VWA5B2

Summary

VWA5B2 (von Willebrand factor A domain containing 5B2, HGNC:25144) is a protein-coding gene on chromosome 3q27.1, encoding von Willebrand factor A domain-containing protein 5B2 (Q8N398).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 201 total
• MANE Select transcript: NM_001390846

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25144
Approved symbol	VWA5B2
Name	von Willebrand factor A domain containing 5B2
Location	3q27.1
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp761K032, LOC90113
Ensembl gene	ENSG00000145198
Ensembl biotype	protein_coding
Entrez	90113

Gene structure

Transcript identifiers

Ensembl transcripts: 32 — 27 protein_coding, 4 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000273794, ENST00000461141, ENST00000474580, ENST00000493493, ENST00000497229, ENST00000691901, ENST00000911178, ENST00000911179, ENST00000911180, ENST00000911181, ENST00000911182, ENST00000911183, ENST00000911184, ENST00000911185, ENST00000911186, ENST00000911187, ENST00000911188, ENST00000911189, ENST00000911190, ENST00000911191, ENST00000911192, ENST00000916216, ENST00000947729, ENST00000947730, ENST00000947731, ENST00000947732, ENST00000947733, ENST00000947734, ENST00000947735, ENST00000947736, ENST00000947737, ENST00000947738

RefSeq mRNA: 10 — MANE Select: NM_001390846 NM_001320373, NM_001390839, NM_001390840, NM_001390841, NM_001390842, NM_001390843, NM_001390844, NM_001390846, NM_001390847, NM_138345

CCDS: CCDS54686

Canonical transcript exons

ENST00000691901 — 20 exons

Exon	Start	End
ENSE00001320679	184234631	184234755
ENSE00001529720	184230747	184230917
ENSE00001754164	184233178	184233397
ENSE00003499130	184237226	184237411
ENSE00003504034	184241187	184241404
ENSE00003556516	184238303	184238474
ENSE00003558691	184236343	184236551
ENSE00003567025	184236152	184236262
ENSE00003570823	184239394	184239583
ENSE00003614302	184236638	184236749
ENSE00003619671	184240791	184240928
ENSE00003622911	184239689	184240036
ENSE00003628926	184235153	184235308
ENSE00003632143	184241490	184242329
ENSE00003636180	184241024	184241107
ENSE00003637027	184238563	184238873
ENSE00003648906	184234266	184234397
ENSE00003654824	184233576	184233733
ENSE00003926516	184230380	184230667
ENSE00003933994	184229585	184229713

Expression profiles

Bgee: expression breadth ubiquitous, 152 present calls, max score 97.10.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0467 / max 37.4669, expressed in 9 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
40152	0.0283	4
40151	0.0184	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	97.10	gold quality
right adrenal gland cortex	UBERON:0035827	96.87	gold quality
right adrenal gland	UBERON:0001233	96.68	gold quality
right frontal lobe	UBERON:0002810	96.34	gold quality
cerebellar hemisphere	UBERON:0002245	96.30	gold quality
cerebellar cortex	UBERON:0002129	96.08	gold quality
left adrenal gland cortex	UBERON:0035825	95.72	gold quality
left adrenal gland	UBERON:0001234	95.62	gold quality
anterior cingulate cortex	UBERON:0009835	93.25	gold quality
Brodmann (1909) area 9	UBERON:0013540	92.96	gold quality
cerebellum	UBERON:0002037	92.79	gold quality
adrenal cortex	UBERON:0001235	92.31	gold quality
adrenal gland	UBERON:0002369	89.87	gold quality
amygdala	UBERON:0001876	89.80	gold quality
prefrontal cortex	UBERON:0000451	88.70	gold quality
adenohypophysis	UBERON:0002196	88.26	gold quality
hypothalamus	UBERON:0001898	88.09	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	87.57	gold quality
nucleus accumbens	UBERON:0001882	87.49	gold quality
putamen	UBERON:0001874	86.92	gold quality
pituitary gland	UBERON:0000007	86.74	gold quality
caudate nucleus	UBERON:0001873	86.41	gold quality
neocortex	UBERON:0001950	84.71	gold quality
frontal cortex	UBERON:0001870	84.08	gold quality
islet of Langerhans	UBERON:0000006	83.72	gold quality
right uterine tube	UBERON:0001302	83.35	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.94	gold quality
forebrain	UBERON:0001890	81.83	gold quality
brain	UBERON:0000955	81.78	gold quality
cerebral cortex	UBERON:0000956	81.24	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-125970	yes	5.97
E-ANND-3	yes	5.79

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

38 targeting VWA5B2, 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-574-5P	100.00	66.01	989
HSA-MIR-4481	100.00	66.42	1669
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-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-4745-5P	99.98	65.95	1028
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-448	99.79	72.37	2103
HSA-MIR-4658	99.77	64.94	514
HSA-MIR-6790-5P	99.77	65.24	505
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-6715B-5P	99.64	69.63	1420
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-6797-5P	99.61	66.55	2084
HSA-MIR-4472	99.56	66.08	1478

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	vwa5b2	ENSDARG00000075886
mus_musculus	Vwa5b2	ENSMUSG00000046613
rattus_norvegicus	Vwa5b2	ENSRNOG00000001707

Paralogs (11): ITIH4 (ENSG00000055955), ITIH1 (ENSG00000055957), ITIH6 (ENSG00000102313), PARP4 (ENSG00000102699), VWA5A (ENSG00000110002), ITIH5 (ENSG00000123243), ITIH2 (ENSG00000151655), VWA5B1 (ENSG00000158816), ITIH3 (ENSG00000162267), VWA3B (ENSG00000168658), VWA3A (ENSG00000175267)

Protein

Protein identifiers

von Willebrand factor A domain-containing protein 5B2 — Q8N398 (reviewed: Q8N398)

All UniProt accessions (1): Q8N398

RefSeq proteins (10): NP_001307302, NP_001377768, NP_001377769, NP_001377770, NP_001377771, NP_001377772, NP_001377773, NP_001377775, NP_001377776, NP_612354 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002035	VWF_A	Domain
IPR013694	VIT	Domain
IPR036465	vWFA_dom_sf	Homologous_superfamily
IPR052627	VWA_domain-containing	Family

Pfam: PF13757, PF13768

UniProt features (14 total): region of interest 6, compositionally biased region 4, domain 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N398-F1	65.54	0.25

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 58 (showing top): LEIN_PONS_MARKERS, MARTENS_TRETINOIN_RESPONSE_DN, ZWANG_CLASS_1_TRANSIENTLY_INDUCED_BY_EGF, GSE13547_WT_VS_ZFX_KO_BCELL_ANTI_IGM_STIM_12H_UP, MIER1_TARGET_GENES, NABA_ECM_GLYCOPROTEINS, RYBP_TARGET_GENES, ZNF223_TARGET_GENES, ZNF391_TARGET_GENES, ZNF423_TARGET_GENES, MIR4728_5P, MIR6785_5P, MIR137_3P, MIR32_5P, MIR92A_3P

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

818 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
VWA5B2	CLBA1	Q96F83	610
VWA5B2	LRWD1	Q9UFC0	483
VWA5B2	C2orf81	A6NN90	477
VWA5B2	KIF9	Q9HAQ2	474
VWA5B2	FAM131A	Q6UXB0	469
VWA5B2	SH3RF3	Q8TEJ3	441
VWA5B2	RBM34	P42696	437
VWA5B2	LRATD2	Q96KN1	429
VWA5B2	TICRR	Q7Z2Z1	417
VWA5B2	CEP126	Q9P2H0	416
VWA5B2	RELT	Q969Z4	404
VWA5B2	TEDDM1	Q5T9Z0	398
VWA5B2	MAP6D1	Q9H9H5	390
VWA5B2	LRP3	O75074	383
VWA5B2	ZNF280A	P59817	379

IntAct

30 interactions, top by confidence:

A	B	Type	Score
DNAJB4	DNAJB5	psi-mi:“MI:0914”(association)	0.730
DNAJC7	PLD2	psi-mi:“MI:0914”(association)	0.640
GPR156	PLD2	psi-mi:“MI:0914”(association)	0.640
RCCD1	SPAG9	psi-mi:“MI:0914”(association)	0.640
RAB3A	RAB3B	psi-mi:“MI:0914”(association)	0.530
RAB3A	CHM	psi-mi:“MI:0914”(association)	0.530
D2HGDH	ZSWIM8	psi-mi:“MI:0914”(association)	0.350
LOXL4	ARHGAP32	psi-mi:“MI:0914”(association)	0.350
BAG2	PIK3C2A	psi-mi:“MI:0914”(association)	0.350
TRIM35	APAF1	psi-mi:“MI:0914”(association)	0.350
COMMD5	FANCA	psi-mi:“MI:0914”(association)	0.350
CDRT15P3	PEX1	psi-mi:“MI:0914”(association)	0.350
SPRYD7	SLC25A12	psi-mi:“MI:0914”(association)	0.350
CDK20	CDH11	psi-mi:“MI:0914”(association)	0.350
CHIA	SLC25A16	psi-mi:“MI:0914”(association)	0.350
CIAO2A	MAP2K7	psi-mi:“MI:0914”(association)	0.350
HSPA8	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
LECT2	APOD	psi-mi:“MI:0914”(association)	0.350
MYORG	CLGN	psi-mi:“MI:0914”(association)	0.350
NXPH3	NXPH4	psi-mi:“MI:0914”(association)	0.350
P4HA2	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
SNX21	PI4KA	psi-mi:“MI:0914”(association)	0.350
STBD1	ENDOD1	psi-mi:“MI:0914”(association)	0.350
TTLL1	RGS12	psi-mi:“MI:0914”(association)	0.350
TUBB	VWA8	psi-mi:“MI:0914”(association)	0.350
VSIG4	TMEM223	psi-mi:“MI:0914”(association)	0.350
ZDHHC11	NRP1	psi-mi:“MI:0914”(association)	0.350
XRN1	VWA5B2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (15): VWA5B2 (Affinity Capture-MS), VWA5B2 (Affinity Capture-MS), VWA5B2 (Affinity Capture-MS), VWA5B2 (Affinity Capture-MS), VWA5B2 (Affinity Capture-MS), VWA5B2 (Affinity Capture-MS), VWA5B2 (Affinity Capture-MS), VWA5B2 (Affinity Capture-MS), VWA5B2 (Affinity Capture-MS), VWA5B2 (Affinity Capture-MS), VWA5B2 (Affinity Capture-RNA), VWA5B2 (Protein-peptide), VWA5B2 (Proximity Label-MS), VWA5B2 (Proximity Label-MS), VWA5B2 (Two-hybrid)

ESM2 similar proteins: A1L515, A4D2P6, A6QQD2, A8VU90, E1BDF2, O75808, O88995, P0CG25, P22083, Q0IIA6, Q2TA57, Q3B7L1, Q3MIP1, Q3U5Q7, Q3UR50, Q3UR97, Q3UV16, Q400G9, Q5BKX5, Q5EBM0, Q5GH72, Q5SZI1, Q5TM19, Q5U4P2, Q62994, Q659K9, Q6PRD1, Q7Z736, Q861W0, Q86UR1, Q8BNN1, Q8C0R7, Q8CG70, Q8IUW3, Q8IVL6, Q8N398, Q8NAG6, Q8NCW0, Q8R2H1, Q8VCE9

Diamond homologs: A9Z1V5, C7G046, O00534, Q3UR50, Q54CQ8, Q54DU5, Q54DV3, Q54MG1, Q54MG4, Q55G98, Q5TIE3, Q75WE7, Q8N398

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 52 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.

GO biological processes:

GO term	Partners	Fold	FDR
protein folding	6	13.2×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	188
Likely benign	8
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3116 predictions. Top by Δscore:

Variant	Effect	Δscore
3:184230916:GG:G	donor_gain	1.0000
3:184230917:GG:G	donor_gain	1.0000
3:184235259:C:G	donor_gain	1.0000
3:184235266:G:GT	donor_gain	1.0000
3:184235267:G:GT	donor_gain	1.0000
3:184235270:C:G	donor_gain	1.0000
3:184236258:GTGAT:G	donor_gain	1.0000
3:184236260:GAT:G	donor_gain	1.0000
3:184236262:TGT:T	donor_loss	1.0000
3:184236263:G:GG	donor_gain	1.0000
3:184236263:GTGA:G	donor_loss	1.0000
3:184236264:T:G	donor_loss	1.0000
3:184237199:T:G	acceptor_gain	1.0000
3:184237199:T:TA	acceptor_gain	1.0000
3:184237208:T:A	acceptor_gain	1.0000
3:184237210:T:TA	acceptor_gain	1.0000
3:184237211:G:A	acceptor_gain	1.0000
3:184237215:A:AG	acceptor_gain	1.0000
3:184237216:C:G	acceptor_gain	1.0000
3:184237223:C:G	acceptor_gain	1.0000
3:184237224:A:AG	acceptor_gain	1.0000
3:184237224:AGCT:A	acceptor_gain	1.0000
3:184237224:AGCTG:A	acceptor_gain	1.0000
3:184237225:G:GA	acceptor_gain	1.0000
3:184237225:GC:G	acceptor_gain	1.0000
3:184237225:GCTG:G	acceptor_gain	1.0000
3:184237225:GCTGG:G	acceptor_gain	1.0000
3:184237408:AGGG:A	donor_gain	1.0000
3:184237409:GGG:G	donor_gain	1.0000
3:184237409:GGGG:G	donor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000176468 (3:184230153 C>A), RS1000234255 (3:184230666 C>A), RS1000282456 (3:184239188 G>A), RS1000499334 (3:184229690 T>C), RS1000869495 (3:184242077 C>A,T), RS1001168013 (3:184232519 G>A), RS1001241352 (3:184232073 G>A), RS1001347533 (3:184240050 G>A), RS1001564900 (3:184233642 C>A), RS1001689630 (3:184238494 T>C), RS1001777404 (3:184239869 T>G), RS1002051090 (3:184236511 C>A,G,T), RS1002200843 (3:184227688 G>A,C), RS1002381774 (3:184238304 G>A), RS1002421953 (3:184236905 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST001469_1	Major depressive disorder	5.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
(+)-JQ1 compound	increases expression	3
Resveratrol	affects cotreatment, decreases expression	2
Benzo(a)pyrene	decreases expression, affects methylation	2
aristolochic acid I	increases expression	1
6,7-dimethoxy-2-(pyrrolidin-1-yl)-N-(5-(pyrrolidin-1-yl)pentyl)quinazolin-4-amine	increases expression	1
OTX015	increases expression	1
mivebresib	increases expression	1
methyleugenol	increases expression	1
propionaldehyde	increases expression	1
ethyl-p-hydroxybenzoate	decreases expression	1
beta-lapachone	decreases expression	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
pentanal	increases expression	1
licochalcone B	increases expression	1
bisphenol S	increases expression	1
Acetaminophen	increases expression	1
Aldehydes	increases expression	1
Copper	affects cotreatment, decreases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Phthalic Acids	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Urethane	increases expression	1
Valproic Acid	increases methylation	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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