RAB3IP

Summary

RAB3IP (RAB3A interacting protein, HGNC:16508) is a protein-coding gene on chromosome 12q15, encoding Rab-3A-interacting protein (Q96QF0). Guanine nucleotide exchange factor (GEF) which may activate RAB8A and RAB8B.

Enables guanyl-nucleotide exchange factor activity and identical protein binding activity. Involved in several processes, including positive regulation of cilium assembly; protein localization to motile cilium; and protein targeting to membrane. Located in centrosome; cytosol; and nucleoplasm.

Source: NCBI Gene 117177 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 77 total
• MANE Select transcript: NM_022456

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16508
Approved symbol	RAB3IP
Name	RAB3A interacting protein
Location	12q15
Locus type	gene with protein product
Status	Approved
Aliases	RABIN3, FLJ22548, RABIN8
Ensembl gene	ENSG00000127328
Ensembl biotype	protein_coding
OMIM	608686
Entrez	117177

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 20 protein_coding, 4 nonsense_mediated_decay, 2 retained_intron

ENST00000247833, ENST00000362025, ENST00000378809, ENST00000378815, ENST00000417413, ENST00000481897, ENST00000483530, ENST00000526994, ENST00000547055, ENST00000547591, ENST00000549760, ENST00000550536, ENST00000550647, ENST00000550847, ENST00000551641, ENST00000552199, ENST00000552610, ENST00000553099, ENST00000867667, ENST00000867668, ENST00000867669, ENST00000867670, ENST00000867671, ENST00000867672, ENST00000867673, ENST00000919863

RefSeq mRNA: 6 — MANE Select: NM_022456 NM_001024647, NM_001278402, NM_022456, NM_175623, NM_175624, NM_175625

CCDS: CCDS41811, CCDS44942, CCDS8993, CCDS8995, CCDS8996

Canonical transcript exons

ENST00000247833 — 11 exons

Exon	Start	End
ENSE00000871994	69800209	69800337
ENSE00000871995	69795141	69795344
ENSE00001247974	69738860	69739031
ENSE00003487837	69756405	69756663
ENSE00003516283	69755384	69755659
ENSE00003524813	69812778	69812877
ENSE00003557273	69815364	69823199
ENSE00003562420	69812964	69813033
ENSE00003652276	69784720	69784815
ENSE00003658979	69794437	69794514
ENSE00003689356	69801609	69801721

Expression profiles

Bgee: expression breadth ubiquitous, 213 present calls, max score 97.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.1370 / max 503.8795, expressed in 1705 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
126747	20.3565	1704
126746	0.2787	129
126751	0.1662	59
126749	0.1644	69
126750	0.1373	55
126745	0.0339	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	97.37	gold quality
left testis	UBERON:0004533	97.30	gold quality
islet of Langerhans	UBERON:0000006	96.45	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	96.00	gold quality
kidney epithelium	UBERON:0004819	95.73	gold quality
testis	UBERON:0000473	94.80	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	94.39	gold quality
cerebellar vermis	UBERON:0004720	94.25	gold quality
metanephros cortex	UBERON:0010533	93.54	gold quality
adult mammalian kidney	UBERON:0000082	92.51	gold quality
pancreas	UBERON:0001264	92.51	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.35	gold quality
body of pancreas	UBERON:0001150	92.09	gold quality
cerebellum	UBERON:0002037	91.64	gold quality
cerebellar cortex	UBERON:0002129	91.49	gold quality
cerebellar hemisphere	UBERON:0002245	91.40	gold quality
mucosa of transverse colon	UBERON:0004991	91.31	gold quality
kidney	UBERON:0002113	91.22	gold quality
rectum	UBERON:0001052	91.18	gold quality
cortex of kidney	UBERON:0001225	91.10	gold quality
adrenal tissue	UBERON:0018303	90.94	gold quality
pigmented layer of retina	UBERON:0001782	90.92	gold quality
retina	UBERON:0000966	90.90	gold quality
adenohypophysis	UBERON:0002196	90.28	gold quality
right hemisphere of cerebellum	UBERON:0014890	90.15	gold quality
bone marrow cell	CL:0002092	89.98	gold quality
pituitary gland	UBERON:0000007	89.83	gold quality
corpus callosum	UBERON:0002336	89.46	gold quality
ileal mucosa	UBERON:0000331	89.33	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	88.95	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-GEOD-93593	yes	585.29
E-HCAD-10	yes	27.41
E-ANND-3	yes	14.89
E-GEOD-135922	yes	13.06
E-GEOD-124858	no	108.69

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

216 targeting RAB3IP, 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-6867-5P	100.00	82.21	3464
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-3163	100.00	77.23	8605
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-3667-3P	99.99	67.17	1636
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-6778-3P	99.96	67.29	2693

Literature-anchored findings (GeneRIF, showing 11)

• RABIN3 interacts with the cancer-related protein SSX2 and a novel nuclear protein, SSX2IP. (PMID:12007189)
• Rabin8 was identified as a direct phospho-substrate of ERK1/2 in response to EGF signaling. (PMID:25535387)
• Rab11-FIP3 coordinates the interactions of ASAP1 and Rab11a with Rabin8. (PMID:25673879)
• the role of Rabin8 (a mammalian ortholog of Sec2p) with Rab8-nucleotide-exchange factor activity in autophagy in mammalian cells, was examined. (PMID:25787272)
• Authors show that Rab11-GMPPNP-FIP3-Rabin8 is more stable than Rab11-GMPPNP-Rabin8, owing to direct interaction between Rabin8 and FIP3 within the dual effector-bound complex. (PMID:26258637)
• The crystal structure of tetrameric Rabin8, guanine nucleotide exchange factors (GEFs) domain reveals an occluded Rab8 binding site suggesting that this oligomer is enzymatically inactive, a notion that’s verified experimentally using Rabin8/Rab8 GEF assays. (PMID:29318657)
• role of Rab3IP in inducing an invasive phenotype in gastric cancer cells, in addition to its involvement in EMT. (PMID:30005870)
• C7orf43 directly binds to Rabin8 and that C7orf43 knockdown diminishes Rabin8 preciliary centrosome accumulation. (PMID:31467083)
• Long noncoding RNA NEAT1 knockdown inhibits MPP(+)-induced apoptosis, in fl ammation and cytotoxicity in SK-N-SH cells by regulating miR-212-5p/RAB3IP axis. (PMID:32442477)
• Rab8 and Rabin8-Mediated Tumor Formation by Hyperactivated EGFR Signaling via FGFR Signaling. (PMID:33092268)
• LINC00943 knockdown attenuates MPP(+)-induced neuronal damage via miR-15b-5p/RAB3IP axis in SK-N-SH cells. (PMID:33208053)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	rab3ip	ENSDARG00000101908
mus_musculus	Rab3ip	ENSMUSG00000064181
rattus_norvegicus	Rab3ip	ENSRNOG00000005362
caenorhabditis_elegans		WBGENE00010045

Paralogs (1): RAB3IL1 (ENSG00000167994)

Protein

Protein identifiers

Rab-3A-interacting protein — Q96QF0 (reviewed: Q96QF0)

Alternative names: Rabin-3, Rabin8, SSX2-interacting protein

All UniProt accessions (8): Q96QF0, F8VNX9, F8VTR6, H0YD03, H0YHP4, H0YI02, H0YI66, J3KPG1

UniProt curated annotations — full annotation on UniProt →

Function. Guanine nucleotide exchange factor (GEF) which may activate RAB8A and RAB8B. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. Mediates the release of GDP from RAB8A and RAB8B but not from RAB3A or RAB5. Modulates actin organization and promotes polarized transport of RAB8A-specific vesicles to the cell surface. Together with RAB11A, RAB8A, the exocyst complex, PARD3, PRKCI, ANXA2, CDC42 and DNMBP promotes transcytosis of PODXL to the apical membrane initiation sites (AMIS), apical surface formation and lumenogenesis. Part of the ciliary targeting complex containing Rab11, ASAP1, RAB3IP and RAB11FIP3 and ARF4 that promotes RAB3IP preciliary vesicle trafficking to mother centriole and ciliogenesis initiation.

Subunit / interactions. Homodimer. Interacts with the N-terminal region of SSX2. Interacts with the GDP-bound forms of RAB8A and RAB8B. The interaction with RAB8A is prevented by phosphorylation of RAB8A at ‘Thr-72’. Interacts with the GDP-bound forms of RAB3A and RAB3D. Interacts with DCDC1. Interacts (via the N-terminal region) with TRAPPC14; this interaction mediates RAB3IP association with the TRAPP II complex. Forms a heterotetramer with RAB11A where RAB3IP homodimer binds two RAB11A subunits. Forms a complex with RAB11A and RAB11FIP3, probably a heterohexamer with two of each protein subunit, where Rabin8/RAB3IP and RAB11FIP3 simultaneously bind to RAB11A; the complex promotes preciliary trafficking. Forms a complex containing RAB11A, ASAP1, RAB3IP, RAP11FIP3 and ARF4; the complex promotes preciliary trafficking; the complex binds to RHO in photoreceptor cells and promotes RHO ciliary transport.

Subcellular location. Cytoplasm. Nucleus. Cytoskeleton. Cell projection. Lamellipodium. Vesicle. Microtubule organizing center. Centrosome.

Tissue specificity. Expressed in brain, kidney, heart, pancreas and placenta. Not detected in skeletal muscle or liver.

Post-translational modifications. Phosphorylated by AKT1; the phosphorylation alters its GEF activity.

Activity regulation. Phosphorylation by ATK1 alters its GEF activity. Complex formation with RAB11A and RAB11FIP3 and ciliogenesis function are competitively inhibited by RAB11A-WDR44 interaction.

Similarity. Belongs to the SEC2 family.

Isoforms (8)

UniProt ID	Names	Canonical?
Q96QF0-1	2, alpha2	yes
Q96QF0-2	1, alpha1
Q96QF0-3	3, beta1
Q96QF0-4	4, beta2
Q96QF0-5	5, gamma1
Q96QF0-6	6, gamma2
Q96QF0-7	7
Q96QF0-8	8

RefSeq proteins (6): NP_001019818, NP_001265331, NP_071901, NP_783322, NP_783323, NP_783324 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009449	Sec2_N	Domain
IPR040351	RAB3IL/RAB3IP/Sec2	Family

Pfam: PF06428, PF25555

UniProt features (40 total): splice variant 8, helix 7, modified residue 6, sequence conflict 4, strand 4, mutagenesis site 3, turn 3, region of interest 2, chain 1, coiled-coil region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

7 structures.

PDB	Method	Resolution (Å)
6F6P	X-RAY DIFFRACTION	2.45
4UJ5	X-RAY DIFFRACTION	2.6
4UJ3	X-RAY DIFFRACTION	3
4LHX	X-RAY DIFFRACTION	3.05
4LHY	X-RAY DIFFRACTION	3.1
4LHZ	X-RAY DIFFRACTION	3.2
4UJ4	X-RAY DIFFRACTION	4.2

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96QF0-F1	71.93	0.51

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): 296, 163, 165, 263, 266, 288

Mutagenesis-validated functional residues (3):

Position	Phenotype
435	reduced complex formation with rab11a; when associated with a-439 and a-444.
439	reduced complex formation with rab11a; when associated with a-435 and a-444.
444	reduced complex formation with rab11a; when associated with a-435 and a-439.

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-5620912	Anchoring of the basal body to the plasma membrane
R-HSA-5620916	VxPx cargo-targeting to cilium
R-HSA-5620922	BBSome-mediated cargo-targeting to cilium
R-HSA-8876198	RAB GEFs exchange GTP for GDP on RABs

MSigDB gene sets: 297 (showing top): PEREZ_TP63_TARGETS, GOBP_PROTEIN_TARGETING, GOBP_VESICLE_MEDIATED_TRANSPORT, HNF1_Q6, REACTOME_MEMBRANE_TRAFFICKING, GOMF_GTPASE_BINDING, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_MEMBRANE_DOCKING, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, CEBP_Q2, CAGCAGG_MIR370, GOBP_GOLGI_TO_PLASMA_MEMBRANE_TRANSPORT, GOBP_PROTEIN_TARGETING_TO_MEMBRANE, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION

GO Biological Process (6): protein targeting to membrane (GO:0006612), Golgi to plasma membrane transport (GO:0006893), protein transport (GO:0015031), negative regulation of filopodium assembly (GO:0051490), cilium assembly (GO:0060271), obsolete ciliary basal body-plasma membrane docking (GO:0097711)

GO Molecular Function (4): guanyl-nucleotide exchange factor activity (GO:0005085), identical protein binding (GO:0042802), GTPase binding (GO:0051020), protein binding (GO:0005515)

GO Cellular Component (12): nucleus (GO:0005634), nucleoplasm (GO:0005654), centrosome (GO:0005813), cytosol (GO:0005829), lamellipodium (GO:0030027), vesicle (GO:0031982), ciliary basal body (GO:0036064), perinuclear region of cytoplasm (GO:0048471), proximal dendrite (GO:1990635), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Cargo trafficking to the periciliary membrane	2
Assembly of the 9+0 primary cilium	1
Rab regulation of trafficking	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
microtubule organizing center	2
cytoplasm	2
protein targeting	1
establishment of protein localization to membrane	1
post-Golgi vesicle-mediated transport	1
vesicle-mediated transport to the plasma membrane	1
transport	1
intracellular protein localization	1
establishment of protein localization	1
filopodium assembly	1
regulation of filopodium assembly	1
negative regulation of plasma membrane bounded cell projection assembly	1
axoneme assembly	1
intraciliary transport involved in cilium assembly	1
cilium organization	1
protein localization to cilium	1
organelle assembly	1
trans-Golgi to periciliary membrane compartment transport	1
plasma membrane bounded cell projection assembly	1
ciliary transition zone assembly	1
GTP binding	1
GDP binding	1
GTPase regulator activity	1
protein binding	1
enzyme binding	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
centriole	1
cell leading edge	1
plasma membrane bounded cell projection	1
membrane-bounded organelle	1
cilium	1
dendrite	1
intracellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

1440 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RAB3IP	RAB8A	P24407	999
RAB3IP	BBS1	Q8NFJ9	995
RAB3IP	RAB11A	P24410	994
RAB3IP	BBS4	Q96RK4	914
RAB3IP	RABIF	P47224	898
RAB3IP	EXOC6	Q8TAG9	881
RAB3IP	BBS5	Q8N3I7	873
RAB3IP	BBS7	Q8IWZ6	871
RAB3IP	BBS2	Q9BXC9	870
RAB3IP	BBS9	P78514	863
RAB3IP	RAB3A	P20336	823
RAB3IP	CEP164	Q9UPV0	797
RAB3IP	RAB11FIP3	O75154	794
RAB3IP	TTC8	Q8TAM2	789
RAB3IP	RAC2	P15153	773

IntAct

171 interactions, top by confidence:

A	B	Type	Score
RAB3IL1	RAB3IP	psi-mi:“MI:0915”(physical association)	0.890
RAB3IP	RAB3IL1	psi-mi:“MI:0915”(physical association)	0.890
	RAB8A	psi-mi:“MI:0915”(physical association)	0.820
RAB3IP	RAB8A	psi-mi:“MI:0407”(direct interaction)	0.780
RAB8A	RAB3IP	psi-mi:“MI:0915”(physical association)	0.780
RAB3IP	TRAPPC10	psi-mi:“MI:0915”(physical association)	0.770
TRAPPC10	RAB3IP	psi-mi:“MI:0403”(colocalization)	0.770
CCDC146	GMNN	psi-mi:“MI:0914”(association)	0.740
TRAPPC9	RAB3IP	psi-mi:“MI:0403”(colocalization)	0.720
RAB3IP	TRAPPC3	psi-mi:“MI:0914”(association)	0.700
RAB3IP	TRAPPC3	psi-mi:“MI:0915”(physical association)	0.700
PLOD3	RAB3IP	psi-mi:“MI:0915”(physical association)	0.670
RAB3IP	TRAPPC6A	psi-mi:“MI:0915”(physical association)	0.670
SSX2	RAB3IP	psi-mi:“MI:0915”(physical association)	0.670
RAB3IP	PLOD3	psi-mi:“MI:0915”(physical association)	0.670
RAB3IP	SSX2	psi-mi:“MI:0915”(physical association)	0.670

BioGRID (155): RAB3IP (Two-hybrid), RAB3IP (Two-hybrid), RAB3IP (Two-hybrid), RAB3IP (Two-hybrid), RAB3IP (Two-hybrid), RAB3IP (Two-hybrid), RAB3IP (Two-hybrid), RAB3IP (Two-hybrid), RAB3IP (Two-hybrid), RAB3IP (Two-hybrid), RAB3IP (Two-hybrid), RAB3IP (Two-hybrid), KRT40 (Two-hybrid), FAM124A (Two-hybrid), RAB3IP (Affinity Capture-MS)

ESM2 similar proteins: A0A088MLT8, A2AQ25, B3KU38, B5DF41, E9PSK7, O15079, O35274, P0DPB3, P0DPB4, P12755, P49140, P85299, Q0D2I5, Q14DQ1, Q1LY51, Q3B7M3, Q3SYW5, Q4KMA0, Q4R3X1, Q50H33, Q5F3L9, Q5FVG6, Q5RD40, Q5XKK7, Q60698, Q6ZNC4, Q6ZUS6, Q6ZWB6, Q80U23, Q80U62, Q80XA6, Q812A5, Q86YI8, Q8BXL9, Q8K2W6, Q8ND83, Q8NFH8, Q8QFX1, Q8TEK3, Q924W7

Diamond homologs: O13930, Q2KJ58, Q62739, Q68EF0, Q8TBN0, Q8VDV3, Q96QF0, Q99NH3

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
AKT1	“up-regulates activity”	RAB3IP	phosphorylation
STK38	“up-regulates activity”	RAB3IP	phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 113 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
RAB GEFs exchange GTP for GDP on RABs	13	20.7×	1e-11
COPII-mediated vesicle transport	8	16.7×	4e-06
RAB geranylgeranylation	5	11.1×	9e-03
CDC42 GTPase cycle	7	6.5×	9e-03

GO biological processes:

GO term	Partners	Fold	FDR
obsolete vesicle tethering	8	77.8×	2e-11
COPII vesicle coat assembly	6	41.3×	1e-06
endoplasmic reticulum to Golgi vesicle-mediated transport	9	12.0×	1e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	55
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1967 predictions. Top by Δscore:

Variant	Effect	Δscore
12:69739484:G:GT	donor_gain	1.0000
12:69739812:TGG:T	donor_gain	1.0000
12:69755380:ATAG:A	acceptor_gain	1.0000
12:69755381:T:G	acceptor_gain	1.0000
12:69755381:TA:T	acceptor_loss	1.0000
12:69755382:A:AG	acceptor_gain	1.0000
12:69755383:G:GA	acceptor_loss	1.0000
12:69755383:G:GG	acceptor_gain	1.0000
12:69755383:GGTT:G	acceptor_gain	1.0000
12:69755657:CAG:C	donor_loss	1.0000
12:69755658:AGGTA:A	donor_loss	1.0000
12:69755659:GGTA:G	donor_loss	1.0000
12:69755660:G:C	donor_loss	1.0000
12:69756402:CA:C	acceptor_loss	1.0000
12:69756403:A:AG	acceptor_gain	1.0000
12:69756403:A:AT	acceptor_loss	1.0000
12:69756404:G:GG	acceptor_gain	1.0000
12:69756660:GAGG:G	donor_gain	1.0000
12:69756661:AGGGT:A	donor_loss	1.0000
12:69756662:GG:G	donor_gain	1.0000
12:69756662:GGGTA:G	donor_loss	1.0000
12:69756663:GG:G	donor_gain	1.0000
12:69756663:GGTA:G	donor_loss	1.0000
12:69756665:T:G	donor_loss	1.0000
12:69784714:TCTTA:T	acceptor_loss	1.0000
12:69784715:CTTAG:C	acceptor_loss	1.0000
12:69784716:TTAG:T	acceptor_loss	1.0000
12:69784718:AGG:A	acceptor_loss	1.0000
12:69794510:GAAAA:G	donor_gain	1.0000
12:69794511:A:T	donor_gain	1.0000

AlphaMissense

2996 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:69756647:T:C	L181P	1.000
12:69756655:G:C	A184P	1.000
12:69784724:T:C	L188P	1.000
12:69784754:T:C	L198P	1.000
12:69784766:G:C	R202P	1.000
12:69784775:T:C	L205P	1.000
12:69784796:T:A	L212H	1.000
12:69784796:T:C	L212P	1.000
12:69784799:C:T	T213I	1.000
12:69784801:G:C	A214P	1.000
12:69784808:T:A	L216Q	1.000
12:69784808:T:C	L216P	1.000
12:69784810:T:A	F217I	1.000
12:69784810:T:C	F217L	1.000
12:69784810:T:G	F217V	1.000
12:69784811:T:C	F217S	1.000
12:69784811:T:G	F217C	1.000
12:69784812:T:A	F217L	1.000
12:69784812:T:G	F217L	1.000
12:69794440:G:C	A220P	1.000
12:69794441:C:A	A220D	1.000
12:69794461:G:C	A227P	1.000
12:69794482:G:C	A234P	1.000
12:69794495:T:C	L238P	1.000
12:69794503:G:C	A241P	1.000
12:69795151:T:C	L248P	1.000
12:69795156:G:C	A250P	1.000
12:69795168:G:C	A254P	1.000
12:69795172:T:C	L255S	1.000
12:69800234:T:C	F321S	1.000

dbSNP variants (sampled 300 via entrez): RS1000068644 (12:69821421 AT>A), RS1000070182 (12:69749628 A>G), RS1000122453 (12:69791445 A>G,T), RS1000124379 (12:69821435 G>T), RS1000160475 (12:69760161 C>G,T), RS1000180897 (12:69770775 A>C,G), RS1000223700 (12:69790926 C>T), RS1000271722 (12:69753592 A>C), RS1000283187 (12:69782324 G>A,C), RS1000334304 (12:69782195 C>T), RS1000367932 (12:69780458 G>T), RS1000451901 (12:69771115 T>C), RS1000461252 (12:69822572 G>A), RS1000520057 (12:69822959 T>C,G), RS1000577013 (12:69808046 C>G)

Disease associations

OMIM: gene MIM:608686 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST007006_11	Logical memory (delayed recall) in normal cognition	4.000000e-07
GCST007094_146	Diastolic blood pressure	4.000000e-08
GCST008163_437	Height	3.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004874	memory performance
EFO:0006336	diastolic blood pressure

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	4
sodium arsenite	increases abundance, increases expression, affects cotreatment, decreases expression	2
Panobinostat	affects cotreatment, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
aristolochic acid I	decreases expression	1
TL8-506	affects cotreatment, increases expression	1
dicrotophos	decreases expression	1
bisphenol A	increases methylation	1
trichostatin A	decreases expression, increases expression	1
beta-lapachone	decreases expression	1
methylparaben	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
perfluorooctanoic acid	increases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
coumarin	affects phosphorylation	1
epigallocatechin gallate	decreases expression, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases 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
perfluorohexanesulfonic acid	decreases expression	1
belinostat	affects cotreatment, decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
PCI 5002	increases expression, affects cotreatment	1
Sunitinib	increases expression	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Benzo(a)pyrene	decreases methylation	1
Caffeine	increases phosphorylation	1

Clinical trials (associated diseases)

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