MSANTD4

Summary

MSANTD4 (Myb/SANT DNA binding domain containing 4 with coiled-coils, HGNC:29383) is a protein-coding gene on chromosome 11q22.3, encoding Myb/SANT-like DNA-binding domain-containing protein 4 (Q8NCY6).

Located in nucleus.

Source: NCBI Gene 84437 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 47 total
• MANE Select transcript: NM_032424

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29383
Approved symbol	MSANTD4
Name	Myb/SANT DNA binding domain containing 4 with coiled-coils
Location	11q22.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000170903
Ensembl biotype	protein_coding
Entrez	84437

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 13 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000301919, ENST00000529805, ENST00000530108, ENST00000530788, ENST00000534458, ENST00000874422, ENST00000874423, ENST00000874424, ENST00000874425, ENST00000874426, ENST00000874427, ENST00000874428, ENST00000917869, ENST00000917870

RefSeq mRNA: 5 — MANE Select: NM_032424 NM_001318747, NM_001318748, NM_001318749, NM_001318750, NM_032424

CCDS: CCDS31663

Canonical transcript exons

ENST00000301919 — 3 exons

Exon	Start	End
ENSE00001135045	106007899	106010110
ENSE00001137591	106020962	106022240
ENSE00001251836	106010456	106011067

Expression profiles

Bgee: expression breadth ubiquitous, 253 present calls, max score 94.40.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.5031 / max 215.3042, expressed in 1614 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
122095	5.7640	1591
122094	0.7392	432

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tendon of biceps brachii	UBERON:0008188	94.40	gold quality
medial globus pallidus	UBERON:0002477	92.95	gold quality
calcaneal tendon	UBERON:0003701	92.11	gold quality
tendon	UBERON:0000043	92.05	gold quality
endothelial cell	CL:0000115	91.18	gold quality
ganglionic eminence	UBERON:0004023	91.11	gold quality
embryo	UBERON:0000922	91.10	gold quality
globus pallidus	UBERON:0001875	90.75	gold quality
tibialis anterior	UBERON:0001385	89.91	silver quality
heart right ventricle	UBERON:0002080	89.84	gold quality
corpus callosum	UBERON:0002336	89.45	gold quality
cortical plate	UBERON:0005343	89.45	gold quality
pigmented layer of retina	UBERON:0001782	89.38	gold quality
cauda epididymis	UBERON:0004360	89.38	gold quality
islet of Langerhans	UBERON:0000006	89.35	gold quality
cerebellar vermis	UBERON:0004720	87.97	gold quality
left ventricle myocardium	UBERON:0006566	87.32	gold quality
deltoid	UBERON:0001476	87.01	gold quality
ventricular zone	UBERON:0003053	86.88	gold quality
biceps brachii	UBERON:0001507	86.86	gold quality
adrenal tissue	UBERON:0018303	86.81	gold quality
Brodmann (1909) area 46	UBERON:0006483	86.75	gold quality
germinal epithelium of ovary	UBERON:0001304	86.56	gold quality
substantia nigra pars compacta	UBERON:0001965	85.69	gold quality
colonic epithelium	UBERON:0000397	85.66	gold quality
myocardium	UBERON:0002349	85.39	gold quality
lateral nuclear group of thalamus	UBERON:0002736	85.31	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	85.09	gold quality
postcentral gyrus	UBERON:0002581	85.07	gold quality
cardiac muscle of right atrium	UBERON:0003379	84.93	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.86

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2558.1	MSANTD4	Myb-SANT

JASPAR matrix evidence (PMIDs): PMID:39605368

miRNA regulators (miRDB)

101 targeting MSANTD4, 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-656-3P	100.00	72.15	2788
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-548Y	99.94	71.28	3514
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	msantd4	ENSDARG00000018040
mus_musculus	Msantd4	ENSMUSG00000041124
rattus_norvegicus	Msantd4	ENSRNOG00000022245

Protein

Protein identifiers

Myb/SANT-like DNA-binding domain-containing protein 4 — Q8NCY6 (reviewed: Q8NCY6)

Alternative names: Myb/SANT-like DNA-binding domain containing 4 with coiled-coils

All UniProt accessions (4): Q8NCY6, E9PKC8, E9PLV2, E9PRK0

RefSeq proteins (5): NP_001305676, NP_001305677, NP_001305678, NP_001305679, NP_115800* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026162	MSANTD4	Family
IPR028002	Myb_DNA-bind_5	Domain

Pfam: PF13873

UniProt features (12 total): cross-link 6, modified residue 2, chain 1, domain 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NCY6-F1	70.10	0.25

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 (8): 254, 273, 106, 188, 9, 114, 142, 237

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 81 (showing top): chr11q22, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GARY_CD5_TARGETS_DN, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, SENESE_HDAC1_TARGETS_UP, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, ZHAN_MULTIPLE_MYELOMA_MS_DN, VANOEVELEN_MYOGENESIS_SIN3A_TARGETS, ASH1L_TARGET_GENES, CEBPZ_TARGET_GENES, CHAMP1_TARGET_GENES, CREB3L4_TARGET_GENES, LHX9_TARGET_GENES, PAX7_TARGET_GENES, PRKDC_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

516 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MSANTD4	TMEM107	Q6UX40	544
MSANTD4	CCDC117	Q8IWD4	533
MSANTD4	FAM110B	Q8TC76	506
MSANTD4	ANKRD49	Q8WVL7	489
MSANTD4	AP1S2	P56377	479
MSANTD4	SDHAF3	Q9NRP4	474
MSANTD4	VEPH1	Q14D04	452
MSANTD4	AASDHPPT	Q9NRN7	448
MSANTD4	KBTBD3	Q8NAB2	436
MSANTD4	ZDHHC4	Q9NPG8	432
MSANTD4	XKR4	Q5GH76	425
MSANTD4	ENY2	Q9NPA8	421
MSANTD4	CMC2	Q9NRP2	419
MSANTD4	MRPS15	P82914	417
MSANTD4	FBXO8	Q9NRD0	405

IntAct

33 interactions, top by confidence:

A	B	Type	Score
RALBP1	MSANTD4	psi-mi:“MI:0915”(physical association)	0.740
RALBP1	JUN	psi-mi:“MI:0914”(association)	0.640
BYSL	MSANTD4	psi-mi:“MI:0915”(physical association)	0.560
MSANTD4	DAXX	psi-mi:“MI:0915”(physical association)	0.560
MSANTD4	LNX1	psi-mi:“MI:0915”(physical association)	0.560
MSANTD4	PNKP	psi-mi:“MI:0915”(physical association)	0.560
GNGT1	MSANTD4	psi-mi:“MI:0915”(physical association)	0.560
PSMA1	MSANTD4	psi-mi:“MI:0915”(physical association)	0.560
TCEA2	MSANTD4	psi-mi:“MI:0915”(physical association)	0.560
PARD6B	PARD3	psi-mi:“MI:0914”(association)	0.350
RALBP1	AP2A1	psi-mi:“MI:0914”(association)	0.350
DYRK1A	TEX13D	psi-mi:“MI:0914”(association)	0.350
SYNGAP1	POM121C	psi-mi:“MI:0914”(association)	0.350
GOLGA6A	STRN	psi-mi:“MI:0914”(association)	0.350
PTBP3		psi-mi:“MI:0914”(association)	0.350
RALBP1	MSANTD4	psi-mi:“MI:0915”(physical association)	0.000
DAXX	MSANTD4	psi-mi:“MI:0915”(physical association)	0.000
LNX1	MSANTD4	psi-mi:“MI:0915”(physical association)	0.000
TCEA2	MSANTD4	psi-mi:“MI:0915”(physical association)	0.000
GNGT1	MSANTD4	psi-mi:“MI:0915”(physical association)	0.000
PSMA1	MSANTD4	psi-mi:“MI:0915”(physical association)	0.000
PNKP	MSANTD4	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (20): MSANTD4 (Affinity Capture-MS), MSANTD4 (Affinity Capture-MS), MSANTD4 (Two-hybrid), MSANTD4 (Two-hybrid), MSANTD4 (Two-hybrid), MSANTD4 (Two-hybrid), MSANTD4 (Two-hybrid), TCEA2 (Two-hybrid), DAXX (Two-hybrid), MSANTD4 (Affinity Capture-MS), MSANTD4 (Affinity Capture-MS), MSANTD4 (Affinity Capture-MS), MSANTD4 (Affinity Capture-MS), MSANTD4 (Reconstituted Complex), MSANTD4 (Affinity Capture-MS)

ESM2 similar proteins: A0A1W2PQ72, D3ZXW3, F4JZ68, O13839, O17862, O35260, O73622, O95073, P01103, P06536, P06537, P06876, P10242, P21705, P32314, P40847, P46200, P49843, P49844, P59667, P92189, Q09262, Q09663, Q0P4H6, Q10026, Q18171, Q18248, Q1LXZ9, Q22811, Q2KJB9, Q501L3, Q5H9I0, Q66J77, Q6FSB1, Q6GLA1, Q6ZTZ1, Q757W2, Q7TSZ8, Q7ZXG4, Q8AYI2

Diamond homologs: Q2KJB9, Q501L3, Q6GLA1, Q8NCY6, Q91YU3, A7MBH3, G3V7P1, O15400, O70257, Q3ZBT5, Q5R602, Q5RBW6, Q5ZI27, Q69YI7, Q6PFD7, Q86Y82, Q96NA8, Q9BE21, Q9ER00

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	43
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

628 predictions. Top by Δscore:

Variant	Effect	Δscore
11:106010111:C:CC	acceptor_gain	1.0000
11:106011063:AATTC:A	acceptor_gain	1.0000
11:106011064:ATTC:A	acceptor_gain	1.0000
11:106011065:TTC:T	acceptor_gain	1.0000
11:106011066:TC:T	acceptor_gain	1.0000
11:106011066:TCC:T	acceptor_loss	1.0000
11:106011067:CC:C	acceptor_gain	1.0000
11:106011068:C:CC	acceptor_gain	1.0000
11:106011068:CTA:C	acceptor_loss	1.0000
11:106010106:TCAAA:T	acceptor_gain	0.9900
11:106010107:CAAA:C	acceptor_gain	0.9900
11:106010107:CAAAC:C	acceptor_gain	0.9900
11:106010452:TTA:T	donor_loss	0.9900
11:106010453:TACTT:T	donor_loss	0.9900
11:106010454:A:AC	donor_gain	0.9900
11:106010454:AC:A	donor_loss	0.9900
11:106010455:C:CG	donor_gain	0.9900
11:106010455:CTT:C	donor_gain	0.9900
11:106011064:ATTCC:A	acceptor_gain	0.9900
11:106011065:TTCCT:T	acceptor_gain	0.9900
11:106010108:AAA:A	acceptor_gain	0.9800
11:106010108:AAAC:A	acceptor_loss	0.9800
11:106010109:AAC:A	acceptor_loss	0.9800
11:106010110:ACTA:A	acceptor_loss	0.9800
11:106010112:T:C	acceptor_loss	0.9800
11:106010450:ACTT:A	donor_loss	0.9800
11:106010455:CT:C	donor_gain	0.9800
11:106011066:TCCT:T	acceptor_gain	0.9800
11:106011068:C:T	acceptor_gain	0.9800
11:106021508:C:CT	acceptor_gain	0.9800

AlphaMissense

2288 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:106010701:A:C	Y73D	1.000
11:106010702:C:A	R72S	1.000
11:106010702:C:G	R72S	1.000
11:106010703:C:A	R72M	1.000
11:106010703:C:G	R72T	1.000
11:106010708:T:A	K70N	1.000
11:106010708:T:G	K70N	1.000
11:106010726:C:A	R64S	1.000
11:106010726:C:G	R64S	1.000
11:106010727:C:A	R64M	1.000
11:106010727:C:G	R64T	1.000
11:106010774:C:A	W48C	1.000
11:106010774:C:G	W48C	1.000
11:106010775:C:G	W48S	1.000
11:106010776:A:G	W48R	1.000
11:106010776:A:T	W48R	1.000
11:106010786:C:A	K44N	1.000
11:106010786:C:G	K44N	1.000
11:106010859:A:G	L20P	1.000
11:106010859:A:T	L20H	1.000
11:106010882:A:C	F12L	1.000
11:106010882:A:T	F12L	1.000
11:106010883:A:C	F12C	1.000
11:106010883:A:G	F12S	1.000
11:106010884:A:G	F12L	1.000
11:106010885:A:C	N11K	1.000
11:106010885:A:T	N11K	1.000
11:106010893:T:C	K9E	1.000
11:106010894:C:A	R8S	1.000
11:106010894:C:G	R8S	1.000

dbSNP variants (sampled 300 via entrez): RS1000200735 (11:106013800 T>C), RS1000228572 (11:106008928 C>T), RS1000304806 (11:106020649 T>TGACAGCAGC), RS1000348247 (11:106018543 T>C), RS1000789696 (11:106017425 T>C), RS1000893512 (11:106012526 C>A,T), RS1000903910 (11:106017148 T>A,C), RS1001378745 (11:106010252 G>T), RS1001417315 (11:106023218 C>T), RS1001534841 (11:106021584 C>T), RS1001974941 (11:106021908 C>CCT), RS1002098651 (11:106015187 G>A,T), RS1002106465 (11:106013737 C>G), RS1002279572 (11:106015480 T>C), RS1002597442 (11:106011863 A>T)

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

2 associations (top):

Study	Trait	p-value
GCST009391_1371	Metabolite levels	3.000000e-06
GCST010002_247	Refractive error	4.000000e-39

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010367	lysophosphatidylethanolamine 18:0 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, increases expression	3
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
FR900359	decreases phosphorylation	1
bisphenol F	affects cotreatment, increases expression	1
TAK-243	increases sumoylation	1
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
trichostatin A	decreases expression	1
sodium arsenite	increases abundance, increases expression	1
coumarin	decreases phosphorylation	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	1
ICG 001	increases expression	1
abrine	increases expression	1
dorsomorphin	decreases expression, affects cotreatment	1
Temozolomide	increases expression	1
Vorinostat	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	increases abundance, increases expression	1
Atrazine	decreases expression	1
Cadmium	increases expression	1
Coal	decreases expression, increases abundance	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Smoke	decreases expression, increases abundance	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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