VPS29

Summary

VPS29 (VPS29 retromer complex component, HGNC:14340) is a protein-coding gene on chromosome 12q24.11, encoding Vacuolar protein sorting-associated protein 29 (Q9UBQ0). Component of the commander complex that is essential for endosomal recycling of transmembrane cargos; the commander complex is composed of the CCC subcomplex and the retriever subcomplex. It is a selective cancer dependency (DepMap: 32.9% of cell lines).

This gene belongs to a group of vacuolar protein sorting (VPS) genes that, when functionally impaired, disrupt the efficient delivery of vacuolar hydrolases. The protein encoded by this gene is a component of a large multimeric complex, termed the retromer complex, which is involved in retrograde transport of proteins from endosomes to the trans-Golgi network. This VPS protein may be involved in the formation of the inner shell of the retromer coat for retrograde vesicles leaving the prevacuolar compartment. Alternative splice variants encoding different isoforms and representing non-protein coding transcripts have been found for this gene.

Source: NCBI Gene 51699 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 16 total
• Cancer dependency (DepMap): dependent in 32.9% of screened cell lines
• MANE Select transcript: NM_016226

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14340
Approved symbol	VPS29
Name	VPS29 retromer complex component
Location	12q24.11
Locus type	gene with protein product
Status	Approved
Aliases	PEP11, DC7, DC15
Ensembl gene	ENSG00000111237
Ensembl biotype	protein_coding
OMIM	606932
Entrez	51699

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 7 protein_coding, 3 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000360579, ENST00000447578, ENST00000546588, ENST00000548259, ENST00000548539, ENST00000549578, ENST00000549970, ENST00000550267, ENST00000551655, ENST00000552130, ENST00000553128, ENST00000621131

RefSeq mRNA: 4 — MANE Select: NM_016226 NM_001282150, NM_001282151, NM_016226, NM_057180

CCDS: CCDS41832, CCDS53832, CCDS73525

Canonical transcript exons

ENST00000549578 — 4 exons

Exon	Start	End
ENSE00002373823	110502049	110502111
ENSE00002402754	110491083	110492122
ENSE00003499968	110496012	110496203
ENSE00003612453	110492996	110493231

Expression profiles

Bgee: expression breadth ubiquitous, 255 present calls, max score 98.98.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 64.2991 / max 886.3918, expressed in 1827 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
133239	64.1730	1827
133238	0.1261	34

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
monocyte	CL:0000576	98.98	gold quality
leukocyte	CL:0000738	98.89	gold quality
tibialis anterior	UBERON:0001385	98.82	gold quality
ileal mucosa	UBERON:0000331	98.79	gold quality
smooth muscle tissue	UBERON:0001135	98.78	gold quality
left ventricle myocardium	UBERON:0006566	98.76	gold quality
mucosa of stomach	UBERON:0001199	98.70	gold quality
rectum	UBERON:0001052	98.69	gold quality
cardiac muscle of right atrium	UBERON:0003379	98.65	gold quality
right coronary artery	UBERON:0001625	98.56	gold quality
lower esophagus muscularis layer	UBERON:0035833	98.56	gold quality
lower esophagus	UBERON:0013473	98.55	gold quality
vermiform appendix	UBERON:0001154	98.52	gold quality
tibial artery	UBERON:0007610	98.52	gold quality
popliteal artery	UBERON:0002250	98.51	gold quality
myocardium	UBERON:0002349	98.46	gold quality
body of pancreas	UBERON:0001150	98.45	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	98.39	gold quality
gall bladder	UBERON:0002110	98.35	gold quality
small intestine Peyer’s patch	UBERON:0003454	98.32	gold quality
islet of Langerhans	UBERON:0000006	98.29	gold quality
left coronary artery	UBERON:0001626	98.28	gold quality
aorta	UBERON:0000947	98.25	gold quality
muscle layer of sigmoid colon	UBERON:0035805	98.23	gold quality
transverse colon	UBERON:0001157	98.22	gold quality
granulocyte	CL:0000094	98.20	gold quality
descending thoracic aorta	UBERON:0002345	98.18	gold quality
esophagus	UBERON:0001043	98.13	gold quality
left uterine tube	UBERON:0001303	98.00	gold quality
colon	UBERON:0001155	97.97	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

59 targeting VPS29, 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-3646	100.00	73.56	5283
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-6505-5P	99.73	69.25	1595
HSA-MIR-548M	99.70	68.87	1749
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-488-3P	99.61	68.79	1731
HSA-MIR-892A	99.54	68.16	1141
HSA-MIR-3609	99.52	69.89	2587

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 32.9% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 15)

• analysis of the phosphodiesterase/nuclease-like fold and two protein-protein interaction sites in human VPS29 (PMID:15788412)
• It was demonstrated that recombinant human Vps29 displays in vitro phosphatase activity towards a serine-phosphorylated peptide, containing the acidic-cluster dileucine motif of the cytoplasmatic tail of the CI-M6PR. (PMID:16737443)
• These observations indicate that the mammalian retromer complex assembles by sequential association of SNX1/2 and Vps26-Vps29-Vps35 subcomplexes on endosomal membranes and that SNX1 and SNX2 play interchangeable but essential roles. (PMID:17101778)
• crystal structure of a VPS29-VPS35 subcomplex showing how the metallophosphoesterase-fold subunit VPS29 acts as a scaffold for the carboxy-terminal half of VPS35 (PMID:17891154)
• Membrane recruitment of the cargo-selective retromer subcomplex VPS35/29/26 is catalysed by the small GTPase Rab7 and inhibited by the Rab-GAP TBC1D5. (PMID:19531583)
• Conclusion is that VPS29 is a metal ion-independent, rigid scaffolding domain, which is essential but not sufficient for incorporation of retromer into functional endosomal transport assemblies. (PMID:21629666)
• Mutations in the gene composing the retromer cargo recognition subunit are not a common cause of Parkinson’s disease. (PMID:24684791)
• This study demonstrated that Genetic variability of VPS29 in parkinsonism. (PMID:25475142)
• Data indicate that vesicular transport proteins VPS35 and VPS29 influence the levels of the other subunit of retromer. (PMID:25937119)
• The retromer complex is a highly conserved membrane trafficking assembly composed of three proteins - Vps26, Vps29 and Vps35, which are impaired in neurodegenerative diseases. (Review) (PMID:26965691)
• Heterotrimer composed of DSCR3, C16orf62 and VPS29 orchestrates endosomal cargo retrieval and recycling. (PMID:28892079)
• RidL is critical for binding of the L. pneumophila effector to the Vps29 retromer subunit and displacement of the regulator TBC1D5. (PMID:29146912)
• Retromer stabilization results in neuroprotection in a model of Amyotrophic Lateral Sclerosis. (PMID:32737286)
• Mechanism and evolution of the Zn-fingernail required for interaction of VARP with VPS29. (PMID:33024112)
• Potential functions and causal associations of VPS29 in hepatocellular carcinoma: a bioinformatic and Mendelian randomization study. (PMID:37916325)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	vps29	ENSDARG00000069521
mus_musculus	Vps29	ENSMUSG00000029462
rattus_norvegicus	Vps29	ENSRNOG00000001274
drosophila_melanogaster	Vps29	FBGN0031310
caenorhabditis_elegans		WBGENE00014234

Protein

Protein identifiers

Vacuolar protein sorting-associated protein 29 — Q9UBQ0 (reviewed: Q9UBQ0)

Alternative names: PEP11 homolog, Vesicle protein sorting 29

All UniProt accessions (4): Q9UBQ0, A0A384MR19, F8VXU5, Q05DG7

UniProt curated annotations — full annotation on UniProt →

Function. Component of the commander complex that is essential for endosomal recycling of transmembrane cargos; the commander complex is composed of the CCC subcomplex and the retriever subcomplex. Component of the retriever complex, which is a heterotrimeric complex related to retromer cargo-selective complex (CSC) and essential for retromer-independent retrieval and recycling of numerous cargos such as integrin alpha-5/beta-1 (ITGA5:ITGB1). Component of the retromer cargo-selective complex (CSC). The CSC is believed to be the core functional component of retromer or respective retromer complex variants acting to prevent missorting of selected transmembrane cargo proteins into the lysosomal degradation pathway. The recruitment of the CSC to the endosomal membrane involves RAB7A and SNX3. The SNX-BAR retromer mediates retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN) and is involved in endosome-to-plasma membrane transport for cargo protein recycling. The SNX3-retromer mediates the retrograde endosome-to-TGN transport of WLS distinct from the SNX-BAR retromer pathway. The SNX27-retromer is believed to be involved in endosome-to-plasma membrane trafficking and recycling of a broad spectrum of cargo proteins. The CSC seems to act as recruitment hub for other proteins, such as the WASH complex and TBC1D5. Required to regulate transcytosis of the polymeric immunoglobulin receptor (pIgR-pIgA). In the endosomes, retriever complex drives the retrieval and recycling of NxxY-motif-containing cargo proteins by coupling to SNX17, a cargo essential for the homeostatic maintenance of numerous cell surface proteins associated with processes that include cell migration, cell adhesion, nutrient supply and cell signaling. The recruitment of the retriever complex to the endosomal membrane involves CCC and WASH complexes. Involved in GLUT1 endosome-to-plasma membrane trafficking; the function is dependent of association with ANKRD27. (Microbial infection) The heterotrimeric retromer cargo-selective complex (CSC) mediates the exit of human papillomavirus from the early endosome and the delivery to the Golgi apparatus.

Subunit / interactions. Component of the commander complex consisting of the CCC subcomplex and the retriever subcomplex. Component of the heterotrimeric retriever complex formed by VPS26C, VPS29 and VPS35L; within the complex interacts with VPS35L. Component of the heterotrimeric retromer cargo-selective complex (CSC), also described as vacuolar protein sorting subcomplex (VPS), formed by VPS26 (VPS26A or VPS26B), VPS29 and VPS35. The CSC has a highly elongated structure with VPS26 and VPS29 binding independently at opposite distal ends of VPS35 as central platform. The CSC is believed to associate with variable sorting nexins to form functionally distinct retromer complex variants. The originally described retromer complex (also called SNX-BAR retromer) is a pentamer containing the CSC and a heterodimeric membrane-deforming subcomplex formed between SNX1 or SNX2 and SNX5 or SNX6 (also called SNX-BAR subcomplex); the respective CSC and SNX-BAR subcomplexes associate with low affinity. The CSC associates with SNX3 to form a SNX3-retromer complex. The CSC associates with SNX27, the WASH complex and the SNX-BAR subcomplex to form the SNX27-retromer complex. Interacts with VPS26A, VPS35, SNX1, SNX2, SNX3, SNX27, WASHC5. Interacts with TBC1D5; this interaction is blocked by VPS35L in the retriever complex. Interacts with SNX17; the interaction is indirect; SNX17 (via its C-terminus) interacts with the retriever complex (via VPS26C and VPS35L). Interacts with VPS26B and ANKRD27. (Microbial infection) Interacts with human papillomavirus 16 minor capsid protein L2 (via C-terminus); this interaction mediates the transport of the capsid from the early endosome to the Golgi apparatus.

Subcellular location. Cytoplasm. Membrane. Endosome membrane. Early endosome. Late endosome.

Tissue specificity. Ubiquitous. Highly expressed in heart, lung, placenta, spleen, peripheral blood leukocytes, thymus, colon skeletal muscle, kidney and brain.

Similarity. Belongs to the VPS29 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9UBQ0-1	1	yes
Q9UBQ0-2	2

RefSeq proteins (4): NP_001269079, NP_001269080, NP_057310, NP_476528 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000979	Phosphodiesterase_MJ0936/Vps29	Family
IPR024654	Calcineurin-like_PHP_lpxH	Domain
IPR028661	Vps29	Family
IPR029052	Metallo-depent_PP-like	Homologous_superfamily

Pfam: PF12850

UniProt features (48 total): strand 17, mutagenesis site 13, binding site 8, helix 3, sequence conflict 2, turn 2, chain 1, splice variant 1, modified residue 1

Structure

Experimental structures (PDB)

21 structures.

PDB	Method	Resolution (Å)
8ESE	X-RAY DIFFRACTION	1.35
5GTU	X-RAY DIFFRACTION	1.5
6XS7	X-RAY DIFFRACTION	1.58
6XSA	X-RAY DIFFRACTION	1.83
6XS5	X-RAY DIFFRACTION	2.01
1W24	X-RAY DIFFRACTION	2.1
8R0J	X-RAY DIFFRACTION	2.4
5WYH	X-RAY DIFFRACTION	2.46
8R02	X-RAY DIFFRACTION	2.5
5OSI	X-RAY DIFFRACTION	2.52
6XS9	X-RAY DIFFRACTION	2.69
2R17	X-RAY DIFFRACTION	2.8
8SYN	ELECTRON MICROSCOPY	2.94
8SYO	ELECTRON MICROSCOPY	2.94
8RKS	X-RAY DIFFRACTION	3.1
8SYM	ELECTRON MICROSCOPY	3.2
9AU7	ELECTRON MICROSCOPY	3.4
5OSH	X-RAY DIFFRACTION	4.3
8P0V	ELECTRON MICROSCOPY	6.5
8P0X	ELECTRON MICROSCOPY	7.5
7BLN	ELECTRON MICROSCOPY	8.9

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UBQ0-F1	96.64	0.99

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (8): 8; 10; 39; 39; 62; 86; 115; 117

Post-translational modifications (1): 50

Mutagenesis-validated functional residues (13):

Position	Phenotype
8	loss of in vitro protein phosphatase activity.
39	loss of in vitro protein phosphatase activity.
39	no effect on in vitro protein phosphatase activity.
62	loss of in vitro protein phosphatase activity.
67	impairs interaction with vps35l.
86	loss of in vitro protein phosphatase activity.
90	impairs interaction with vps35.
91	impairs interaction with vps35. impairs interaction with vps35l and ccc complex association.
93	impairs interaction with vps35l and ccc complex association.
117	loss of in vitro protein phosphatase activity.
152	impairs interaction with tbc1d5. impairs interaction with vps35l.
165	impairs interaction with vps35l.
174	impairs interaction with vps35l.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-3238698	WNT ligand biogenesis and trafficking

MSigDB gene sets: 165 (showing top): RNGTGGGC_UNKNOWN, GOBP_REGULATION_OF_AUTOPHAGY, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_VESICLE_MEDIATED_TRANSPORT, GATA3_01, GOBP_REGULATION_OF_CATABOLIC_PROCESS, RAHMAN_TP53_TARGETS_PHOSPHORYLATED, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13, GOBP_ENDOCYTIC_RECYCLING, GOBP_RETROGRADE_TRANSPORT_ENDOSOME_TO_GOLGI, GOBP_LOCALIZATION_WITHIN_MEMBRANE, DANG_BOUND_BY_MYC, GOBP_CYTOSOLIC_TRANSPORT, GOCC_RETROMER_COMPLEX, GOCC_MEMBRANE_PROTEIN_COMPLEX

GO Biological Process (5): intracellular protein transport (GO:0006886), endocytic recycling (GO:0032456), retrograde transport, endosome to Golgi (GO:0042147), RNA processing (GO:0006396), protein transport (GO:0015031)

GO Molecular Function (2): metal ion binding (GO:0046872), protein binding (GO:0005515)

GO Cellular Component (10): endosome (GO:0005768), early endosome (GO:0005769), late endosome (GO:0005770), cytosol (GO:0005829), endosome membrane (GO:0010008), retromer complex (GO:0030904), retromer, cargo-selective complex (GO:0030906), nucleolus (GO:0005730), cytoplasm (GO:0005737), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Signaling by WNT	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
endosome	3
cellular anatomical structure	3
intracellular protein localization	2
endosomal transport	2
endomembrane system	2
membrane protein complex	2
protein transport	1
intracellular transport	1
vesicle-mediated transport to the plasma membrane	1
intercellular transport	1
cytosolic transport	1
gene expression	1
RNA biosynthetic process	1
primary metabolic process	1
transport	1
establishment of protein localization	1
cation binding	1
binding	1
cytoplasmic vesicle	1
cytoplasm	1
cytoplasmic vesicle membrane	1
bounding membrane of organelle	1
retromer complex	1
nuclear lumen	1
intracellular membraneless organelle	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

3144 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
VPS29	SNX1	Q13596	999
VPS29	VPS26A	O75436	999
VPS29	VPS35	Q96QK1	999
VPS29	VPS26B	Q4G0F5	997
VPS29	SNX2	P82862	997
VPS29	VPS26C	O14972	995
VPS29	VPS35L	Q7Z3J2	994
VPS29	RNF168	Q8IYW5	985
VPS29	TBC1D5	Q92609	985
VPS29	SNX5	Q9Y5X3	980
VPS29	SNX3	O60493	970
VPS29	SNX6	Q9UNH7	969
VPS29	SNX27	Q96L92	957
VPS29	SERPINE2	P07093	894
VPS29	ANXA7	P20073	778

IntAct

128 interactions, top by confidence:

A	B	Type	Score
VPS35	VPS26A	psi-mi:“MI:0914”(association)	0.980
VPS26A	VPS35	psi-mi:“MI:0915”(physical association)	0.980
VPS35	VPS26A	psi-mi:“MI:0915”(physical association)	0.980
VPS26A	VPS35	psi-mi:“MI:0914”(association)	0.980
VPS35	VPS29	psi-mi:“MI:0915”(physical association)	0.970
VPS29	VPS35	psi-mi:“MI:0915”(physical association)	0.970
VPS29	VPS35	psi-mi:“MI:0407”(direct interaction)	0.970
VPS35	VPS29	psi-mi:“MI:0407”(direct interaction)	0.970
VPS26A	VPS29	psi-mi:“MI:0915”(physical association)	0.930
VPS29	VPS26A	psi-mi:“MI:0914”(association)	0.930
COMMD2	CCDC22	psi-mi:“MI:0914”(association)	0.930
VPS29	VPS26A	psi-mi:“MI:0915”(physical association)	0.930
VPS35L	CCDC22	psi-mi:“MI:0914”(association)	0.900
VPS29	TBC1D5	psi-mi:“MI:0915”(physical association)	0.860
VPS29	TBC1D5	psi-mi:“MI:0914”(association)	0.860
VPS29	VPS35L	psi-mi:“MI:0915”(physical association)	0.840

BioGRID (277): VPS29 (Two-hybrid), VPS35 (Two-hybrid), VPS29 (Affinity Capture-MS), VPS29 (Affinity Capture-MS), VPS29 (Affinity Capture-MS), VPS29 (Reconstituted Complex), VPS29 (Reconstituted Complex), GRHPR (Co-fractionation), HAT1 (Co-fractionation), KIAA1598 (Co-fractionation), OTUB1 (Co-fractionation), PSMD6 (Co-fractionation), SAC3D1 (Co-fractionation), VPS29 (Co-fractionation), VPS29 (Co-fractionation)

ESM2 similar proteins: A0Q6C0, A4IXW6, A5ICM2, A7NCA3, A8ETA7, A8ZXG7, B2RZ78, B2SGK4, B4S561, B4SCC0, D5V0N9, O42615, P46493, P60502, P96655, Q0BLV0, Q11WK3, Q14HJ0, Q2A3D4, Q3AT13, Q3AU36, Q3B6A2, Q3K150, Q3T0M0, Q54IF7, Q5NG38, Q5R9Z1, Q5WVX4, Q5X4I9, Q5ZIL2, Q5ZUS0, Q6DEU3, Q6GP62, Q7MN25, Q7ZV68, Q81ST7, Q87RS1, Q8DFC3, Q8DZQ7, Q8E5F5

Diamond homologs: B2RZ78, P38759, Q3T0M0, Q54IF7, Q58040, Q5R9Z1, Q5ZIL2, Q6DEU3, Q6GP62, Q7ZV68, Q9QZ88, Q9STT2, Q9UBQ0, Q9UTI5, O27802, P75349, Q58346, A9BF32

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 71 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
Neddylation	11	11.1×	8e-07

GO biological processes:

GO term	Partners	Fold	FDR
endocytic recycling	9	40.8×	4e-10
retrograde transport, endosome to Golgi	8	27.9×	8e-08
intracellular protein transport	9	9.9×	3e-05
protein transport	11	8.2×	1e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	11
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

824 predictions. Top by Δscore:

Variant	Effect	Δscore
12:110492118:TGTTT:T	acceptor_gain	1.0000
12:110492119:GTTT:G	acceptor_gain	1.0000
12:110492120:TTT:T	acceptor_gain	1.0000
12:110492121:TT:T	acceptor_gain	1.0000
12:110492122:TCTAG:T	acceptor_loss	1.0000
12:110492123:C:CC	acceptor_gain	1.0000
12:110492123:CTAGA:C	acceptor_loss	1.0000
12:110492124:T:A	acceptor_loss	1.0000
12:110492994:A:AC	donor_gain	1.0000
12:110492995:C:CC	donor_gain	1.0000
12:110493237:A:C	acceptor_gain	1.0000
12:110496211:G:GC	acceptor_gain	1.0000
12:110496921:T:A	donor_gain	1.0000
12:110502051:T:TA	donor_gain	1.0000
12:110492990:AC:A	donor_loss	0.9900
12:110492991:C:CT	donor_loss	0.9900
12:110492992:T:TA	donor_loss	0.9900
12:110492993:C:CT	donor_loss	0.9900
12:110492994:A:AT	donor_loss	0.9900
12:110492995:CGTTT:C	donor_gain	0.9900
12:110493230:TT:T	acceptor_gain	0.9900
12:110493232:C:CC	acceptor_gain	0.9900
12:110496007:ATCAC:A	donor_loss	0.9900
12:110496008:TCACC:T	donor_loss	0.9900
12:110496009:CAC:C	donor_loss	0.9900
12:110496010:ACC:A	donor_loss	0.9900
12:110496011:C:A	donor_loss	0.9900
12:110496200:CCAA:C	acceptor_gain	0.9900
12:110496201:CAACT:C	acceptor_gain	0.9900
12:110496204:C:CC	acceptor_gain	0.9900

AlphaMissense

1196 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:110496094:C:A	G38V	1.000
12:110496094:C:T	G38E	1.000
12:110492061:A:C	Y165D	0.999
12:110492099:A:G	L152S	0.999
12:110492104:A:C	F150L	0.999
12:110492104:A:T	F150L	0.999
12:110492106:A:G	F150L	0.999
12:110493018:C:A	G137W	0.999
12:110493023:G:T	A135D	0.999
12:110493029:C:T	G133D	0.999
12:110493030:C:G	G133R	0.999
12:110493086:C:T	G114E	0.999
12:110493095:A:G	L111P	0.999
12:110493167:C:T	G87E	0.999
12:110493176:A:G	L84P	0.999
12:110493179:C:T	G83D	0.999
12:110496025:C:A	G61V	0.999
12:110496025:C:T	G61E	0.999
12:110496026:C:G	G61R	0.999
12:110496026:C:T	G61R	0.999
12:110496095:C:G	G38R	0.999
12:110496095:C:T	G38R	0.999
12:110496187:C:A	G7V	0.999
12:110496187:C:T	G7E	0.999
12:110496188:C:G	G7R	0.999
12:110496188:C:T	G7R	0.999
12:110492061:A:G	Y165H	0.998
12:110492067:A:C	Y163D	0.998
12:110492099:A:C	L152W	0.998
12:110492105:A:G	F150S	0.998

dbSNP variants (sampled 300 via entrez): RS1000044920 (12:110493651 T>A), RS1000077256 (12:110493284 TA>T,TAA), RS1000117245 (12:110491038 T>A), RS1000278529 (12:110497882 C>G), RS1000278726 (12:110497621 T>C), RS1000573927 (12:110490765 C>T), RS1000621094 (12:110495843 T>G), RS1000812733 (12:110502758 C>G), RS1000878489 (12:110504100 C>T), RS1001264840 (12:110502445 C>G,T), RS1001290328 (12:110493861 G>A), RS1001497706 (12:110497211 T>C), RS1001631813 (12:110501122 G>A), RS1001834873 (12:110495509 G>A,C), RS1001885700 (12:110495231 A>G)

Disease associations

OMIM: gene MIM:606932 | 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

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	3
Smoke	decreases expression, increases abundance	3
bisphenol A	decreases expression, increases expression	2
Air Pollutants	affects expression, increases abundance, decreases expression	2
Vehicle Emissions	decreases expression, decreases reaction, increases abundance, increases expression	2
Valproic Acid	affects expression, increases expression	2
Particulate Matter	decreases expression, decreases reaction, increases abundance, increases expression	2
aristolochic acid I	decreases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	decreases expression	1
arsenite	affects binding, increases reaction	1
perfluorooctanoic acid	decreases expression	1
chloropicrin	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
nutlin 3	affects cotreatment, increases secretion	1
bisphenol B	increases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases expression, decreases reaction	1
LDN 193189	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Arsenic	increases expression, decreases expression, affects cotreatment, increases abundance	1
Benzo(a)pyrene	increases expression	1
Dactinomycin	affects cotreatment, increases secretion	1
Dinitrochlorobenzene	affects binding	1
Doxorubicin	increases expression	1
Homocysteine	affects cotreatment, affects expression	1
Ivermectin	decreases expression	1
Methionine	affects cotreatment, affects expression	1
Ozone	affects expression, increases abundance	1

Clinical trials (associated diseases)

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