MSANTD3

Summary

MSANTD3 (Myb/SANT DNA binding domain containing 3, HGNC:23370) is a protein-coding gene on chromosome 9q31.1, encoding Myb/SANT-like DNA-binding domain-containing protein 3 (Q96H12).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 14 total
• MANE Select transcript: NM_080655

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23370
Approved symbol	MSANTD3
Name	Myb/SANT DNA binding domain containing 3
Location	9q31.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC17337
Ensembl gene	ENSG00000066697
Ensembl biotype	protein_coding
Entrez	91283

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 11 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000374885, ENST00000374886, ENST00000395067, ENST00000398977, ENST00000489377, ENST00000613183, ENST00000622639, ENST00000882519, ENST00000914271, ENST00000914272, ENST00000914273, ENST00000967989

RefSeq mRNA: 4 — MANE Select: NM_080655 NM_001198805, NM_001198806, NM_001198807, NM_080655

CCDS: CCDS56579, CCDS6749

Canonical transcript exons

ENST00000395067 — 3 exons

Exon	Start	End
ENSE00001465026	100441906	100442356
ENSE00001659938	100427143	100427393
ENSE00003613463	100450557	100451734

Expression profiles

Bgee: expression breadth ubiquitous, 245 present calls, max score 94.38.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.5081 / max 355.3866, expressed in 1810 samples.

FANTOM5 promoters (11 alternative TSS)

Promoter ID	TPM avg	Samples expressed
97711	5.9125	1661
97714	4.9053	1598
97712	4.8406	1647
97715	4.0353	1575
97716	2.5533	1357
97719	0.7450	275
97713	0.6470	421
97710	0.3623	168
97709	0.3379	159
97718	0.1454	65

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cartilage tissue	UBERON:0002418	94.38	gold quality
ganglionic eminence	UBERON:0004023	92.77	gold quality
cortical plate	UBERON:0005343	92.15	gold quality
islet of Langerhans	UBERON:0000006	91.99	gold quality
stromal cell of endometrium	CL:0002255	91.67	gold quality
oviduct epithelium	UBERON:0004804	91.47	gold quality
buccal mucosa cell	CL:0002336	90.08	gold quality
gastrocnemius	UBERON:0001388	87.37	gold quality
monocyte	CL:0000576	87.16	gold quality
muscle of leg	UBERON:0001383	87.01	gold quality
leukocyte	CL:0000738	86.51	gold quality
oocyte	CL:0000023	86.21	gold quality
prefrontal cortex	UBERON:0000451	86.17	gold quality
ventricular zone	UBERON:0003053	86.15	gold quality
smooth muscle tissue	UBERON:0001135	86.08	gold quality
secondary oocyte	CL:0000655	85.66	gold quality
heart left ventricle	UBERON:0002084	85.63	gold quality
cardiac ventricle	UBERON:0002082	85.30	gold quality
pancreas	UBERON:0001264	85.09	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.01	gold quality
gall bladder	UBERON:0002110	84.96	gold quality
hindlimb stylopod muscle	UBERON:0004252	84.93	gold quality
heart	UBERON:0000948	84.39	gold quality
tendon	UBERON:0000043	84.30	gold quality
right atrium auricular region	UBERON:0006631	84.30	gold quality
cardiac atrium	UBERON:0002081	84.05	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	84.05	gold quality
apex of heart	UBERON:0002098	83.98	gold quality
calcaneal tendon	UBERON:0003701	83.75	gold quality
vermiform appendix	UBERON:0001154	83.59	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.22

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA1523.1	MSANTD3	Myb/SANT domain factors
MA1523.2	MSANTD3	Myb/SANT domain factors

JASPAR matrix evidence (PMIDs): PMID:12354778

miRNA regulators (miRDB)

44 targeting MSANTD3, 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-4531	99.99	69.70	3181
HSA-MIR-196A-1-3P	99.99	72.15	2772
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-3529-3P	99.90	73.55	3045
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-10393-5P	99.65	68.01	1368
HSA-MIR-4452	99.50	68.45	1493
HSA-MIR-12131	99.48	68.72	1673
HSA-MIR-3915	99.45	68.49	1905
HSA-MIR-4735-5P	99.43	68.49	1780
HSA-MIR-449B-3P	99.20	67.24	1047
HSA-MIR-892C-5P	99.16	70.56	2116
HSA-MIR-6071	99.16	67.77	1780
HSA-MIR-548AS-3P	99.12	69.12	2294
HSA-MIR-6074	98.89	69.64	2187
HSA-MIR-1245B-5P	98.88	66.55	576
HSA-MIR-3142	98.88	66.09	529
HSA-MIR-606	98.72	67.34	960
HSA-MIR-384	98.71	67.34	1229
HSA-MIR-1301-3P	98.64	68.27	1071
HSA-MIR-5047	98.64	68.62	1035
HSA-MIR-3668	98.52	68.76	951
HSA-MIR-3944-5P	98.50	67.55	997
HSA-MIR-548AT-3P	98.37	64.98	580
HSA-MIR-548AY-3P	98.37	65.14	562

Literature-anchored findings (GeneRIF, showing 2)

• MSANTD3 rearrangement as a recurrent event in salivary gland AcCC (PMID:28212443)
• we find the HTN3-MSANTD3 gene fusion to be a recurrent event in acinic cell carcinoma with prominent serous differentiation and an indolent clinical course (PMID:30520817)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Msantd3	ENSMUSG00000039693
rattus_norvegicus	Msantd3	ENSRNOG00000008159

Protein

Protein identifiers

Myb/SANT-like DNA-binding domain-containing protein 3 — Q96H12 (reviewed: Q96H12)

All UniProt accessions (3): Q96H12, X6R907, X6RL08

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed in brain.

Similarity. Belongs to the MSANTD3 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96H12-1	1	yes
Q96H12-2	2

RefSeq proteins (4): NP_001185734, NP_001185735, NP_001185736, NP_542386* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR028002	Myb_DNA-bind_5	Domain

Pfam: PF13873

UniProt features (9 total): modified residue 3, splice variant 2, chain 1, domain 1, coiled-coil region 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96H12-F1	74.81	0.52

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 (4): 96, 98, 274, 154

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 108 (showing top): LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN, LIAO_METASTASIS, ACEVEDO_LIVER_CANCER_UP, ZHAN_MULTIPLE_MYELOMA_CD1_AND_CD2_DN, CHEN_METABOLIC_SYNDROM_NETWORK, CHYLA_CBFA2T3_TARGETS_UP, BRUINS_UVC_RESPONSE_EARLY_LATE, KOINUMA_TARGETS_OF_SMAD2_OR_SMAD3, KRIEG_HYPOXIA_NOT_VIA_KDM3A, CSR_EARLY_UP.V1_UP, HES2_TARGET_GENES, MAFG_TARGET_GENES, NFE2L1_TARGET_GENES, TFEB_TARGET_GENES, UBN1_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

298 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MSANTD3	HTN3	P15516	621
MSANTD3	NR4A3	Q92570	497
MSANTD3	MSANTD2	Q6P1R3	481
MSANTD3	PRB3	Q04118	445
MSANTD3	SUV39H1	O43463	415
MSANTD3	ANO1	Q5XXA6	415
MSANTD3	TBC1D21	Q8IYX1	401
MSANTD3	ZNF275	Q9NSD4	393
MSANTD3	RUNDC1	Q96C34	367
MSANTD3	ZYG11A	Q6WRX3	353
MSANTD3	ZNF232	Q9UNY5	350
MSANTD3	TMEM245	Q9H330	348
MSANTD3	ZNF768	Q9H5H4	323
MSANTD3	CRTC1	Q6UUV9	318
MSANTD3	MRPL49	Q13405	314

IntAct

37 interactions, top by confidence:

A	B	Type	Score
MSANTD3	CHAT	psi-mi:“MI:0915”(physical association)	0.560
MSANTD3	FGFR3	psi-mi:“MI:0915”(physical association)	0.560
GRIN2C	MSANTD3	psi-mi:“MI:0915”(physical association)	0.560
MSANTD3	GSN	psi-mi:“MI:0915”(physical association)	0.560
MSANTD3		psi-mi:“MI:0915”(physical association)	0.560
MSANTD3	SMC3	psi-mi:“MI:0915”(physical association)	0.400
MSANTD3	FXR1	psi-mi:“MI:0915”(physical association)	0.370
MSANTD3	FXR2	psi-mi:“MI:0915”(physical association)	0.370
MSANTD3	TSC1	psi-mi:“MI:0915”(physical association)	0.370
MSANTD3	SUV39H1	psi-mi:“MI:0915”(physical association)	0.370
GNAS	MSANTD3	psi-mi:“MI:0915”(physical association)	0.370
PFN2	MSANTD3	psi-mi:“MI:0915”(physical association)	0.370
MSANTD3	TMEM129	psi-mi:“MI:0915”(physical association)	0.370
VSTM2A	MSANTD3	psi-mi:“MI:0915”(physical association)	0.370
MSANTD3	BMPR1A	psi-mi:“MI:0915”(physical association)	0.370
MSANTD3	BUB1	psi-mi:“MI:0915”(physical association)	0.370
CDH1	MSANTD3	psi-mi:“MI:0915”(physical association)	0.370
MSANTD3	MCC	psi-mi:“MI:0915”(physical association)	0.370
MSANTD3	MLH3	psi-mi:“MI:0915”(physical association)	0.370
MSANTD3	MUTYH	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (23): MSANTD3 (Two-hybrid), MSANTD3 (Proximity Label-MS), MSANTD3 (Affinity Capture-MS), SMC3 (Proximity Label-MS), MSANTD3 (Two-hybrid), MSANTD3 (Two-hybrid), MSANTD3 (Two-hybrid), MSANTD3 (Two-hybrid), MSANTD3 (Two-hybrid), MSANTD3 (Two-hybrid), MSANTD3 (Two-hybrid), GNAS (Two-hybrid), PFN2 (Two-hybrid), TMEM129 (Two-hybrid), VSTM2A (Two-hybrid)

ESM2 similar proteins: A1YG61, A2T737, A4IGQ8, B5XCB8, O60934, O70273, P28715, Q08B72, Q0III0, Q13546, Q28J92, Q2KJE0, Q32LN0, Q3B8D4, Q3T0G1, Q3US16, Q4R3Q6, Q5R4U3, Q5RCE4, Q5RCV3, Q5SZJ8, Q5U208, Q5U560, Q5VVJ2, Q60855, Q69Z66, Q6DDT6, Q6DIN8, Q6IR68, Q6PFX2, Q6TGZ4, Q7L4P6, Q7ZYM8, Q86VP1, Q86VV4, Q8BSV3, Q8C6D4, Q8CHW1, Q8IW35, Q8N302

Diamond homologs: Q0III0, Q28J92, Q7ZYM8, Q96H12, Q9CR78

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	13
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

957 predictions. Top by Δscore:

Variant	Effect	Δscore
9:100427389:TGCAG:T	donor_loss	1.0000
9:100427390:GCAGG:G	donor_loss	1.0000
9:100427391:CAGGT:C	donor_loss	1.0000
9:100427392:AG:A	donor_loss	1.0000
9:100427393:GGTAG:G	donor_loss	1.0000
9:100427394:G:GA	donor_loss	1.0000
9:100427395:T:G	donor_loss	1.0000
9:100441904:A:AG	acceptor_gain	1.0000
9:100441905:G:GG	acceptor_gain	1.0000
9:100441905:GGATA:G	acceptor_gain	1.0000
9:100444200:G:GT	donor_gain	1.0000
9:100450555:A:AG	acceptor_gain	1.0000
9:100450556:G:GG	acceptor_gain	1.0000
9:100450862:G:GT	donor_gain	1.0000
9:100441901:TACA:T	acceptor_loss	0.9900
9:100441903:CA:C	acceptor_loss	0.9900
9:100441904:A:C	acceptor_loss	0.9900
9:100441904:AG:A	acceptor_gain	0.9900
9:100441905:GG:G	acceptor_gain	0.9900
9:100441905:GGAT:G	acceptor_gain	0.9900
9:100442353:CAAG:C	donor_loss	0.9900
9:100442357:G:T	donor_loss	0.9900
9:100444190:T:G	donor_gain	0.9900
9:100450551:TTTCA:T	acceptor_loss	0.9900
9:100450552:TTCA:T	acceptor_loss	0.9900
9:100450554:CA:C	acceptor_loss	0.9900
9:100450555:A:AC	acceptor_loss	0.9900
9:100450556:G:GT	acceptor_loss	0.9900
9:100450556:GA:G	acceptor_gain	0.9900
9:100450556:GAATC:G	acceptor_gain	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000193863 (9:100447307 A>G), RS1000303119 (9:100440592 T>TG), RS1000438601 (9:100440929 A>C,G,T), RS1000506854 (9:100434694 C>G), RS1000652341 (9:100447599 T>G), RS1000702653 (9:100442677 C>T), RS1000704514 (9:100434459 G>A), RS1000830916 (9:100441104 T>A,G), RS1001012642 (9:100429078 G>A), RS1001015241 (9:100428309 T>C), RS1001028555 (9:100449061 G>A), RS1001096157 (9:100440576 G>T), RS1001244692 (9:100445910 T>C), RS1001399449 (9:100435855 T>A), RS1001513014 (9:100432638 A>G)

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
GCST010106_5	Conjunctival UV autofluorescence (CUVAF)	7.000000e-07

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004731	eye measurement
EFO:0010729	sun exposure measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
trichostatin A	affects cotreatment, decreases expression, affects expression	3
Aflatoxin B1	affects expression, increases expression	3
Arsenic	increases abundance, increases expression, affects cotreatment	2
Benzo(a)pyrene	increases expression	2
Estradiol	affects cotreatment, increases expression	2
Valproic Acid	affects expression, decreases expression	2
Cyclosporine	increases expression	2
TAK-243	decreases sumoylation	1
triphenyl phosphate	affects expression	1
sodium arsenate	increases abundance, increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
coumarin	increases phosphorylation	1
avobenzone	increases expression	1
2-palmitoylglycerol	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
ICG 001	increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Temozolomide	decreases expression	1
Sunitinib	increases expression	1
Air Pollutants, Occupational	affects expression	1
Caffeine	decreases phosphorylation	1
Diethylhexyl Phthalate	decreases expression	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Phthalic Acids	increases methylation	1
Quercetin	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_E1KT	HyCyte HeLa KO-hMSANTD3	Cancer cell line	Female

Clinical trials (associated diseases)

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