptor activation	7	48.0×	9e-10
Signaling by FGFR2 IIIa TM	8	43.3×	2e-10
Abortive elongation of HIV-1 transcript in the absence of Tat	9	40.3×	2e-11
FGFR2 alternative splicing	9	34.3×	1e-10
RNA Polymerase III Chain Elongation	6	34.3×	1e-07
Pausing and recovery of Tat-mediated HIV elongation	10	33.2×	2e-11
Tat-mediated HIV elongation arrest and recovery	10	33.2×	2e-11
RNA Pol II CTD phosphorylation and interaction with CE during HIV infection	9	33.1×	1e-10

GO biological processes:

GO term	Partners	Fold	FDR
spliceosomal snRNP assembly	5	20.3×	9e-04
mRNA splicing, via spliceosome	13	8.3×	5e-06
transcription by RNA polymerase II	12	5.9×	4e-04
RNA splicing	9	5.5×	6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	12
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2603 predictions. Top by Δscore:

Variant	Effect	Δscore
20:38040433:A:AG	acceptor_gain	1.0000
20:38040434:G:GG	acceptor_gain	1.0000
20:38040434:GCC:G	acceptor_gain	1.0000
20:38040434:GCCA:G	acceptor_gain	1.0000
20:38048341:T:A	acceptor_gain	1.0000
20:38048342:G:A	acceptor_gain	1.0000
20:38048346:A:AG	acceptor_gain	1.0000
20:38048347:G:GG	acceptor_gain	1.0000
20:38048347:GA:G	acceptor_gain	1.0000
20:38048793:G:GT	donor_gain	1.0000
20:38048851:GA:G	donor_gain	1.0000
20:38048852:A:G	donor_gain	1.0000
20:38057525:T:A	acceptor_gain	1.0000
20:38057529:TAGC:T	acceptor_loss	1.0000
20:38057530:A:AG	acceptor_gain	1.0000
20:38057530:AGCAA:A	acceptor_loss	1.0000
20:38057531:G:GG	acceptor_gain	1.0000
20:38057531:GC:G	acceptor_gain	1.0000
20:38057531:GCA:G	acceptor_gain	1.0000
20:38057531:GCAA:G	acceptor_gain	1.0000
20:38057531:GCAAC:G	acceptor_gain	1.0000
20:38057621:G:GT	donor_gain	1.0000
20:38059386:T:G	acceptor_gain	1.0000
20:38059390:ACAGA:A	acceptor_loss	1.0000
20:38059392:A:AG	acceptor_gain	1.0000
20:38059393:G:GG	acceptor_gain	1.0000
20:38059393:GA:G	acceptor_gain	1.0000
20:38059393:GAC:G	acceptor_gain	1.0000
20:38059393:GACT:G	acceptor_gain	1.0000
20:38059484:G:GT	donor_gain	1.0000

AlphaMissense

2101 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:38033973:T:C	L9P	1.000
20:38033985:T:C	L13P	1.000
20:38033994:T:C	L16P	1.000
20:38034024:T:C	L26P	1.000
20:38034026:T:C	S27P	1.000
20:38034027:C:A	S27Y	1.000
20:38034027:C:T	S27F	1.000
20:38034030:T:C	L28P	1.000
20:38034032:T:A	W29R	1.000
20:38034032:T:C	W29R	1.000
20:38034033:G:C	W29S	1.000
20:38034034:G:C	W29C	1.000
20:38034034:G:T	W29C	1.000
20:38034036:T:C	L30P	1.000
20:38034041:C:A	H32N	1.000
20:38034041:C:G	H32D	1.000
20:38034042:A:C	H32P	1.000
20:38034043:C:A	H32Q	1.000
20:38034043:C:G	H32Q	1.000
20:38034044:C:G	H33D	1.000
20:38034045:A:C	H33P	1.000
20:38034047:C:A	R34S	1.000
20:38034048:G:C	R34P	1.000
20:38034069:T:A	V41D	1.000
20:38034077:T:A	W44R	1.000
20:38034077:T:C	W44R	1.000
20:38034078:G:C	W44S	1.000
20:38034079:G:C	W44C	1.000
20:38034079:G:T	W44C	1.000
20:38034090:T:C	L48P	1.000

dbSNP variants (sampled 300 via entrez): RS1000007465 (20:38052492 C>G,T), RS1000021589 (20:38048263 ATTTCT>A), RS1000022581 (20:38074259 G>A), RS1000025020 (20:38089229 G>A), RS1000161416 (20:38071877 C>G), RS1000163831 (20:38065852 C>G,T), RS1000208114 (20:38088351 G>C,T), RS1000299285 (20:38084244 G>A), RS1000313798 (20:38058912 C>A), RS1000328130 (20:38036103 C>G,T), RS1000342522 (20:38078120 A>G), RS1000369242 (20:38082354 T>G), RS1000458519 (20:38077797 A>G), RS1000477949 (20:38048679 C>T), RS1000506615 (20:38047913 T>G)

Disease associations

OMIM: gene MIM:614694 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

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
Valproic Acid	increases methylation, affects expression, decreases expression	2
Cadmium Chloride	increases abundance, increases expression	2
FR900359	increases phosphorylation	1
bisphenol F	affects cotreatment, increases expression	1
bisphenol A	increases expression	1
nobiletin	decreases reaction, increases expression	1
sodium arsenate	decreases reaction, increases expression	1
2,4,5,2’,4’,5’-hexachlorobiphenyl	decreases expression	1
methylparaben	decreases expression	1
sodium arsenite	affects expression	1
coumarin	decreases phosphorylation	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	increases expression	1
LDN 193189	affects cotreatment, increases expression	1
Fulvestrant	increases methylation	1
Acetaminophen	decreases expression	1
Air Pollutants	increases abundance, affects methylation	1
Benzo(a)pyrene	decreases expression	1
Cadmium	increases abundance, increases expression	1
Caffeine	decreases phosphorylation	1
Dexamethasone	affects cotreatment, increases expression	1
Fluorouracil	increases expression, affects response to substance	1
Folic Acid	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Nitrogen Oxides	increases abundance, affects methylation	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Copper Sulfate	increases expression	1
Raloxifene Hydrochloride	affects response to substance	1

Clinical trials (associated diseases)

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