RABEP1

Summary

RABEP1 (rabaptin, RAB GTPase binding effector protein 1, HGNC:17677) is a protein-coding gene on chromosome 17p13.2, encoding Rab GTPase-binding effector protein 1 (Q15276). Rab effector protein acting as linker between gamma-adaptin, RAB4A and RAB5A.

Enables protein domain specific binding activity and protein homodimerization activity. Involved in vesicle-mediated transport. Located in cytosol; endocytic vesicle; and endosome. Part of protein-containing complex.

Source: NCBI Gene 9135 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 104 total
• MANE Select transcript: NM_004703

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17677
Approved symbol	RABEP1
Name	rabaptin, RAB GTPase binding effector protein 1
Location	17p13.2
Locus type	gene with protein product
Status	Approved
Aliases	neurocrescin, RAB5EP, RABPT5, rabaptin-5
Ensembl gene	ENSG00000029725
Ensembl biotype	protein_coding
OMIM	603616
Entrez	9135

Gene structure

Transcript identifiers

Ensembl transcripts: 30 — 29 protein_coding, 1 retained_intron

ENST00000341923, ENST00000537505, ENST00000570487, ENST00000572250, ENST00000574568, ENST00000575475, ENST00000575991, ENST00000876342, ENST00000876343, ENST00000876344, ENST00000876345, ENST00000876346, ENST00000876347, ENST00000876348, ENST00000876349, ENST00000876350, ENST00000876351, ENST00000876352, ENST00000911616, ENST00000911617, ENST00000911618, ENST00000911619, ENST00000911620, ENST00000947555, ENST00000947556, ENST00000947557, ENST00000947558, ENST00000947559, ENST00000947560, ENST00000947561

RefSeq mRNA: 3 — MANE Select: NM_004703 NM_001083585, NM_001291581, NM_004703

CCDS: CCDS42243, CCDS45592

Canonical transcript exons

ENST00000537505 — 18 exons

Exon	Start	End
ENSE00001539174	5282284	5282520
ENSE00001578091	5308694	5308822
ENSE00001579466	5381389	5381505
ENSE00001649230	5383122	5386340
ENSE00002805862	5378177	5378232
ENSE00002816462	5380364	5380462
ENSE00003476845	5365122	5365238
ENSE00003491771	5377116	5377305
ENSE00003586739	5331949	5332152
ENSE00003616034	5335184	5335344
ENSE00003620182	5354359	5354490
ENSE00003622269	5368370	5368468
ENSE00003640626	5362912	5363016
ENSE00003654511	5346790	5346925
ENSE00003676230	5350451	5350629
ENSE00003676306	5373314	5373454
ENSE00003683673	5361208	5361675
ENSE00003688561	5338019	5338138

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 96.79.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 42.9936 / max 775.0952, expressed in 1823 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
159025	39.6246	1823
159026	3.3690	1510

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	96.79	gold quality
cortical plate	UBERON:0005343	96.20	gold quality
calcaneal tendon	UBERON:0003701	96.03	gold quality
biceps brachii	UBERON:0001507	95.43	gold quality
sural nerve	UBERON:0015488	95.22	gold quality
tendon	UBERON:0000043	95.16	gold quality
postcentral gyrus	UBERON:0002581	94.94	gold quality
medial globus pallidus	UBERON:0002477	94.91	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	94.82	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	94.53	gold quality
adrenal tissue	UBERON:0018303	94.40	gold quality
gastrocnemius	UBERON:0001388	94.33	gold quality
muscle of leg	UBERON:0001383	94.20	gold quality
globus pallidus	UBERON:0001875	94.09	gold quality
middle temporal gyrus	UBERON:0002771	94.00	gold quality
parietal lobe	UBERON:0001872	93.85	gold quality
superior frontal gyrus	UBERON:0002661	93.66	gold quality
entorhinal cortex	UBERON:0002728	93.66	gold quality
spinal cord	UBERON:0002240	93.46	gold quality
ganglionic eminence	UBERON:0004023	93.44	gold quality
corpus callosum	UBERON:0002336	93.20	gold quality
tendon of biceps brachii	UBERON:0008188	92.97	gold quality
hindlimb stylopod muscle	UBERON:0004252	92.86	gold quality
temporal lobe	UBERON:0001871	92.59	gold quality
lateral nuclear group of thalamus	UBERON:0002736	92.56	gold quality
cerebellar hemisphere	UBERON:0002245	92.55	gold quality
right frontal lobe	UBERON:0002810	92.51	gold quality
cerebellar cortex	UBERON:0002129	92.45	gold quality
caudate nucleus	UBERON:0001873	92.40	gold quality
right hemisphere of cerebellum	UBERON:0014890	92.40	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.77
E-MTAB-7606	no	173.85

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

111 targeting RABEP1, 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-3163	100.00	77.23	8605
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-5682	99.89	72.56	1005
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-629-3P	99.85	67.99	1875

Literature-anchored findings (GeneRIF, showing 10)

• GGAs, a family of Arf-dependent clathrin adaptors involved in selection of TGN cargo, interact with the Rabaptin-5-Rabex-5 complex, a Rab4/Rab5 effector regulating endosome fusion (PMID:12505986)
• The authors determined that increased listeriolysin O-independent dissolution of vacuoles during RABEP1 knockdown required the Listeria monocytogenes broad-range phospholipase C (PC-PLC). (PMID:19500109)
• Breast cancer cell line studies showed that microRNA, miR-373, was capable of promoting breast cancer invasion and metastasis via translational inhibition of TXNIP and RABEP1 that were the direct target genes of miR-373. (PMID:21271679)
• Silencing of Rabaptin-5 induces down-regulation of recycling of K(V)10.1 channel in transfected cells and reduction of K(V)10.1 current density in cells natively expressing K(V)10.1, indicating a role of Rabaptin-5 in channel trafficking. (PMID:22841712)
• The disruption of Rabaptin-5 Ser407 phosphorylation reduces persistent cell migration in 2D and alphavbeta3-dependent invasion. (PMID:22975325)
• analysis of Rabex-5 GEF activation by Rabaptin-5 (PMID:24957337)
• The results contradict the model of feedback activation of Rab5 and instead indicate that Rbpt5 is recruited by both Rabex5 recognizing ubiquitylated cargo and by Rab4 to activate Rab5 in a feed-forward manner. (PMID:26430212)
• ITSN2L interacts with RABEP1 and stimulates its degradation in regulation of endocytosis. (PMID:26633357)
• The pleckstrin homology domain (PH) of PLD1 itself promotes degradation of HIF-1alpha, then accelerates EGFR endocytosis via upregulation of rabaptin-5 and suppresses tumor progression. (PMID:26680696)
• SH2B1 and RABEP1 genetic variants are associated with worsening of LDL and glucose parameters in patients treated with psychotropic drugs (PMID:28694205)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Rabep1	ENSMUSG00000020817
rattus_norvegicus	Rabep1	ENSRNOG00000005015
caenorhabditis_elegans		WBGENE00017161

Paralogs (1): RABEP2 (ENSG00000177548)

Protein

Protein identifiers

Rab GTPase-binding effector protein 1 — Q15276 (reviewed: Q15276)

Alternative names: Rabaptin-4, Rabaptin-5, Rabaptin-5alpha, Renal carcinoma antigen NY-REN-17

All UniProt accessions (5): A0A087WZZ3, Q15276, I3L2B8, I3L456, K7ENJ9

UniProt curated annotations — full annotation on UniProt →

Function. Rab effector protein acting as linker between gamma-adaptin, RAB4A and RAB5A. Involved in endocytic membrane fusion and membrane trafficking of recycling endosomes. Involved in KCNH1 channels trafficking to and from the cell membrane. Forms a complex with RABGEF1 that stimulates RABGEF1-mediated nucleotide exchange on RAB5A. Mediates the traffic of PKD1:PKD2 complex from the endoplasmic reticulum through the Golgi to the cilium.

Subunit / interactions. Homodimer when bound to RAB5A. Heterodimer with RABGEF1. The heterodimer binds RAB4A and RAB5A that have been activated by GTP-binding. Interacts with TSC2. Interacts with GGA1 (via GAE domain), GGA2 (via GAE domain) and GGA3 (via GAE domain). Interacts with AP1G1 (via GAE domain). Interacts with AP1G2 (via GAE domain). Interacts with ECPAS. Interacts with KCNH1. Interacts with PKD1 (via C-terminal domain) and GGA1; the interactions recruit PKD1:PKD2 complex to GGA1 and ARL3 at trans-Golgi network.

Subcellular location. Cytoplasm. Early endosome. Recycling endosome. Cytoplasmic vesicle.

Post-translational modifications. Proteolytic cleavage by caspases in apoptotic cells causes loss of endosome fusion activity.

Similarity. Belongs to the rabaptin family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q15276-1	1, Rabaptin-5	yes
Q15276-2	2, Rabaptin-4

RefSeq proteins (3): NP_001077054, NP_001278510, NP_004694* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003914	Rabaptin	Family
IPR015390	Rabaptin_Rab5-bd_dom	Domain
IPR018514	Rabaptin_CC	Domain

Pfam: PF03528, PF09311

UniProt features (35 total): mutagenesis site 15, modified residue 7, helix 3, region of interest 2, sequence conflict 2, coiled-coil region 2, initiator methionine 1, chain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

6 structures.

PDB	Method	Resolution (Å)
1P4U	X-RAY DIFFRACTION	2.2
4N3Y	X-RAY DIFFRACTION	2.2
1TU3	X-RAY DIFFRACTION	2.31
1X79	X-RAY DIFFRACTION	2.41
4N3Z	X-RAY DIFFRACTION	3.1
4Q9U	X-RAY DIFFRACTION	4.62

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q15276-F1	79.16	0.54

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 (7): 407, 408, 410, 2, 282, 374, 377

Mutagenesis-validated functional residues (15):

Position	Phenotype
439	abolishes the interaction with ap1g1, ap1g2, gga1, gga2 and gga3.
440	abolishes the interaction with ap1g1, ap1g2, gga1, gga2 and gga3.
441	reduces the interaction with ap1g1 and gga3.
441	abolishes the interaction with ap1g2, gga1 and gga2.
441	reduces the interaction with ap1g2, gga1, gga2.
441	abolishes the interaction with ap1g1, ap1g2, gga1, gga2 and gga3.
442	abolishes the interaction with ap1g1, ap1g2, gga1, gga2 and gga3.
812	no effect on rab5a binding affinity.
815	no effect on rab5a binding affinity.
818	strongly decreases rab5a binding affinity.
820	strongly decreases rab5a binding affinity.
821	strongly decreases rab5a binding affinity.
822	strongly decreases rab5a binding affinity.
826	strongly decreases rab5a binding affinity.
829	strongly decreases rab5a binding affinity.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-8854214	TBC/RABGAPs

MSigDB gene sets: 205 (showing top): GCM_PTPRD, GOBP_PROTEIN_LOCALIZATION_TO_CILIUM, GOZGIT_ESR1_TARGETS_DN, GOBP_MEMBRANE_FUSION, GOMF_GROWTH_FACTOR_ACTIVITY, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_6, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT, GOBP_GOLGI_TO_PLASMA_MEMBRANE_TRANSPORT, GOBP_REGULATION_OF_RECEPTOR_INTERNALIZATION, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, SMID_BREAST_CANCER_LUMINAL_B_UP, GOBP_REGULATION_OF_RECEPTOR_MEDIATED_ENDOCYTOSIS

GO Biological Process (9): Golgi to plasma membrane transport (GO:0006893), endocytosis (GO:0006897), apoptotic process (GO:0006915), protein transport (GO:0015031), vesicle-mediated transport (GO:0016192), membrane fusion (GO:0061025), regulation of postsynaptic neurotransmitter receptor internalization (GO:0099149), protein localization to ciliary membrane (GO:1903441), signal transduction (GO:0007165)

GO Molecular Function (5): GTPase activator activity (GO:0005096), growth factor activity (GO:0008083), protein domain specific binding (GO:0019904), protein homodimerization activity (GO:0042803), protein binding (GO:0005515)

GO Cellular Component (10): endosome (GO:0005768), early endosome (GO:0005769), cytosol (GO:0005829), endocytic vesicle (GO:0030139), early endosome membrane (GO:0031901), protein-containing complex (GO:0032991), recycling endosome (GO:0055037), glutamatergic synapse (GO:0098978), cytoplasm (GO:0005737), cytoplasmic vesicle (GO:0031410)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Rab regulation of trafficking	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transport	2
cellular process	2
cytoplasmic vesicle	2
endosome	2
cytoplasm	2
cellular anatomical structure	2
post-Golgi vesicle-mediated transport	1
vesicle-mediated transport to the plasma membrane	1
vesicle budding from membrane	1
membrane invagination	1
vesicle-mediated transport	1
import into cell	1
programmed cell death	1
apoptotic signaling pathway	1
execution phase of apoptosis	1
intracellular protein localization	1
establishment of protein localization	1
membrane organization	1
regulation of receptor internalization	1
regulation of biological quality	1
postsynaptic neurotransmitter receptor internalization	1
protein localization to cilium	1
protein localization to membrane	1
protein localization to cell periphery	1
cell communication	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
GTPase activity	1
enzyme activator activity	1
GTPase regulator activity	1
receptor ligand activity	1
protein binding	1
identical protein binding	1
protein dimerization activity	1
binding	1
endomembrane system	1
early endosome	1
endosome membrane	1
cellular_component	1

Protein interactions and networks

STRING

1572 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RABEP1	RABGEF1	Q9UJ41	999
RABEP1	RAB5A	P20339	998
RABEP1	RAB4A	P20338	975
RABEP1	EEA1	Q15075	966
RABEP1	GGA1	Q9UJY5	960
RABEP1	IFT54	Q8TDR0	948
RABEP1	RAB8A	P24407	850
RABEP1	RBSN	Q9H1K0	834
RABEP1	RAB22A	Q9UL26	759
RABEP1	TSC2	P49815	736
RABEP1	GAPVD1	Q14C86	731
RABEP1	MON1A	Q86VX9	714
RABEP1	RABIF	P47224	698
RABEP1	AP1G1	O43747	689
RABEP1	GGA3	Q9NZ52	688

IntAct

259 interactions, top by confidence:

A	B	Type	Score
GGA1	RABEP1	psi-mi:“MI:0407”(direct interaction)	0.840
RABEP1	GGA1	psi-mi:“MI:0407”(direct interaction)	0.840
GGA1	RABEP1	psi-mi:“MI:0915”(physical association)	0.840
RABEP1	GGA1	psi-mi:“MI:0915”(physical association)	0.840
RABEP1	GGA2	psi-mi:“MI:0915”(physical association)	0.820
GGA2	RABEP1	psi-mi:“MI:0915”(physical association)	0.820
YWHAH	ABLIM1	psi-mi:“MI:0914”(association)	0.800
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
GGA3	RABEP1	psi-mi:“MI:0407”(direct interaction)	0.700
GGA3	RABEP1	psi-mi:“MI:0915”(physical association)	0.700
RABEP1	GGA3	psi-mi:“MI:0915”(physical association)	0.700
YWHAG	BLTP3B	psi-mi:“MI:2364”(proximity)	0.640
YWHAH	PLEKHG3	psi-mi:“MI:0914”(association)	0.610
RABGEF1	RABEP1	psi-mi:“MI:0407”(direct interaction)	0.590
YWHAH	BLTP3B	psi-mi:“MI:2364”(proximity)	0.570
ODAD3	RABEP1	psi-mi:“MI:0915”(physical association)	0.560
RABEP1	CEP57	psi-mi:“MI:0915”(physical association)	0.560
RABEP1	MAT2B	psi-mi:“MI:0915”(physical association)	0.560
RAB4B	RABEP1	psi-mi:“MI:0915”(physical association)	0.560
RABEP1	ZNF438	psi-mi:“MI:0915”(physical association)	0.560
RABEP1	BARD1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (297): RABGEF1 (Affinity Capture-Western), RABEP1 (Affinity Capture-MS), RABEP1 (Affinity Capture-MS), RABEP1 (Affinity Capture-MS), RABEP1 (Affinity Capture-MS), RAB5A (Two-hybrid), AP1G2 (Two-hybrid), AP1G1 (Two-hybrid), GGA3 (Two-hybrid), GGA2 (Two-hybrid), GGA1 (Two-hybrid), RABEP1 (Biochemical Activity), RABEP1 (Proximity Label-MS), RABEP1 (Affinity Capture-MS), RABEP1 (Affinity Capture-MS)

ESM2 similar proteins: A0A2R8QCI3, A0JMK8, A3KGV1, A7YH32, A9X1A5, B0KWC9, B6MFW3, B8JK76, G5E861, G9G127, O35550, O35551, P59242, P85120, Q15276, Q3V6T2, Q502I3, Q5BJF6, Q5RG45, Q5SNZ0, Q5TZ80, Q5ZJ27, Q5ZKK5, Q66GS9, Q66KE8, Q6AYX5, Q6DIX6, Q6NRB0, Q6P402, Q6P5D4, Q6PGZ0, Q6VGS5, Q6ZU80, Q7TMK6, Q80UF4, Q80YF0, Q80YT7, Q86SQ7, Q8BIL5, Q8CJ99

Diamond homologs: O35550, O35551, Q15276

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
RABEP1	up-regulates	RAB5A	binding
RABEP1	up-regulates	RABGEF1	binding
PRKD1	“up-regulates activity”	RABEP1	phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 119 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
Activation of BAD and translocation to mitochondria	5	44.3×	6e-06
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	5	39.1×	9e-06
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	5	39.1×	9e-06
Activation of BH3-only proteins	5	28.9×	4e-05
RHO GTPases activate PKNs	7	25.8×	1e-06
TBC/RABGAPs	8	24.1×	3e-07
Translocation of SLC2A4 (GLUT4) to the plasma membrane	10	17.9×	8e-08
Intrinsic Pathway for Apoptosis	5	17.0×	4e-04

GO biological processes:

GO term	Partners	Fold	FDR
Golgi to plasma membrane transport	8	42.0×	8e-09
intracellular protein localization	8	7.8×	3e-03
protein transport	11	4.5×	6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	74
Likely benign	5
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

3703 predictions. Top by Δscore:

Variant	Effect	Δscore
17:5282438:G:GT	donor_gain	1.0000
17:5308692:A:AG	acceptor_gain	1.0000
17:5308693:G:A	acceptor_loss	1.0000
17:5308693:G:GT	acceptor_gain	1.0000
17:5308693:GT:G	acceptor_gain	1.0000
17:5308693:GTT:G	acceptor_gain	1.0000
17:5308693:GTTT:G	acceptor_gain	1.0000
17:5308693:GTTTC:G	acceptor_gain	1.0000
17:5308818:AGAGG:A	donor_gain	1.0000
17:5308819:GAGG:G	donor_gain	1.0000
17:5308819:GAGGG:G	donor_gain	1.0000
17:5308821:GG:G	donor_gain	1.0000
17:5308821:GGGTA:G	donor_loss	1.0000
17:5308822:GG:G	donor_gain	1.0000
17:5308823:G:GG	donor_gain	1.0000
17:5308823:GTA:G	donor_loss	1.0000
17:5308824:TAAGT:T	donor_loss	1.0000
17:5331936:C:G	acceptor_gain	1.0000
17:5331945:CCAGA:C	acceptor_gain	1.0000
17:5331946:CAGAG:C	acceptor_gain	1.0000
17:5331947:A:AG	acceptor_gain	1.0000
17:5331947:A:T	acceptor_loss	1.0000
17:5331947:AGAG:A	acceptor_gain	1.0000
17:5331947:AGAGG:A	acceptor_gain	1.0000
17:5331948:G:GC	acceptor_gain	1.0000
17:5331948:GA:G	acceptor_gain	1.0000
17:5331948:GAGG:G	acceptor_gain	1.0000
17:5331948:GAGGA:G	acceptor_gain	1.0000
17:5332122:G:GT	donor_gain	1.0000
17:5332140:GCTGT:G	donor_gain	1.0000

AlphaMissense

5687 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:5338041:T:C	L184P	1.000
17:5350504:T:A	W280R	1.000
17:5350504:T:C	W280R	1.000
17:5350506:G:C	W280C	1.000
17:5350506:G:T	W280C	1.000
17:5350525:T:C	F287L	1.000
17:5350526:T:C	F287S	1.000
17:5350527:T:A	F287L	1.000
17:5350527:T:G	F287L	1.000
17:5362945:T:C	C533R	1.000
17:5308788:A:C	R43S	0.999
17:5308788:A:T	R43S	0.999
17:5338031:G:C	A181P	0.999
17:5346842:T:C	L234P	0.999
17:5346856:G:C	A239P	0.999
17:5346860:T:A	V240D	0.999
17:5346884:T:C	L248P	0.999
17:5346905:T:C	L255P	0.999
17:5350475:G:C	R270P	0.999
17:5350493:T:C	L276S	0.999
17:5350513:G:C	A283P	0.999
17:5350514:C:A	A283D	0.999
17:5350526:T:G	F287C	0.999
17:5350529:T:C	L288P	0.999
17:5350534:T:C	S290P	0.999
17:5350580:T:C	L305P	0.999
17:5361641:T:A	V510D	0.999
17:5361655:T:A	W515R	0.999
17:5361655:T:C	W515R	0.999
17:5361657:G:C	W515C	0.999

dbSNP variants (sampled 300 via entrez): RS1000030758 (17:5311737 A>G), RS1000034689 (17:5357453 C>T), RS1000097130 (17:5362847 G>A,T), RS1000110843 (17:5358625 T>G), RS1000131992 (17:5319058 G>A), RS1000139003 (17:5283414 C>T), RS1000162055 (17:5336618 T>G), RS1000190462 (17:5283699 T>G), RS1000232539 (17:5362617 T>G), RS1000240692 (17:5302658 G>A), RS1000241522 (17:5322600 A>G), RS1000245196 (17:5311078 G>T), RS1000260017 (17:5324885 A>G), RS1000270762 (17:5379069 C>G), RS1000274024 (17:5342524 A>G)

Disease associations

OMIM: gene MIM:603616 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): teratoma (MONDO:0002601)

Orphanet (0):

HPO phenotypes

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

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST002783_392	Body mass index	2.000000e-08
GCST002783_478	Body mass index	1.000000e-08
GCST002783_581	Body mass index	2.000000e-06
GCST004379_4	Red blood cell density in sickle cell anemia	1.000000e-07
GCST004610_150	White blood cell count	4.000000e-12
GCST004904_187	Body mass index	9.000000e-09
GCST90002388_484	Lymphocyte count	5.000000e-10
GCST90002395_269	Mean platelet volume	5.000000e-14

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0004587	lymphocyte count

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D013724	Teratoma	C04.557.465.910

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB clinical annotations

1 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs1000940	Other	3	amisulpride;aripiprazole;clozapine;lithium;mirtazapine;olanzapine;paliperidone;quetiapine;risperidone;valproic acid	Bipolar Disorder;Depressive Disorder;Psychotic Disorder;Schizoaffective disorder

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs1000940	RABEP1	3	2.25	1	amisulpride;aripiprazole;clozapine;lithium;mirtazapine;olanzapine;paliperidone;quetiapine;risperidone;valproic acid

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases methylation, increases expression, affects expression	3
trichostatin A	decreases expression, affects cotreatment	2
Benzo(a)pyrene	affects methylation, decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
dicrotophos	decreases expression	1
geldanamycin	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
beta-lapachone	decreases expression	1
benzo(e)pyrene	increases methylation	1
coumarin	decreases phosphorylation	1
beta-methylcholine	affects expression	1
K 7174	increases expression	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
PCI 5002	affects cotreatment, increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Atrazine	decreases expression	1
Caffeine	decreases phosphorylation	1
Carbamazepine	affects expression	1
Cisplatin	increases expression, affects cotreatment	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Estradiol	affects binding, increases reaction	1
Ethyl Methanesulfonate	decreases expression	1
Ivermectin	decreases expression	1
Methapyrilene	increases methylation	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_C7YJ	HAP1 RABEP1 (-) 1	Cancer cell line	Male
CVCL_C7YK	HAP1 RABEP1 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00104676	PHASE3	COMPLETED	Combination Chemotherapy in Treating Patients With Stage II or Stage III Germ Cell Tumors
NCT02375204	PHASE3	ACTIVE_NOT_RECRUITING	Standard-Dose Combination Chemotherapy or High-Dose Combination Chemotherapy and Stem Cell Transplant in Treating Patients with Relapsed or Refractory Germ Cell Tumors
NCT00002931	PHASE2	COMPLETED	Combination Chemotherapy Plus Peripheral Stem Cell Transplantation in Treating Patients With Relapsed Germ Cell Cancer
NCT00301782	PHASE2	COMPLETED	Combination Chemotherapy in Treating Male Patients With Germ Cell Tumors
NCT00432094	PHASE2	COMPLETED	Autologous Peripheral Blood Stem Cell Transplant for Germ Cell Tumors
NCT00453232	PHASE2	COMPLETED	Combination Chemotherapy and Pegfilgrastim in Treating Men With Metastatic Germ Cell Tumors
NCT00453310	PHASE2	COMPLETED	Sunitinib in Treating Patients With Metastatic Germ Cell Tumors That Have Relapsed or Not Responded to Treatment
NCT00470366	PHASE2	COMPLETED	Combination Chemotherapy and Pegfilgrastim in Treating Patients With Previously Untreated Germ Cell Tumors
NCT02300987	PHASE2	COMPLETED	A Randomized, Blinded, Placebo-controlled, Phase II Trial of LEE011 in Patients With Relapsed, Refractory, Incurable Teratoma With Recent Progression
NCT00003643	PHASE2/PHASE3	UNKNOWN	Combination Chemotherapy in Treating Men With Germ Cell Cancer
NCT00423852	PHASE1/PHASE2	COMPLETED	Paclitaxel, Ifosfamide, and Carboplatin Followed By Autologous Stem Cell Transplant in Treating Patients With Germ Cell Tumors That Did Not Respond to Cisplatin
NCT00687778	Not specified	UNKNOWN	11C-Acetate PET/CT Non-FDG-Avid Tumors
NCT00836121	Not specified	COMPLETED	Anterior Mediastinum Teratoma: A Case Report
NCT05179850	Not specified	UNKNOWN	Computer Aided Diagnostic Tool on Computed Tomography Images for Diagnosis of Retroperitoneal Tumor in Children
NCT05187923	Not specified	UNKNOWN	Computer Aided Tool for Diagnosis of Neck Masses in Children
NCT05564026	Not specified	RECRUITING	Molecular Epidemiology of Pediatric Germ Cell Tumors
NCT06421805	Not specified	RECRUITING	Establishing Prospective Mediastinal Tumor Database of PUMCH
NCT07199699	Not specified	NOT_YET_RECRUITING	Subxiphoid VATS for Giant Mediastinal Teratoma