CDC40

Summary

CDC40 (cell division cycle 40, HGNC:17350) is a protein-coding gene on chromosome 6q21, encoding Pre-mRNA-processing factor 17 (O60508). Required for pre-mRNA splicing as component of the activated spliceosome. It is a selective cancer dependency (DepMap: 86.3% of cell lines).

Pre-mRNA splicing occurs in two sequential transesterification steps. The protein encoded by this gene is found to be essential for the catalytic step II in pre-mRNA splicing process. It is found in the spliceosome, and contains seven WD repeats, which function in protein-protein interactions. This protein has a sequence similarity to yeast Prp17 protein, which functions in two different cellular processes: pre-mRNA splicing and cell cycle progression. It suggests that this protein may play a role in cell cycle progression.

Source: NCBI Gene 51362 — RefSeq curated summary.

At a glance

• Gene–disease (curated): pontocerebellar hypoplasia, type 15 (Limited, GenCC)
• GWAS associations: 1
• Clinical variants (ClinVar): 62 total
• Phenotypes (HPO): 26
• Cancer dependency (DepMap): dependent in 86.3% of screened cell lines
• MANE Select transcript: NM_015891

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17350
Approved symbol	CDC40
Name	cell division cycle 40
Location	6q21
Locus type	gene with protein product
Status	Approved
Aliases	PRP17, EHB3, PRPF17, FLJ10564
Ensembl gene	ENSG00000168438
Ensembl biotype	protein_coding
OMIM	605585
Entrez	51362

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 2 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000307731, ENST00000368930, ENST00000368932, ENST00000431461, ENST00000445340, ENST00000453107, ENST00000606893, ENST00000924587, ENST00000950458

RefSeq mRNA: 1 — MANE Select: NM_015891 NM_015891

CCDS: CCDS5081

Canonical transcript exons

ENST00000307731 — 15 exons

Exon	Start	End
ENSE00001234459	110229954	110232232
ENSE00003686082	110201558	110201687
ENSE00003695056	110228832	110228976
ENSE00003696344	110219364	110219479
ENSE00003697430	110213086	110213160
ENSE00003697652	110219736	110219869
ENSE00003698331	110209084	110209223
ENSE00003699466	110207506	110207589
ENSE00003700085	110217702	110217803
ENSE00003700151	110193182	110193268
ENSE00003701242	110226167	110226243
ENSE00003701707	110215286	110215331
ENSE00003849227	110180427	110180633
ENSE00003892143	110212133	110212272
ENSE00003892647	110210707	110210803

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 94.03.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.2253 / max 717.6807, expressed in 1809 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
69249	25.3058	1805
69248	6.3195	1673
69246	0.3766	135
69247	0.2234	73

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
middle temporal gyrus	UBERON:0002771	94.03	gold quality
sperm	CL:0000019	91.73	gold quality
mononuclear cell	CL:0000842	91.31	gold quality
calcaneal tendon	UBERON:0003701	91.26	gold quality
monocyte	CL:0000576	91.25	gold quality
leukocyte	CL:0000738	91.02	gold quality
adrenal tissue	UBERON:0018303	90.74	gold quality
secondary oocyte	CL:0000655	90.66	gold quality
ileal mucosa	UBERON:0000331	90.55	gold quality
skin of hip	UBERON:0001554	90.55	gold quality
male germ cell	CL:0000015	90.53	gold quality
bone marrow	UBERON:0002371	90.16	gold quality
oocyte	CL:0000023	90.07	gold quality
upper leg skin	UBERON:0004262	90.03	gold quality
deltoid	UBERON:0001476	89.75	gold quality
parietal pleura	UBERON:0002400	89.72	gold quality
palpebral conjunctiva	UBERON:0001812	89.70	gold quality
Brodmann (1909) area 23	UBERON:0013554	89.66	gold quality
trabecular bone tissue	UBERON:0002483	89.61	gold quality
bone element	UBERON:0001474	89.49	gold quality
epithelium of nasopharynx	UBERON:0001951	89.43	gold quality
nasopharynx	UBERON:0001728	89.41	gold quality
pleura	UBERON:0000977	89.09	gold quality
superficial temporal artery	UBERON:0001614	88.82	gold quality
eye	UBERON:0000970	88.80	gold quality
diaphragm	UBERON:0001103	88.64	silver quality
synovial joint	UBERON:0002217	88.62	gold quality
gluteal muscle	UBERON:0002000	88.55	gold quality
tibialis anterior	UBERON:0001385	88.37	gold quality
superior frontal gyrus	UBERON:0002661	88.24	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.71

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

90 targeting CDC40, 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-3613-3P	100.00	76.36	7965
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-3686	99.90	70.53	2432

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 86.3% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

• HBx activates NF-kappaB to promote the expression of miR1269b, which augments CDC40 expression, contributing to malignancy in hepatocellular cancer. (PMID:27349221)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	cdc40	ENSDARG00000041226
mus_musculus	Cdc40	ENSMUSG00000038446
rattus_norvegicus	Cdc40	ENSRNOG00000000581
drosophila_melanogaster	CG6015	FBGN0038927
caenorhabditis_elegans	prp-17	WBGENE00018625
caenorhabditis_elegans		WBGENE00021877

Paralogs (2): WDR87 (ENSG00000171804), WDR25 (ENSG00000176473)

Protein

Protein identifiers

Pre-mRNA-processing factor 17 — O60508 (reviewed: O60508)

Alternative names: Cell division cycle 40 homolog, EH-binding protein 3, PRP17 homolog

All UniProt accessions (2): O60508, Q5SRN1

UniProt curated annotations — full annotation on UniProt →

Function. Required for pre-mRNA splicing as component of the activated spliceosome. Plays an important role in embryonic brain development; this function does not require proline isomerization.

Subunit / interactions. Component of the pre-catalytic and catalytic spliceosome complexes. Component of the postcatalytic spliceosome P complex. Interacts with PPIL1; this interaction leads to CDC40 isomerization.

Subcellular location. Nucleus. Nucleus speckle.

Post-translational modifications. Undergoes isomerization of the peptide bond between Gly-94 and Pro-95. The reaction is catalyzed by PPIL1.

Disease relevance. Pontocerebellar hypoplasia 15 (PCH15) [MIM:619302] A form of pontocerebellar hypoplasia, a disorder characterized by structural defects of the pons and cerebellum, evident upon brain imaging. PCH15 is a severe autosomal recessive form characterized by progressive microcephaly, and poor or absent psychomotor development with severely impaired intellectual development apparent from birth. Other features may include spastic quadriplegia, early-onset seizures, and chronic anemia and thrombocytopenia. The disease is caused by variants affecting the gene represented in this entry.

RefSeq proteins (1): NP_056975* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001680	WD40_rpt	Repeat
IPR015943	WD40/YVTN_repeat-like_dom_sf	Homologous_superfamily
IPR019775	WD40_repeat_CS	Conserved_site
IPR032847	PRPF17	Family
IPR036322	WD40_repeat_dom_sf	Homologous_superfamily

Pfam: PF00400

UniProt features (71 total): strand 40, turn 9, repeat 7, helix 5, sequence conflict 3, region of interest 2, chain 1, compositionally biased region 1, modified residue 1, sequence variant 1, mutagenesis site 1

Structure

Experimental structures (PDB)

28 structures.

PDB	Method	Resolution (Å)
8C6J	ELECTRON MICROSCOPY	2.8
6ID1	ELECTRON MICROSCOPY	2.86
6ID0	ELECTRON MICROSCOPY	2.9
6ICZ	ELECTRON MICROSCOPY	3
8I0T	ELECTRON MICROSCOPY	3
8I0V	ELECTRON MICROSCOPY	3
9R3D	ELECTRON MICROSCOPY	3.12
6QDV	ELECTRON MICROSCOPY	3.3
8I0U	ELECTRON MICROSCOPY	3.3
9FMD	ELECTRON MICROSCOPY	3.3
6FF4	ELECTRON MICROSCOPY	3.4
6ZYM	ELECTRON MICROSCOPY	3.4
8I0W	ELECTRON MICROSCOPY	3.4
8RO2	ELECTRON MICROSCOPY	3.5
5XJC	ELECTRON MICROSCOPY	3.6
7W59	ELECTRON MICROSCOPY	3.6
7W5A	ELECTRON MICROSCOPY	3.6
5YZG	ELECTRON MICROSCOPY	4.1
7AAV	ELECTRON MICROSCOPY	4.2
7W5B	ELECTRON MICROSCOPY	4.3
6FF7	ELECTRON MICROSCOPY	4.5
7A5P	ELECTRON MICROSCOPY	5
5Z56	ELECTRON MICROSCOPY	5.1
5MQF	ELECTRON MICROSCOPY	5.9
8CH6	ELECTRON MICROSCOPY	5.9
5Z57	ELECTRON MICROSCOPY	6.5
7ABI	ELECTRON MICROSCOPY	8
9R8V	ELECTRON MICROSCOPY	8.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O60508-F1	86.76	0.71

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 (1): 46

Mutagenesis-validated functional residues (1):

Position	Phenotype
95	loss of isomerization. can rescue splicing defects when transfected in knockout cells.

Function

Pathways and Gene Ontology

Reactome pathways

6 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-9770562	mRNA Polyadenylation
R-HSA-9918481	Dengue Virus-Host Interactions
R-HSA-73856	RNA Polymerase II Transcription Termination

MSigDB gene sets: 241 (showing top): BROWNE_HCMV_INFECTION_30MIN_DN, GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, BROWNE_HCMV_INFECTION_6HR_DN, YAGI_AML_WITH_INV_16_TRANSLOCATION, MODULE_151, AACYNNNNTTCCS_UNKNOWN, BROWNE_HCMV_INFECTION_16HR_UP, BROWNE_HCMV_INFECTION_12HR_UP, BROWNE_HCMV_INFECTION_48HR_DN, REACTOME_MRNA_3_END_PROCESSING, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, GOBP_RNA_SPLICING, REACTOME_MRNA_SPLICING, SCHLOSSER_SERUM_RESPONSE_DN

GO Biological Process (4): mRNA splicing, via spliceosome (GO:0000398), embryonic brain development (GO:1990403), mRNA processing (GO:0006397), RNA splicing (GO:0008380)

GO Molecular Function (3): RNA binding (GO:0003723), mRNA binding (GO:0003729), protein binding (GO:0005515)

GO Cellular Component (6): nucleoplasm (GO:0005654), nuclear speck (GO:0016607), U2-type catalytic step 2 spliceosome (GO:0071007), catalytic step 2 spliceosome (GO:0071013), nucleus (GO:0005634), spliceosomal complex (GO:0005681)

Reactome top-level categories

Rollup of top-6 pathways:

Category	Pathways
Transport of Mature Transcript to Cytoplasm	1
mRNA Splicing	1
Processing of Capped Intron-Containing Pre-mRNA	1
mRNA 3’-end processing	1
Dengue Virus Infection	1
RNA Polymerase II Transcription	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
embryonic organ development	1
mRNA metabolic process	1
nucleic acid binding	1
RNA binding	1
binding	1
nuclear lumen	1
cellular anatomical structure	1
nuclear ribonucleoprotein granule	1
U2-type spliceosomal complex	1
U2 snRNP	1
U6 snRNP	1
catalytic step 2 spliceosome	1
Prp19 complex	1
spliceosomal complex	1
U5 snRNP	1
catalytic complex	1
intracellular membrane-bounded organelle	1
nuclear protein-containing complex	1
ribonucleoprotein complex	1

Protein interactions and networks

STRING

2289 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CDC40	DHX38	Q92620	991
CDC40	PRPF18	Q99633	984
CDC40	CDC5L	Q99459	876
CDC40	XAB2	Q9HCS7	814
CDC40	SLU7	O95391	811
CDC40	RBM22	Q9NW64	790
CDC40	BCAS2	O75934	781
CDC40	DHX8	Q14562	764
CDC40	SNW1	Q13573	764
CDC40	CRNKL1	Q9BZJ0	726
CDC40	CWC25	Q9NXE8	707
CDC40	YJU2	Q9BW85	704
CDC40	SYF2	O95926	693
CDC40	SF3A1	Q15459	656
CDC40	PPIL1	Q9Y3C6	643

IntAct

153 interactions, top by confidence:

A	B	Type	Score
SNRPF	GEMIN2	psi-mi:“MI:0914”(association)	0.910
PPIE	AQR	psi-mi:“MI:0914”(association)	0.810
PRPF19	AQR	psi-mi:“MI:0914”(association)	0.790
SNRPE	GEMIN2	psi-mi:“MI:0914”(association)	0.770
ISY1	AQR	psi-mi:“MI:0914”(association)	0.740
CCT2	TXNDC9	psi-mi:“MI:0914”(association)	0.730
SYF2	AQR	psi-mi:“MI:0914”(association)	0.730
PRPF19	CDC40	psi-mi:“MI:0915”(physical association)	0.720
CDC40	PRPF19	psi-mi:“MI:0915”(physical association)	0.720
SNRPG	GEMIN2	psi-mi:“MI:0914”(association)	0.710
SNRPB	PRMT5	psi-mi:“MI:0914”(association)	0.670
SNW1	AQR	psi-mi:“MI:0914”(association)	0.650
PNN	CASC3	psi-mi:“MI:0914”(association)	0.640
SNRPA1	HTATSF1	psi-mi:“MI:0914”(association)	0.640
DHX8	AHCYL1	psi-mi:“MI:0914”(association)	0.640
SF3B1	SAP18	psi-mi:“MI:0914”(association)	0.640
SNRPA1	U2SURP	psi-mi:“MI:0914”(association)	0.640
ILF2	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
SNRPE	PRMT5	psi-mi:“MI:0914”(association)	0.530
SNRPN	PRMT5	psi-mi:“MI:0914”(association)	0.530
SNIP1	CASC3	psi-mi:“MI:0914”(association)	0.530

BioGRID (189): CDC40 (Affinity Capture-RNA), CDC40 (Affinity Capture-RNA), CDC40 (Affinity Capture-MS), CDC40 (Affinity Capture-MS), CDC40 (Affinity Capture-MS), CDC40 (Affinity Capture-MS), CDC40 (Affinity Capture-MS), CDC40 (Affinity Capture-MS), CDC40 (Affinity Capture-MS), CDC40 (Affinity Capture-MS), CDC40 (Affinity Capture-MS), CDC40 (Affinity Capture-MS), CCDC12 (Co-fractionation), CDC40 (Co-fractionation), CDC40 (Co-fractionation)

ESM2 similar proteins: A2A690, A5D7H2, F1LTE0, O43237, O43815, O55106, O60508, O60941, O70585, O88447, P37285, P54198, P58405, P70483, P79987, P84060, Q07866, Q13033, Q14161, Q15542, Q1RMU5, Q4KUS2, Q4R5P6, Q5R581, Q5RAC9, Q5RE09, Q5SRX1, Q61666, Q676U5, Q6DFF9, Q6P6Y1, Q6PDL0, Q80YA9, Q86UE8, Q8C092, Q8C0V0, Q8QFR2, Q8WXI2, Q90ZY6, Q91YE7

Diamond homologs: A1CJY4, A1D7I5, A2QEV8, A3LX18, A4RDD7, A5DGL8, A5DVY3, A6RUL1, A6ZMK5, A7EF03, A7RM20, A7TH19, A8QBF3, A8WVX8, B0BNA7, B0XFT7, B0XYC8, B3MVL6, B3N4C7, B4GSH1, B4I195, B4JB43, B4KGX9, B4LUA5, B4N0L0, B4NW98, B4Q354, B5FZ19, E3LB80, O02195, O60508, P0CS32, P0CS33, P36408, P40217, P79083, P79147, Q0CXH9, Q0V320, Q13347

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 136 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
Metabolism of non-coding RNA	6	40.1×	2e-07
mRNA Splicing	29	33.5×	2e-35
RNA Polymerase II Transcription Termination	12	27.7×	5e-13
Processing of Capped Intron-Containing Pre-mRNA	32	27.7×	3e-36
mRNA Splicing - Major Pathway	46	26.5×	4e-53
Transport of Mature Transcript to Cytoplasm	6	24.0×	4e-06
mRNA Splicing - Minor Pathway	10	23.6×	4e-10
mRNA 3’-end processing	11	22.8×	6e-11

GO biological processes:

GO term	Partners	Fold	FDR
U2-type prespliceosome assembly	12	65.7×	1e-17
spliceosomal snRNP assembly	9	45.9×	2e-11
spliceosomal complex assembly	7	37.0×	6e-08
mRNA splicing, via spliceosome	44	35.4×	4e-55
negative regulation of mRNA splicing, via spliceosome	5	33.6×	2e-05
RNA splicing, via transesterification reactions	6	32.9×	2e-06
RNA splicing	23	17.8×	3e-20
mRNA export from nucleus	6	15.6×	1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	49
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2454 predictions. Top by Δscore:

Variant	Effect	Δscore
6:110180631:AAGGT:A	donor_loss	1.0000
6:110180633:GGTA:G	donor_loss	1.0000
6:110180634:G:GG	donor_gain	1.0000
6:110180635:T:A	donor_loss	1.0000
6:110193177:TTTA:T	acceptor_loss	1.0000
6:110193180:A:AG	acceptor_gain	1.0000
6:110193180:AG:A	acceptor_gain	1.0000
6:110193181:G:GA	acceptor_gain	1.0000
6:110193181:GG:G	acceptor_gain	1.0000
6:110193181:GGA:G	acceptor_gain	1.0000
6:110193181:GGAA:G	acceptor_gain	1.0000
6:110193266:GAG:G	donor_gain	1.0000
6:110193269:G:GG	donor_gain	1.0000
6:110193270:T:G	donor_loss	1.0000
6:110201548:A:AG	acceptor_gain	1.0000
6:110201549:A:G	acceptor_gain	1.0000
6:110201556:A:AG	acceptor_gain	1.0000
6:110201557:G:GA	acceptor_gain	1.0000
6:110207497:T:TA	acceptor_gain	1.0000
6:110207503:CAG:C	acceptor_loss	1.0000
6:110207504:A:AG	acceptor_gain	1.0000
6:110207504:A:C	acceptor_loss	1.0000
6:110207504:AG:A	acceptor_gain	1.0000
6:110207505:G:GA	acceptor_gain	1.0000
6:110207505:GG:G	acceptor_gain	1.0000
6:110207505:GGT:G	acceptor_gain	1.0000
6:110207505:GGTT:G	acceptor_gain	1.0000
6:110207505:GGTTA:G	acceptor_gain	1.0000
6:110207588:AGG:A	donor_loss	1.0000
6:110207589:GGTAA:G	donor_loss	1.0000

AlphaMissense

3833 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:110201664:A:C	Q128P	1.000
6:110209179:T:A	W196R	1.000
6:110209179:T:C	W196R	1.000
6:110209181:G:C	W196C	1.000
6:110209181:G:T	W196C	1.000
6:110217717:T:A	V335D	1.000
6:110217758:A:C	S349R	1.000
6:110217760:T:A	S349R	1.000
6:110217760:T:G	S349R	1.000
6:110217788:T:A	W359R	1.000
6:110217788:T:C	W359R	1.000
6:110219453:G:T	G394W	1.000
6:110219454:G:A	G394E	1.000
6:110219736:T:A	W403R	1.000
6:110219736:T:C	W403R	1.000
6:110219769:T:C	Y414H	1.000
6:110219778:C:G	H417D	1.000
6:110219780:T:A	H417Q	1.000
6:110219780:T:G	H417Q	1.000
6:110219791:T:A	V421D	1.000
6:110219832:A:C	S435R	1.000
6:110219834:C:A	S435R	1.000
6:110219834:C:G	S435R	1.000
6:110219838:T:C	S437P	1.000
6:110219839:C:A	S437Y	1.000
6:110219839:C:T	S437F	1.000
6:110219841:G:C	D438H	1.000
6:110219844:G:C	D439H	1.000
6:110219844:G:T	D439Y	1.000
6:110219845:A:C	D439A	1.000

dbSNP variants (sampled 300 via entrez): RS1000109896 (6:110194105 T>C), RS1000214946 (6:110206908 A>G), RS1000280317 (6:110220520 C>A,T), RS1000367041 (6:110192527 G>A), RS1000413684 (6:110186322 C>G), RS1000473790 (6:110226913 G>T), RS1000491819 (6:110199510 T>C,G), RS1000496431 (6:110181589 T>G), RS1000539519 (6:110213538 C>T), RS1000573829 (6:110226613 T>A,C), RS1000624165 (6:110179773 C>A), RS1000675179 (6:110179533 C>A,T), RS1000822891 (6:110199867 G>A), RS1000892196 (6:110219091 A>G,T), RS1000918955 (6:110221714 T>C,G)

Disease associations

OMIM: gene MIM:605585 | disease phenotypes: MIM:619302

GenCC curated gene-disease

Disease	Classification	Inheritance
pontocerebellar hypoplasia, type 15	Limited	Unknown

Mondo (1): pontocerebellar hypoplasia, type 15 (MONDO:0030259)

Orphanet (0):

HPO phenotypes

26 total (26 of 26 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000238	Hydrocephalus
HP:0001252	Hypotonia
HP:0001274	Agenesis of corpus callosum
HP:0001276	Hypertonia
HP:0001321	Cerebellar hypoplasia
HP:0001332	Dystonia
HP:0001338	Partial agenesis of the corpus callosum
HP:0001348	Brisk reflexes
HP:0001522	Death in infancy
HP:0001873	Thrombocytopenia
HP:0001903	Anemia
HP:0002069	Bilateral tonic-clonic seizure
HP:0002188	Delayed CNS myelination
HP:0002194	Delayed gross motor development
HP:0002365	Hypoplasia of the brainstem
HP:0002510	Spastic tetraplegia
HP:0003577	Congenital onset
HP:0007359	Focal-onset seizure
HP:0009879	Simplified gyral pattern
HP:0010862	Delayed fine motor development
HP:0010864	Severe intellectual disability
HP:0012434	Delayed early-childhood social milestone development
HP:0012469	Infantile spasms
HP:0032794	Myoclonic seizure
HP:0410252	Persistently decreased total neutrophil count

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST003518_86	Daytime sleep phenotypes	3.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007828	daytime rest measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
trichostatin A	affects cotreatment, decreases expression	3
GSK-J4	increases expression	1
FR900359	decreases phosphorylation	1
triphenyl phosphate	affects expression	1
cobaltous chloride	increases expression	1
cupric oxide	increases expression	1
resorcinol	decreases expression	1
pinostrobin	increases phosphorylation	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	increases expression	1
bisphenol S	affects cotreatment, decreases expression	1
jinfukang	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Cisplatin	increases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Fluorouracil	increases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Polycyclic Aromatic Hydrocarbons	affects expression	1
Ribonucleotides	affects binding	1
Silicon Dioxide	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	increases expression	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

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