MSANTD1

Summary

MSANTD1 (Myb/SANT DNA binding domain containing 1, HGNC:33741) is a protein-coding gene on chromosome 4p16.3, encoding Myb/SANT-like DNA-binding domain-containing protein 1 (Q6ZTZ1).

Predicted to be involved in positive regulation of DNA-templated transcription. Predicted to be active in nuclear body.

Source: NCBI Gene 345222 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 60 total
• MANE Select transcript: NM_001042690

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33741
Approved symbol	MSANTD1
Name	Myb/SANT DNA binding domain containing 1
Location	4p16.3
Locus type	gene with protein product
Status	Approved
Aliases	LOC345222
Ensembl gene	ENSG00000188981
Ensembl biotype	protein_coding
Entrez	345222

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 nonsense_mediated_decay

ENST00000438480, ENST00000505599, ENST00000507492, ENST00000510580

RefSeq mRNA: 2 — MANE Select: NM_001042690 NM_001042690, NM_001330620

CCDS: CCDS47003, CCDS82907

Canonical transcript exons

ENST00000438480 — 3 exons

Exon	Start	End
ENSE00001380098	3253207	3253482
ENSE00001688087	3255725	3256613
ENSE00002054626	3249159	3249542

Expression profiles

Bgee: expression breadth ubiquitous, 147 present calls, max score 78.30.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2827 / max 28.0395, expressed in 77 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
46678	0.2483	74
46679	0.0344	18

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of stomach	UBERON:0001199	78.30	gold quality
prefrontal cortex	UBERON:0000451	71.78	gold quality
nucleus accumbens	UBERON:0001882	71.30	gold quality
caudate nucleus	UBERON:0001873	70.03	gold quality
putamen	UBERON:0001874	69.83	gold quality
right frontal lobe	UBERON:0002810	68.91	gold quality
anterior cingulate cortex	UBERON:0009835	68.47	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	68.14	gold quality
Brodmann (1909) area 9	UBERON:0013540	68.00	gold quality
frontal cortex	UBERON:0001870	67.64	gold quality
hypothalamus	UBERON:0001898	67.53	gold quality
neocortex	UBERON:0001950	67.17	gold quality
cerebral cortex	UBERON:0000956	65.27	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	65.01	gold quality
forebrain	UBERON:0001890	64.72	gold quality
lower esophagus mucosa	UBERON:0035834	64.09	gold quality
amygdala	UBERON:0001876	64.03	gold quality
left testis	UBERON:0004533	63.94	gold quality
right testis	UBERON:0004534	63.38	gold quality
brain	UBERON:0000955	63.22	gold quality
hindlimb stylopod muscle	UBERON:0004252	63.16	gold quality
right hemisphere of cerebellum	UBERON:0014890	62.90	gold quality
gastrocnemius	UBERON:0001388	62.63	gold quality
buccal mucosa cell	CL:0002336	62.33	gold quality
cerebellar hemisphere	UBERON:0002245	62.02	gold quality
cerebellar cortex	UBERON:0002129	61.90	gold quality
cortical plate	UBERON:0005343	61.83	gold quality
testis	UBERON:0000473	61.65	gold quality
Ammon’s horn	UBERON:0001954	61.57	gold quality
muscle of leg	UBERON:0001383	61.54	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.76

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2598.1	MSANTD1	Myb-SANT

JASPAR matrix evidence (PMIDs): PMID:39605530

miRNA regulators (miRDB)

30 targeting MSANTD1, 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-4673	100.00	66.64	1490
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-26A-5P	99.78	73.52	2303
HSA-MIR-26B-5P	99.78	73.51	2305
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-4465	99.71	72.56	2096
HSA-MIR-3934-5P	99.67	64.04	846
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-6727-3P	99.49	65.92	1333
HSA-MIR-147B-5P	99.45	70.62	2432
HSA-MIR-889-3P	99.40	69.76	2103
HSA-MIR-5697	99.39	67.74	1249
HSA-MIR-185-5P	99.35	68.60	2497
HSA-MIR-4644	99.35	69.12	2514
HSA-MIR-3160-3P	99.07	64.78	955
HSA-MIR-4695-5P	99.06	64.87	1151
HSA-MIR-548L	99.06	70.90	2560
HSA-MIR-382-3P	98.83	67.10	1074
HSA-MIR-3135B	98.61	65.33	1470
HSA-MIR-31-5P	98.58	68.35	1239
HSA-MIR-4317	98.49	67.09	987
HSA-MIR-1912-5P	97.94	67.98	832
HSA-MIR-4669	97.94	62.71	224
HSA-MIR-5192	96.89	63.35	879
HSA-MIR-616-3P	96.82	66.99	784
HSA-MIR-1287-5P	96.80	65.30	743
HSA-MIR-6735-3P	96.10	63.81	600
HSA-MIR-550B-3P	95.43	67.73	599

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	msantd1	ENSDARG00000078801
mus_musculus	Msantd1	ENSMUSG00000051246
rattus_norvegicus	Msantd1	ENSRNOG00000064777
drosophila_melanogaster	vers	FBGN0011335
drosophila_melanogaster	CG7239	FBGN0031740
drosophila_melanogaster	ssp	FBGN0036248
drosophila_melanogaster	CG18766	FBGN0042111

Protein

Protein identifiers

Myb/SANT-like DNA-binding domain-containing protein 1 — Q6ZTZ1 (reviewed: Q6ZTZ1)

All UniProt accessions (4): D6R9L8, D6RD98, D6RDG6, Q6ZTZ1

UniProt curated annotations — full annotation on UniProt →

RefSeq proteins (2): NP_001036155, NP_001317549 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026095	Myb/SANT-like_DNA-bd_dom_prot	Family
IPR044822	Myb_DNA-bind_4	Domain

Pfam: PF13837

UniProt features (5 total): region of interest 2, chain 1, domain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZTZ1-F1	72.75	0.43

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 27 (showing top): chr4p16, GOCC_NUCLEAR_BODY, WANG_TUMOR_INVASIVENESS_DN, MIR889_3P, MIR4673, MIR4645_5P, GSE11924_TH1_VS_TH17_CD4_TCELL_UP, MIR3135B, GSE13493_DP_VS_CD4INTCD8POS_THYMOCYTE_UP, MANNE_COVID19_COMBINED_COHORT_VS_HEALTHY_DONOR_PLATELETS_UP, DESCARTES_MAIN_FETAL_CCL19_CCL21_POSITIVE_CELLS, GOBP_POSITIVE_REGULATION_OF_RNA_METABOLIC_PROCESS, GSE2706_R848_VS_LPS_8H_STIM_DC_DN, GSE39820_TGFBETA1_VS_TGFBETA3_IN_IL6_IL23A_TREATED_CD4_TCELL_DN, GSE7460_CTRL_VS_TGFB_TREATED_ACT_TCONV_UP

GO Biological Process (1): positive regulation of DNA-templated transcription (GO:0045893)

GO Molecular Function (0):

GO Cellular Component (1): nuclear body (GO:0016604)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA-templated transcription	1
regulation of DNA-templated transcription	1
positive regulation of RNA biosynthetic process	1
nucleoplasm	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

294 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MSANTD1	OR52W1	Q6IF63	571
MSANTD1	SAP130	Q9H0E3	570
MSANTD1	OSTM1	Q86WC4	569
MSANTD1	CATSPER3	Q86XQ3	532
MSANTD1	OR52B2	Q96RD2	519
MSANTD1	OR10S1	Q8NGN2	507
MSANTD1	RCL1	Q9Y2P8	494
MSANTD1	SNUPN	O95149	490
MSANTD1	SNX29	Q8TEQ0	478
MSANTD1	SMOC2	Q9H3U7	448
MSANTD1	LDLRAD1	Q5T700	447
MSANTD1	BLOC1S5	Q8TDH9	409
MSANTD1	SLCO1B7	G3V0H7	405
MSANTD1	MSRB3	Q8IXL7	383
MSANTD1	UFM1	P61960	381

IntAct

0 interactions, top by confidence:

BioGRID (1): MSANTD1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1W2PQ72, A7J1T0, A7J1T2, A7MBB4, A8MZ59, D3ZXW3, M0R5D6, O36371, O43283, O43310, O73622, O95073, P03177, P10242, P21705, P46200, Q0P4H6, Q1HKZ5, Q1HVD1, Q1LVK9, Q22811, Q2NKQ1, Q3KSQ2, Q3UPF5, Q535K8, Q562B4, Q567C6, Q5R8X7, Q5ZI27, Q6DGX3, Q6INH1, Q6J1H4, Q6PEE2, Q6ZTZ1, Q71M44, Q7SXL7, Q80T85, Q8BFX3, Q8BIL2, Q8BKE5

Diamond homologs: Q6ZTZ1, Q8BIL2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	53
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

625 predictions. Top by Δscore:

Variant	Effect	Δscore
4:3249537:G:GG	donor_gain	1.0000
4:3249539:ACAGG:A	donor_loss	1.0000
4:3249540:CAGG:C	donor_loss	1.0000
4:3249541:AG:A	donor_loss	1.0000
4:3249543:GT:G	donor_loss	1.0000
4:3249544:T:G	donor_loss	1.0000
4:3253202:TTCA:T	acceptor_loss	1.0000
4:3253203:TCAG:T	acceptor_loss	1.0000
4:3253204:CA:C	acceptor_loss	1.0000
4:3253205:A:AG	acceptor_gain	1.0000
4:3253205:AG:A	acceptor_gain	1.0000
4:3253206:G:GA	acceptor_gain	1.0000
4:3253206:GG:G	acceptor_gain	1.0000
4:3253206:GGA:G	acceptor_gain	1.0000
4:3253206:GGAA:G	acceptor_gain	1.0000
4:3253206:GGAAA:G	acceptor_gain	1.0000
4:3253473:T:G	donor_gain	1.0000
4:3253473:T:TG	donor_gain	1.0000
4:3253479:TCAG:T	donor_loss	1.0000
4:3253483:GTAGT:G	donor_loss	1.0000
4:3255719:TTCCA:T	acceptor_loss	1.0000
4:3255720:TCCA:T	acceptor_loss	1.0000
4:3255721:CCA:C	acceptor_loss	1.0000
4:3255723:A:AG	acceptor_gain	1.0000
4:3255723:AGGT:A	acceptor_loss	1.0000
4:3255723:AGGTC:A	acceptor_gain	1.0000
4:3255724:G:GC	acceptor_loss	1.0000
4:3255724:G:GG	acceptor_gain	1.0000
4:3255724:GGTC:G	acceptor_gain	1.0000
4:3255724:GGTCG:G	acceptor_gain	1.0000

AlphaMissense

1818 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:3249358:T:A	W46R	1.000
4:3249358:T:C	W46R	1.000
4:3249359:G:C	W46S	1.000
4:3249360:G:C	W46C	1.000
4:3249360:G:T	W46C	1.000
4:3249383:T:C	L54P	1.000
4:3249394:T:A	W58R	1.000
4:3249394:T:C	W58R	1.000
4:3249396:G:C	W58C	1.000
4:3249396:G:T	W58C	1.000
4:3249430:C:A	R70S	1.000
4:3249510:G:C	K96N	1.000
4:3249510:G:T	K96N	1.000
4:3249514:A:G	K98E	1.000
4:3249516:G:C	K98N	1.000
4:3249516:G:T	K98N	1.000
4:3249525:C:A	N101K	1.000
4:3249525:C:G	N101K	1.000
4:3249532:T:C	F104L	1.000
4:3249534:C:A	F104L	1.000
4:3249534:C:G	F104L	1.000
4:3249542:G:T	R107M	1.000
4:3253250:T:A	W122R	1.000
4:3253250:T:C	W122R	1.000
4:3249358:T:G	W46G	0.999
4:3249383:T:A	L54H	0.999
4:3249392:T:A	V57D	0.999
4:3249395:G:C	W58S	0.999
4:3249416:T:A	L65H	0.999
4:3249416:T:C	L65P	0.999

dbSNP variants (sampled 300 via entrez): RS1000296259 (4:3256104 G>A), RS1000360138 (4:3247037 G>A), RS1000369699 (4:3246776 A>C,G), RS1000671925 (4:3250672 G>A), RS1000742514 (4:3245953 C>T), RS1001255796 (4:3246542 C>T), RS1001509598 (4:3255822 C>A,G,T), RS1001706779 (4:3246329 TCTGGG>T), RS1001716080 (4:3251088 G>A,T), RS1001959487 (4:3254283 A>G), RS1002017261 (4:3249674 G>A), RS1002022601 (4:3255639 G>A,C), RS1002069512 (4:3249575 A>G), RS1002189330 (4:3251215 G>T), RS1002211926 (4:3248554 G>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

9 associations (top):

Study	Trait	p-value
GCST004923_3	Tuberculosis	3.000000e-08
GCST007328_39	Alcohol consumption (drinks per week)	5.000000e-10
GCST007329_37	Automobile speeding propensity	6.000000e-14
GCST008595_42	Cognitive ability, years of educational attainment or schizophrenia (pleiotropy)	1.000000e-08
GCST008757_37	Alcohol consumption	2.000000e-09
GCST009524_122	Household income (MTAG)	3.000000e-08
GCST009524_163	Household income (MTAG)	6.000000e-12
GCST009524_181	Household income (MTAG)	1.000000e-08
GCST90002402_675	Platelet count	2.000000e-09

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0008579	risk-taking behaviour
EFO:0004337	intelligence
EFO:0004784	self reported educational attainment
EFO:0009695	household income
EFO:0004309	platelet count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB clinical annotations

2 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs362267	Efficacy	3	risperidone	Schizophrenia
rs362306	Efficacy	3	risperidone	Schizophrenia

PharmGKB variants

2 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs362267	HTT, MSANTD1	3	0.00	1	risperidone
rs362306	HTT, MSANTD1	3	0.00	1	risperidone

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
mono-(2-ethylhexyl)phthalate	increases abundance, increases methylation	1
Benzo(a)pyrene	decreases methylation	1
Diethylhexyl Phthalate	increases abundance, increases methylation	1
Quercetin	increases expression	1
Smoke	decreases expression	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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