VTI1A

Summary

VTI1A (vesicle transport through interaction with t-SNAREs 1A, HGNC:17792) is a protein-coding gene on chromosome 10q25.2, encoding Vesicle transport through interaction with t-SNAREs homolog 1A (Q96AJ9). V-SNARE that mediates vesicle transport pathways through interactions with t-SNAREs on the target membrane.

The protein encoded by this gene is a member of the family of soluble N-ethylmaleimide-sensitive fusion protein-attachment protein receptors (SNAREs) that function in intracellular trafficking. This family member is involved in vesicular transport between endosomes and the trans-Golgi network. It is a vesicle-associated SNARE (v-SNARE) that interacts with target membrane SNAREs (t-SNAREs). Polymorphisms in this gene have been associated with binocular function, and also with susceptibility to colorectal and lung cancers. A recurrent rearrangement has been found between this gene and the transcription factor 7-like 2 (TCF7L2) gene in colorectal cancers. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 143187 — RefSeq curated summary.

At a glance

• GWAS associations: 30
• Clinical variants (ClinVar): 44 total
• MANE Select transcript: NM_145206

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17792
Approved symbol	VTI1A
Name	vesicle transport through interaction with t-SNAREs 1A
Location	10q25.2
Locus type	gene with protein product
Status	Approved
Aliases	MVti1, Vti1-rp2
Ensembl gene	ENSG00000151532
Ensembl biotype	protein_coding
OMIM	614316
Entrez	143187

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 7 protein_coding_CDS_not_defined, 4 protein_coding

ENST00000393077, ENST00000432306, ENST00000472892, ENST00000480057, ENST00000483122, ENST00000489142, ENST00000489357, ENST00000494728, ENST00000496445, ENST00000705995, ENST00000876660

RefSeq mRNA: 8 — MANE Select: NM_145206 NM_001318203, NM_001318205, NM_001365710, NM_001365711, NM_001365712, NM_001365713, NM_001365714, NM_145206

CCDS: CCDS7575, CCDS91346, CCDS91347

Canonical transcript exons

ENST00000393077 — 8 exons

Exon	Start	End
ENSE00001685704	112538246	112538330
ENSE00001692595	112668937	112668998
ENSE00001694759	112668218	112668288
ENSE00003510762	112527087	112527164
ENSE00003578306	112460524	112460582
ENSE00003649011	112464547	112464657
ENSE00003994484	112447215	112447467
ENSE00003994486	112815290	112818744

Expression profiles

Bgee: expression breadth ubiquitous, 240 present calls, max score 96.05.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 26.2193 / max 349.9411, expressed in 1814 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
107070	24.9476	1813
107069	1.1419	837
205991	0.1297	40

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	96.05	gold quality
calcaneal tendon	UBERON:0003701	92.75	gold quality
pancreatic ductal cell	CL:0002079	92.51	gold quality
buccal mucosa cell	CL:0002336	90.71	gold quality
tendon	UBERON:0000043	88.71	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.72	gold quality
monocyte	CL:0000576	87.47	gold quality
bone marrow cell	CL:0002092	87.31	gold quality
leukocyte	CL:0000738	87.15	gold quality
epithelial cell of pancreas	CL:0000083	84.68	silver quality
cortical plate	UBERON:0005343	84.53	gold quality
corpus callosum	UBERON:0002336	84.44	gold quality
colonic epithelium	UBERON:0000397	83.47	gold quality
bone marrow	UBERON:0002371	83.45	gold quality
blood	UBERON:0000178	83.19	gold quality
adrenal tissue	UBERON:0018303	83.16	gold quality
tendon of biceps brachii	UBERON:0008188	83.05	gold quality
islet of Langerhans	UBERON:0000006	82.83	gold quality
tonsil	UBERON:0002372	82.83	gold quality
muscle of leg	UBERON:0001383	82.69	gold quality
granulocyte	CL:0000094	82.44	gold quality
gastrocnemius	UBERON:0001388	82.37	gold quality
stromal cell of endometrium	CL:0002255	82.23	gold quality
ganglionic eminence	UBERON:0004023	82.01	gold quality
lymph node	UBERON:0000029	81.74	gold quality
medial globus pallidus	UBERON:0002477	81.74	gold quality
secondary oocyte	CL:0000655	81.57	gold quality
rectum	UBERON:0001052	81.37	gold quality
hindlimb stylopod muscle	UBERON:0004252	81.28	gold quality
vermiform appendix	UBERON:0001154	81.20	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-CURD-119	yes	31.96
E-ANND-3	yes	4.83

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

143 targeting VTI1A, 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-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-1-3P	99.93	72.35	1914

Literature-anchored findings (GeneRIF, showing 9)

• The present results suggest that a SNARE complex containing VAMP7 and Vti1a defines a novel traffic pathway to the cell surface in both neuronal and non-neuronal cells. (PMID:19138172)
• We found a colorectal carcinoma cell line harboring the fusion gene to be dependent on VTI1A-TCF7L2 for anchorage-independent growth using RNA interference-mediated knockdown. (PMID:21892161)
• Data indicate that depletion of VAMP4, syntaxin 6, syntaxin 16, and Vti1a disrupted the Golgi ribbon structure. (PMID:23677696)
• Novel variants of VTI1A-TCF7L2 fusion transcripts, including a novel fusion partner gene, RP11-57H14.3, was identified and demonstrated detectable levels in a large fraction of colorectal cancer samples.[RP11-57H14.3] (PMID:24608966)
• analysis of a new susceptibility locus for colorectal cancer in VTI1A [meta-analysis] (PMID:25105248)
• The AA genotype of VTI1A (rs7086803) polymorphism had an increased risk of developing NSCLC compared with the GG genotype. Smoking lung cancer patients with the AA genotype of VTI1A gene (rs7086803) had a poor survival rate. (PMID:25744365)
• our results indicate that genetic variants in VTI1A may modify individual susceptibility to non-GBM of glioma in the Han Chinese population and support the role of the VTI1A genes in the occurrence of glioma. (PMID:28320150)
• Transfection of LS174T cells showed that the VTI1A promoter is highly active compared to the TCF7L2 promoter, and that CDX2 activates transcription of VTI1A. (PMID:29975781)
• Defects in the Maturation of Mitochondrial Iron-Sulfur Proteins: Biophysical Investigation of the MMDS3 Causing Gly104Cys Variant of IBA57. (PMID:39408793)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	vti1a	ENSDARG00000045065
mus_musculus	Vti1a	ENSMUSG00000024983
rattus_norvegicus	Vti1a	ENSRNOG00000042786
drosophila_melanogaster	Vti1a	FBGN0260862
caenorhabditis_elegans		WBGENE00013302

Paralogs (2): VTI1B (ENSG00000100568), GOSR2 (ENSG00000108433)

Protein

Protein identifiers

Vesicle transport through interaction with t-SNAREs homolog 1A — Q96AJ9 (reviewed: Q96AJ9)

Alternative names: Vesicle transport v-SNARE protein Vti1-like 2, Vti1-rp2

All UniProt accessions (2): Q96AJ9, A0A994J5N6

UniProt curated annotations — full annotation on UniProt →

Function. V-SNARE that mediates vesicle transport pathways through interactions with t-SNAREs on the target membrane. These interactions are proposed to mediate aspects of the specificity of vesicle trafficking and to promote fusion of the lipid bilayers. Involved in vesicular transport from the late endosomes to the trans-Golgi network. Along with VAMP7, involved in an non-conventional RAB1-dependent traffic route to the cell surface used by KCNIP1 and KCND2. May be involved in increased cytokine secretion associated with cellular senescence.

Subunit / interactions. Interacts with distinct SNARE complexes that contain either STX5 or STX6. Interacts with NAPA and, to a lesser extent, with NAPG. Identified in a complex containing STX6, STX12, VAMP4 and VTI1A.

Subcellular location. Cytoplasmic vesicle. Golgi apparatus membrane.

Similarity. Belongs to the VTI1 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96AJ9-2	2	yes
Q96AJ9-1	1

RefSeq proteins (8): NP_001305132, NP_001305134, NP_001352639, NP_001352640, NP_001352641, NP_001352642, NP_001352643, NP_660207* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000727	T_SNARE_dom	Domain
IPR007705	Vesicle_trsprt_v-SNARE_N	Domain
IPR010989	SNARE	Homologous_superfamily
IPR027027	GOSR2/Membrin/Bos1	Family
IPR038407	v-SNARE_N_sf	Homologous_superfamily

Pfam: PF05008, PF12352

UniProt features (8 total): topological domain 2, coiled-coil region 2, chain 1, transmembrane region 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96AJ9-F1	85.00	0.42

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-6811438	Intra-Golgi traffic
R-HSA-6811440	Retrograde transport at the Trans-Golgi-Network

MSigDB gene sets: 224 (showing top): GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_VESICLE_ORGANIZATION, GOBP_MEMBRANE_FUSION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_VACUOLAR_TRANSPORT, GOBP_MULTICELLULAR_ORGANISMAL_MOVEMENT, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_INTRA_GOLGI_VESICLE_MEDIATED_TRANSPORT, GOBP_MACROAUTOPHAGY, FONTAINE_PAPILLARY_THYROID_CARCINOMA_UP, GOCC_TRANS_GOLGI_NETWORK, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, GOBP_ORGANELLE_MEMBRANE_FUSION

GO Biological Process (14): intracellular protein transport (GO:0006886), endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), intra-Golgi vesicle-mediated transport (GO:0006891), Golgi to vacuole transport (GO:0006896), autophagy (GO:0006914), macroautophagy (GO:0016236), endocytic recycling (GO:0032456), retrograde transport, endosome to Golgi (GO:0042147), vesicle fusion with Golgi apparatus (GO:0048280), voluntary musculoskeletal movement (GO:0050882), protein transport (GO:0015031), vesicle-mediated transport (GO:0016192), endosomal transport (GO:0016197), membrane fusion (GO:0061025)

GO Molecular Function (3): SNARE binding (GO:0000149), SNAP receptor activity (GO:0005484), protein binding (GO:0005515)

GO Cellular Component (20): Golgi membrane (GO:0000139), endosome (GO:0005768), autophagosome (GO:0005776), endoplasmic reticulum membrane (GO:0005789), Golgi apparatus (GO:0005794), cytosol (GO:0005829), synaptic vesicle (GO:0008021), ER to Golgi transport vesicle membrane (GO:0012507), clathrin-coated vesicle (GO:0030136), SNARE complex (GO:0031201), late endosome membrane (GO:0031902), trans-Golgi network membrane (GO:0032588), neuronal cell body (GO:0043025), neuron projection terminus (GO:0044306), perinuclear region of cytoplasm (GO:0048471), cytoplasm (GO:0005737), endomembrane system (GO:0012505), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410), bounding membrane of organelle (GO:0098588)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Intra-Golgi and retrograde Golgi-to-ER traffic	2

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	6
cellular anatomical structure	6
intracellular transport	3
intercellular transport	3
Golgi vesicle transport	3
organelle membrane	3
intracellular protein localization	2
endosomal transport	2
transport	2
endomembrane system	2
vacuole	2
protein transport	1
post-Golgi vesicle-mediated transport	1
vacuolar transport	1
catabolic process	1
transmembrane transport	1
process utilizing autophagic mechanism	1
autophagosome assembly	1
autophagy	1
vesicle-mediated transport to the plasma membrane	1
cytosolic transport	1
vesicle fusion	1
Golgi organization	1
musculoskeletal movement	1
establishment of protein localization	1
cellular process	1
vesicle-mediated transport	1
membrane organization	1
protein binding	1
protein-macromolecule adaptor activity	1
membrane fusion	1
fusogenic activity	1
binding	1
Golgi apparatus	1
bounding membrane of organelle	1
cytoplasmic vesicle	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
intracellular membrane-bounded organelle	1
exocytic vesicle	1

Protein interactions and networks

STRING

2162 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
VTI1A	STX16	O14662	996
VTI1A	STX6	O43752	995
VTI1A	VAMP4	O75379	993
VTI1A	VAMP7	P51809	986
VTI1A	VAMP3	Q15836	977
VTI1A	STX5	Q13190	972
VTI1A	STX10	O60499	971
VTI1A	BET1	O15155	908
VTI1A	STX12	Q86Y82	792
VTI1A	GOSR1	O95249	768
VTI1A	YKT6	O15498	717
VTI1A	GOSR2	O14653	710
VTI1A	STX7	O15400	709
VTI1A	VPS52	Q8N1B4	708
VTI1A	STX8	Q9UNK0	691

IntAct

72 interactions, top by confidence:

A	B	Type	Score
STX11	SNAP23	psi-mi:“MI:0914”(association)	0.900
STX12	STX6	psi-mi:“MI:0915”(physical association)	0.860
STX12	STX6	psi-mi:“MI:0914”(association)	0.860
STX18	NBAS	psi-mi:“MI:0914”(association)	0.810
STX6	GOSR2	psi-mi:“MI:0914”(association)	0.670
VPS51	STX6	psi-mi:“MI:0914”(association)	0.660
STX7	SNAP23	psi-mi:“MI:0914”(association)	0.640
STX12	SNAP23	psi-mi:“MI:0914”(association)	0.640
VPS45	STX16	psi-mi:“MI:0914”(association)	0.620
NAPA	NBAS	psi-mi:“MI:0914”(association)	0.530
	XPO1	psi-mi:“MI:0914”(association)	0.530
VAMP5	NBAS	psi-mi:“MI:0914”(association)	0.530
TRPC4AP	SMCHD1	psi-mi:“MI:0914”(association)	0.530
HAUS1	BET1	psi-mi:“MI:0914”(association)	0.530
TMEM9	ESYT2	psi-mi:“MI:0914”(association)	0.530
SLC39A4	TMEM120B	psi-mi:“MI:0914”(association)	0.530
STX12	FAM234B	psi-mi:“MI:0914”(association)	0.530
SMPD1	CLGN	psi-mi:“MI:0914”(association)	0.530
ANKH	FAM234B	psi-mi:“MI:0914”(association)	0.530
env	PGRMC1	psi-mi:“MI:0914”(association)	0.460
BET1	SNAP23	psi-mi:“MI:0914”(association)	0.420

BioGRID (119): VTI1A (Affinity Capture-MS), VTI1A (Affinity Capture-MS), VTI1A (Affinity Capture-MS), VTI1A (Affinity Capture-MS), VTI1A (Affinity Capture-MS), VTI1A (Affinity Capture-MS), VTI1A (Affinity Capture-MS), VTI1A (Affinity Capture-MS), VTI1A (Affinity Capture-MS), VTI1A (Affinity Capture-MS), VTI1A (Affinity Capture-MS), VTI1A (Affinity Capture-RNA), VTI1A (Affinity Capture-MS), VTI1A (Affinity Capture-MS), VTI1A (Proximity Label-MS)

ESM2 similar proteins: A8WVD0, O15400, O16000, O35526, O70257, O70439, P32850, P32851, P32856, P32867, P39926, P50279, P61264, P61265, P61266, P61267, P61268, P70452, Q00262, Q08849, Q08850, Q0VCI2, Q12846, Q13277, Q16623, Q16932, Q20024, Q24547, Q3SWZ3, Q3ZBT5, Q42374, Q59YF0, Q5R4L2, Q5R602, Q5TX47, Q64704, Q7XIE2, Q8N4C7, Q8R1Q0, Q8VZU2

Diamond homologs: O88384, O89116, P58200, P78768, Q2KIU0, Q96AJ9, Q9JI51, Q9SEL5, Q9UEU0, Q04338, Q9LVP9, Q9SEL6, Q54CK6

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
VTI1A	“form complex”	“LE-TGN SNARE”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 65 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
Intra-Golgi traffic	8	50.6×	3e-10
Retrograde transport at the Trans-Golgi-Network	6	32.1×	8e-07
Intra-Golgi and retrograde Golgi-to-ER traffic	8	20.4×	3e-07
COPII-mediated vesicle transport	5	19.9×	1e-04
Golgi-to-ER retrograde transport	5	16.2×	3e-04
COPI-dependent Golgi-to-ER retrograde traffic	5	13.5×	6e-04
Transport to the Golgi and subsequent modification	5	12.6×	7e-04
Membrane Trafficking	11	9.9×	4e-07

GO biological processes:

GO term	Partners	Fold	FDR
obsolete vesicle docking	6	79.2×	3e-08
vesicle fusion	6	62.3×	7e-08
membrane fusion	5	53.8×	2e-06
endocytic recycling	6	27.7×	5e-06
intracellular protein transport	11	12.3×	1e-07
protein transport	9	6.8×	3e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	32
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

4357 predictions. Top by Δscore:

Variant	Effect	Δscore
10:112447463:GCCTG:G	donor_gain	1.0000
10:112460516:T:TA	acceptor_gain	1.0000
10:112460521:CA:C	acceptor_loss	1.0000
10:112460522:A:AC	acceptor_loss	1.0000
10:112460522:A:AG	acceptor_gain	1.0000
10:112460523:G:GG	acceptor_gain	1.0000
10:112460523:G:GT	acceptor_loss	1.0000
10:112460579:ACTG:A	donor_gain	1.0000
10:112460580:CTG:C	donor_gain	1.0000
10:112460581:TGGTA:T	donor_loss	1.0000
10:112460582:GGTA:G	donor_loss	1.0000
10:112460583:G:GG	donor_gain	1.0000
10:112464545:A:AG	acceptor_gain	1.0000
10:112464545:AGCTT:A	acceptor_gain	1.0000
10:112464546:G:GC	acceptor_gain	1.0000
10:112464546:GC:G	acceptor_gain	1.0000
10:112464546:GCT:G	acceptor_gain	1.0000
10:112464546:GCTT:G	acceptor_gain	1.0000
10:112464546:GCTTG:G	acceptor_gain	1.0000
10:112464653:ATTTT:A	donor_gain	1.0000
10:112464654:TTTT:T	donor_gain	1.0000
10:112464654:TTTTG:T	donor_loss	1.0000
10:112464655:TTT:T	donor_gain	1.0000
10:112464655:TTTG:T	donor_loss	1.0000
10:112464656:TTGT:T	donor_loss	1.0000
10:112464657:TGTGA:T	donor_loss	1.0000
10:112464658:G:GG	donor_gain	1.0000
10:112464659:T:A	donor_loss	1.0000
10:112527085:A:AG	acceptor_gain	1.0000
10:112527086:G:GG	acceptor_gain	1.0000

AlphaMissense

1426 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:112460571:G:C	A48P	0.998
10:112460581:T:C	L51P	0.998
10:112538318:G:C	A139P	0.998
10:112668248:T:C	L153P	0.998
10:112668277:G:C	A163P	0.998
10:112668967:A:C	S177R	0.998
10:112668969:C:A	S177R	0.998
10:112668969:C:G	S177R	0.998
10:112538256:T:C	L118P	0.997
10:112538277:T:C	L125P	0.997
10:112538288:T:C	S129P	0.997
10:112538298:T:C	L132P	0.997
10:112668227:G:A	G146D	0.997
10:112668938:T:C	L167P	0.997
10:112668980:T:C	L181P	0.997
10:112464554:A:C	Q54P	0.996
10:112538285:T:C	S128P	0.996
10:112668970:T:C	S178P	0.996
10:112538306:G:A	G135R	0.995
10:112538306:G:C	G135R	0.995
10:112538307:G:A	G135E	0.995
10:112538327:A:C	T142P	0.995
10:112668281:G:C	R164P	0.995
10:112815304:G:C	R192P	0.995
10:112815324:G:A	G199R	0.995
10:112815324:G:C	G199R	0.995
10:112447422:G:C	A17P	0.994
10:112538259:T:C	L119P	0.994
10:112668226:G:C	G146R	0.994
10:112464557:T:G	M55R	0.993

dbSNP variants (sampled 300 via entrez): RS1000006285 (10:112645545 C>T), RS1000018895 (10:112593302 T>A,C), RS1000023812 (10:112665421 A>C,G), RS1000025183 (10:112587287 C>A,T), RS1000032557 (10:112731055 CCTT>C), RS1000033846 (10:112852563 C>T), RS1000033978 (10:112447241 G>A,T), RS1000037904 (10:112633675 G>A,C), RS1000065347 (10:112845050 C>A,T), RS1000083659 (10:112505060 A>T), RS1000090393 (10:112502139 C>G,T), RS1000093608 (10:112640758 G>C), RS1000104940 (10:112796250 A>T), RS1000117145 (10:112684010 G>A), RS1000125377 (10:112587518 A>C,T)

Disease associations

OMIM: gene MIM:614316 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): hereditary breast ovarian cancer syndrome (MONDO:0003582)

Orphanet (1): Hereditary breast and/or ovarian cancer syndrome (Orphanet:145)

HPO phenotypes

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

GWAS associations

30 associations (top):

Study	Trait	p-value
GCST001740_5	Lung cancer	4.000000e-18
GCST001860_7	Multiple sclerosis	8.000000e-06
GCST002561_1	Colorectal cancer	1.000000e-09
GCST003227_8	Non-glioblastoma glioma	4.000000e-08
GCST003598_28	QRS duration	1.000000e-09
GCST003598_49	QRS duration	6.000000e-12
GCST003799_8	Colorectal cancer	4.000000e-09
GCST003844_3	QRS duration	1.000000e-14
GCST003901_6	Cognitive decline (age-related)	1.000000e-06
GCST004348_6	Non-glioblastoma glioma	3.000000e-09
GCST005950_12	Body mass index x sex x age interaction (4df test)	8.000000e-12
GCST005951_53	Body mass index	3.000000e-10
GCST005952_5	Body mass index (age>50)	3.000000e-13
GCST006979_606	Heel bone mineral density	3.000000e-12
GCST007227_7	QRS duration	5.000000e-12
GCST007436_7	Carotid intima media thickness	4.000000e-08
GCST007552_10	Colorectal cancer	2.000000e-11
GCST007856_22	Colorectal cancer or advanced adenoma	5.000000e-12
GCST008422_8	QRS duration	8.000000e-10
GCST008834_1	Non-small cell lung cancer	8.000000e-10
GCST010002_225	Refractive error	9.000000e-46
GCST010575_3	Evening vs. morning chronotype (sMEQ score)	5.000000e-06
GCST010796_904	Electrocardiogram morphology (amplitude at temporal datapoints)	3.000000e-40
GCST010796_905	Electrocardiogram morphology (amplitude at temporal datapoints)	3.000000e-40
GCST010796_906	Electrocardiogram morphology (amplitude at temporal datapoints)	3.000000e-38
GCST010796_907	Electrocardiogram morphology (amplitude at temporal datapoints)	7.000000e-41
GCST011010_46	Electrocardiographic traits (multivariate)	1.000000e-11
GCST011205_1	Hypertrophic cardiomyopathy (MTAG)	2.000000e-10
GCST011211_12	Hypertrophic cardiomyopathy	4.000000e-12
GCST012489_30	Heel bone mineral density x serum urate levels interaction	3.000000e-08

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0005054	QRS complex
EFO:0004340	body mass index
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0009270	heel bone mineral density
EFO:0008328	chronotype measurement
EFO:0004327	electrocardiography
EFO:0004531	urate measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D061325	Hereditary Breast and Ovarian Cancer Syndrome	C04.588.180.483; C04.588.322.455.431; C04.700.517; C12.050.351.500.056.630.705.431; C12.050.351.937.418.685.431; C12.100.250.056.630.705.431; C12.900.418.685.431; C16.320.700.517; C17.800.090.500.483; C19.344.410.431; C19.391.630.705.431

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs17129858	VTI1A		0.00	0

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression	5
Valproic Acid	increases expression, affects cotreatment, affects expression	4
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Cadmium Chloride	increases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
bisphenol F	increases expression, affects cotreatment	1
methylmercuric chloride	decreases expression	1
bisphenol A	decreases methylation	1
sodium arsenate	decreases expression	1
sodium arsenite	increases expression	1
perfluorooctanoic acid	increases expression	1
aflatoxin B2	increases methylation	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression, affects expression	1
dorsomorphin	affects cotreatment, decreases expression, affects expression	1
jinfukang	affects cotreatment, decreases expression	1
Irinotecan	decreases expression	1
Resveratrol	increases expression, affects cotreatment	1
Sunitinib	increases expression	1
Air Pollutants	increases abundance, affects expression	1
Arsenic	affects methylation	1
Atrazine	increases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Dexamethasone	increases expression, affects cotreatment	1
Doxorubicin	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Ozone	affects expression, increases abundance	1
Plant Extracts	increases expression, affects cotreatment	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT02562170	PHASE4	COMPLETED	Protexa® Versus TiLoopBra® in Immediate Breast Reconstruction- A Pilot Study
NCT00673335	PHASE3	COMPLETED	Letrozole in Preventing Breast Cancer in Postmenopausal Women With a BRCA1 or BRCA2 Mutation
NCT00685256	PHASE3	COMPLETED	Standard Genetic Counseling With or Without a Decision Guide in Improving Communication Between Mothers Undergoing BRCA1/2 Testing and Their Minor-Age Children
NCT03162276	PHASE3	UNKNOWN	Trial of Inquiry Based Stress Reduction (IBSR) Program for BRCA1/2 Mutation Carriers
NCT00253539	PHASE2	COMPLETED	Arzoxifene or Tamoxifen in Preventing Breast Cancer in Premenopausal Women at High Risk for Breast Cancer
NCT00305695	PHASE2	COMPLETED	Zoledronate or Observation in Maintaining Bone Mineral Density in Patients Who Are Undergoing Surgery to Remove Both Ovaries
NCT00321633	PHASE2	COMPLETED	Carboplatin or Docetaxel in Treating Women With Metastatic Genetic Breast Cancer
NCT01333748	PHASE2	COMPLETED	Search Allelic Imbalance of Expression of BRCA Genes in Hereditary Risk of Breast and/or Ovarian Cancer
NCT01367639	PHASE2	COMPLETED	Trial of Inquiry Based Stress Reduction (IBSR) Program for BRCA1/2 Mutation Carriers
NCT00535119	PHASE1	COMPLETED	Veliparib, Carboplatin, and Paclitaxel in Treating Patients With Advanced Solid Cancer
NCT00892736	PHASE1	COMPLETED	Veliparib in Treating Patients With Malignant Solid Tumors That Do Not Respond to Previous Therapy
NCT03832985	EARLY_PHASE1	COMPLETED	Pediatric Reporting of Adult-Onset Genomic Results
NCT00005095	Not specified	RECRUITING	Specimen and Data Study for Ovarian Cancer Early Detection and Prevention
NCT00609505	Not specified	COMPLETED	Telemedicine vs. Face-to-Face Cancer Genetic Counseling
NCT01273909	Not specified	UNKNOWN	Outcomes After Perforator Flap Reconstruction for Breast Reconstruction and/or Lymphedema Treatment
NCT01445275	Not specified	WITHDRAWN	Cost of Cancer Risk Management in Women at Elevated Genetic Risk for Ovarian Cancer Who Participated on GOG-0199
NCT01608074	Not specified	ACTIVE_NOT_RECRUITING	Radical Fimbriectomy for Young BRCA Mutation Carriers
NCT02087592	Not specified	COMPLETED	Feasibility of Lifestyle Intervention in BRCA1/2 Mutation Carriers
NCT02302742	Not specified	RECRUITING	Triple Negative Breast Cancer and Germline Hereditary Breast and Ovarian Cancer Mutation Carrier Registry
NCT02324062	Not specified	COMPLETED	Cancer Genetics Hereditary Cancer Panel Testing
NCT02516540	Not specified	UNKNOWN	Efficacy of Lifestyle Intervention in BRCA1/2 Mutation Carriers
NCT02653105	Not specified	ACTIVE_NOT_RECRUITING	Women at Risk of Breast Cancer and OLFM4
NCT02705924	Not specified	TERMINATED	Impact of a Psychoeducational Intervention on Expectations and Coping in Young Women Exposed to a High HBOC Risk
NCT02760849	Not specified	ACTIVE_NOT_RECRUITING	Surgery in Preventing Ovarian Cancer in Patients With Genetic Mutations
NCT02786147	Not specified	COMPLETED	Identification and Referral of Women at Risk for Hereditary Breast/Ovarian Cancer
NCT02956681	Not specified	COMPLETED	Statewide Communication to Reach Diverse Low Income Women
NCT03015376	Not specified	UNKNOWN	Inherited Susceptible Genes Among Epithelial Ovarian Cancer
NCT03050268	Not specified	RECRUITING	Familial Investigations of Childhood Cancer Predisposition
NCT03075540	Not specified	COMPLETED	Enhancing At-risk Latina Women’s Use of Genetic Counseling for Hereditary Breast and Ovarian Cancer
NCT03124212	Not specified	RECRUITING	Cascade Genetic Testing for Hereditary Breast/Ovarian Cancer and Lynch Syndrome in Switzerland
NCT03246841	Not specified	ACTIVE_NOT_RECRUITING	Investigation of Tumour Spectrum of Germline Mutations in Breast and Ovarian Cancer Genes.
NCT03294343	Not specified	UNKNOWN	Risk-Reducing Surgeries for Hereditary Ovarian Cancer
NCT03421327	Not specified	COMPLETED	Genetic Risk: Whether, When, and How to Tell Adolescents
NCT03510689	Not specified	COMPLETED	Genetics and Heart Health After Cancer Therapy
NCT03511690	Not specified	COMPLETED	Testing an Intelligent Tutoring System to Enhance Genetic Risk Assessment
NCT03784859	Not specified	COMPLETED	Tissue Expansion in Breast Reconstruction Without Drains
NCT03979612	Not specified	UNKNOWN	Evaluation of the Adhesion to the GENEPY Network
NCT04197856	Not specified	ACTIVE_NOT_RECRUITING	Direct Information to At-risk Relatives
NCT04407611	Not specified	COMPLETED	Scalable Communication Modalities for Returning Genetic Research Results
NCT04508764	Not specified	TERMINATED	Implementation of the Families Accelerating Cascade Testing Toolkit (FACTT) for Hereditary Breast and Ovarian Cancer and Lynch Syndrome