MSANTD2

Summary

MSANTD2 (Myb/SANT DNA binding domain containing 2, HGNC:26266) is a protein-coding gene on chromosome 11q24.2, encoding Myb/SANT-like DNA-binding domain-containing protein 2 (Q6P1R3).

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 65 total
• MANE Select transcript: NM_001308027

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26266
Approved symbol	MSANTD2
Name	Myb/SANT DNA binding domain containing 2
Location	11q24.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ23342
Ensembl gene	ENSG00000120458
Ensembl biotype	protein_coding
Entrez	79684

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000239614, ENST00000374979, ENST00000524950, ENST00000526629, ENST00000527140, ENST00000533514, ENST00000634413, ENST00000650095, ENST00000674284

RefSeq mRNA: 7 — MANE Select: NM_001308027 NM_001308027, NM_001312919, NM_001312920, NM_001312921, NM_001352400, NM_001352401, NM_024631

CCDS: CCDS73408, CCDS76491, CCDS81641, CCDS8454

Canonical transcript exons

ENST00000374979 — 4 exons

Exon	Start	End
ENSE00001133450	124766498	124768028
ENSE00001465312	124774719	124774974
ENSE00002165951	124799871	124800406
ENSE00003565346	124772994	124773054

Expression profiles

Bgee: expression breadth ubiquitous, 276 present calls, max score 91.94.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.0793 / max 58.8933, expressed in 1753 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
122962	6.9305	1697
122963	1.1488	730

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
caput epididymis	UBERON:0004358	91.94	gold quality
right lobe of thyroid gland	UBERON:0001119	90.95	gold quality
left lobe of thyroid gland	UBERON:0001120	90.71	gold quality
thyroid gland	UBERON:0002046	90.29	gold quality
cauda epididymis	UBERON:0004360	89.99	gold quality
corpus epididymis	UBERON:0004359	89.50	gold quality
renal medulla	UBERON:0000362	89.32	gold quality
blood vessel layer	UBERON:0004797	88.81	gold quality
right uterine tube	UBERON:0001302	87.39	gold quality
metanephros cortex	UBERON:0010533	87.18	gold quality
lower lobe of lung	UBERON:0008949	86.81	gold quality
endocervix	UBERON:0000458	86.69	gold quality
body of pancreas	UBERON:0001150	86.45	gold quality
right coronary artery	UBERON:0001625	86.01	gold quality
body of uterus	UBERON:0009853	86.01	gold quality
right ovary	UBERON:0002118	85.93	gold quality
pituitary gland	UBERON:0000007	85.84	gold quality
superficial temporal artery	UBERON:0001614	85.78	gold quality
ventricular zone	UBERON:0003053	85.72	gold quality
left ovary	UBERON:0002119	85.63	gold quality
tibia	UBERON:0000979	85.51	gold quality
popliteal artery	UBERON:0002250	85.42	gold quality
tibial artery	UBERON:0007610	85.40	gold quality
visceral pleura	UBERON:0002401	85.39	gold quality
adenohypophysis	UBERON:0002196	85.33	gold quality
pylorus	UBERON:0001166	85.27	gold quality
endometrium	UBERON:0001295	85.19	gold quality
pericardium	UBERON:0002407	85.00	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.89	gold quality
skin of hip	UBERON:0001554	84.86	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.24

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

42 targeting MSANTD2, 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-4668-3P	100.00	68.74	2635
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-190A-3P	100.00	80.35	5520
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-3662	99.99	73.82	5684
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-12130	99.75	65.47	452
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-5197-5P	99.64	69.08	1494
HSA-MIR-6832-5P	99.58	64.82	1132
HSA-MIR-3136-3P	99.57	66.59	781
HSA-MIR-7155-3P	99.57	66.48	794
HSA-MIR-5007-3P	99.51	68.14	1242
HSA-MIR-12132	99.47	68.90	1341
HSA-MIR-150-3P	99.43	70.51	920
HSA-MIR-4652-3P	99.33	70.02	2742
HSA-MIR-145-3P	99.33	67.66	764
HSA-MIR-3614-5P	99.30	65.25	837
HSA-MIR-3973	99.20	69.19	1990
HSA-MIR-196A-3P	99.19	67.34	1204
HSA-MIR-499A-3P	99.18	69.20	1392
HSA-MIR-499B-3P	99.18	69.27	1391
HSA-MIR-500A-5P	98.76	69.13	1241

Literature-anchored findings (GeneRIF, showing 1)

• LncRNA BCLET variant confers bladder cancer susceptibility through alternative splicing of MSANTD2 exon 1. (PMID:37211917)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	MSANTD2	ENSDARG00000079474
mus_musculus	Msantd2	ENSMUSG00000042138
rattus_norvegicus	Msantd2	ENSRNOG00000009950

Paralogs (2): UTF1 (ENSG00000171794), MSANTD7 (ENSG00000284024)

Protein

Protein identifiers

Myb/SANT-like DNA-binding domain-containing protein 2 — Q6P1R3 (reviewed: Q6P1R3)

All UniProt accessions (4): Q6P1R3, A0A6I8PS01, B4E1M0, E9PPE2

Isoforms (3)

UniProt ID	Names	Canonical?
Q6P1R3-1	1	yes
Q6P1R3-2	2
Q6P1R3-3	3

RefSeq proteins (7): NP_001294956, NP_001299848, NP_001299849, NP_001299850, NP_001339329, NP_001339330, NP_078907 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR042792	MSANTD2	Family
IPR044822	Myb_DNA-bind_4	Domain

Pfam: PF13837

UniProt features (16 total): modified residue 6, cross-link 2, splice variant 2, sequence conflict 2, chain 1, domain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6P1R3-F1	67.06	0.33

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): 268, 343, 13, 24, 27, 32, 48, 436

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 102 (showing top): AAGCAAT_MIR137, GCANCTGNY_MYOD_Q6, SP1_Q2_01, IRF7_01, ACATTCC_MIR1_MIR206, TCCAGAT_MIR5165P, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, RYTTCCTG_ETS2_B, HOOI_ST7_TARGETS_DN, NRF2_01, NERF_Q2, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, GOCC_NUCLEAR_BODY, SCGGAAGY_ELK1_02, MGGAAGTG_GABP_B

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

534 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MSANTD2	KLF16	Q9BXK1	533
MSANTD2	RAB30	Q15771	523
MSANTD2	MSANTD3	Q96H12	481
MSANTD2	DSTYK	Q6XUX3	474
MSANTD2	CAMSAP1	Q5T5Y3	448
MSANTD2	LUC7L3	O95232	440
MSANTD2	DMXL1	Q9Y485	419
MSANTD2	ZMPSTE24	O75844	376
MSANTD2	LMBRD1	Q9NUN5	349
MSANTD2	HNRNPU	Q00839	345
MSANTD2	SLC39A10	Q9ULF5	332
MSANTD2	SCN2A	Q99250	322
MSANTD2	ABCB9	Q9NP78	294
MSANTD2	LRRC57	Q8N9N7	269
MSANTD2	NFAT5	O94916	261

IntAct

16 interactions, top by confidence:

A	B	Type	Score
EN1	NFIB	psi-mi:“MI:2364”(proximity)	0.470
MSANTD2	ERCC3	psi-mi:“MI:0915”(physical association)	0.370
FEV	TAF4	psi-mi:“MI:2364”(proximity)	0.270
KLF8	USP27X	psi-mi:“MI:2364”(proximity)	0.270
MYOD1	BCL9	psi-mi:“MI:2364”(proximity)	0.270
NFIX	TAF4	psi-mi:“MI:2364”(proximity)	0.270
PAX6	SMCHD1	psi-mi:“MI:2364”(proximity)	0.270
SOX5	SMCHD1	psi-mi:“MI:2364”(proximity)	0.270
SP7	IGF2BP3	psi-mi:“MI:2364”(proximity)	0.270
YY1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.270
TLK2	AQR	psi-mi:“MI:2364”(proximity)	0.270
TLK2	SBNO1	psi-mi:“MI:2364”(proximity)	0.270
ZMYM2	ZBTB5	psi-mi:“MI:2364”(proximity)	0.270
MSANTD2	pepT	psi-mi:“MI:0915”(physical association)	0.000
STRN4	MSANTD2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (24): MSANTD2 (Affinity Capture-MS), MSANTD2 (Proximity Label-MS), MSANTD2 (Proximity Label-MS), MSANTD2 (Proximity Label-MS), MSANTD2 (Proximity Label-MS), MSANTD2 (Proximity Label-MS), MSANTD2 (Proximity Label-MS), MSANTD2 (Proximity Label-MS), MSANTD2 (Proximity Label-MS), MSANTD2 (Proximity Label-MS), MSANTD2 (Proximity Label-MS), MSANTD2 (Proximity Label-MS), MSANTD2 (Affinity Capture-MS), MSANTD2 (Proximity Label-MS), MSANTD2 (Proximity Label-MS)

ESM2 similar proteins: A0A1B0GTS1, A0A1B0GWH4, A1A4L6, A1YGI6, A6NDR6, B8QB46, F1MJR8, F1QDF8, O35892, O35893, P09015, P15036, P15037, P23497, P52729, P59598, Q32NH9, Q3KRF1, Q3UM89, Q4G112, Q4V7E1, Q5M7N6, Q5ND04, Q5XIV2, Q5ZHX5, Q66IG8, Q6P1R3, Q6PCX9, Q6PJQ5, Q708W2, Q76I76, Q76I79, Q76N89, Q7M6U3, Q8AXQ4, Q8BVK9, Q8IUE0, Q8IUE1, Q8IWB6, Q8IXJ9

Diamond homologs: Q5ZHX5, Q6NZR2, Q6P1R3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 23 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
transcription by RNA polymerase II	7	22.4×	4e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	58
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1227 predictions. Top by Δscore:

Variant	Effect	Δscore
11:124772992:A:AC	donor_gain	1.0000
11:124772993:C:CC	donor_gain	1.0000
11:124772993:CTGTG:C	donor_gain	1.0000
11:124799866:GTTAC:G	donor_loss	1.0000
11:124799867:TTAC:T	donor_loss	1.0000
11:124799868:TAC:T	donor_loss	1.0000
11:124799869:A:T	donor_loss	1.0000
11:124799870:CCT:C	donor_loss	1.0000
11:124768025:CTTC:C	acceptor_gain	0.9900
11:124768026:TTC:T	acceptor_gain	0.9900
11:124768028:CCTG:C	acceptor_loss	0.9900
11:124768029:C:CC	acceptor_gain	0.9900
11:124768029:CTGGA:C	acceptor_loss	0.9900
11:124768030:T:A	acceptor_loss	0.9900
11:124772986:CTACT:C	donor_loss	0.9900
11:124772987:TACTT:T	donor_loss	0.9900
11:124772988:ACTT:A	donor_loss	0.9900
11:124772989:CTTAC:C	donor_loss	0.9900
11:124772990:T:TC	donor_loss	0.9900
11:124772991:TA:T	donor_loss	0.9900
11:124772992:ACT:A	donor_loss	0.9900
11:124773051:TCATC:T	acceptor_loss	0.9900
11:124773052:CAT:C	acceptor_gain	0.9900
11:124773053:ATCT:A	acceptor_loss	0.9900
11:124773054:TC:T	acceptor_loss	0.9900
11:124773055:C:A	acceptor_loss	0.9900
11:124773055:C:CC	acceptor_gain	0.9900
11:124773056:T:A	acceptor_loss	0.9900
11:124774713:TCTTA:T	donor_loss	0.9900
11:124774714:CTTA:C	donor_loss	0.9900

AlphaMissense

3620 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:124767216:A:G	L547P	1.000
11:124767243:A:G	L538P	1.000
11:124767245:A:C	F537L	1.000
11:124767245:A:T	F537L	1.000
11:124767247:A:G	F537L	1.000
11:124767579:C:T	G426D	1.000
11:124767580:C:G	G426R	1.000
11:124767591:A:G	L422P	1.000
11:124767594:C:T	G421D	1.000
11:124767595:C:G	G421R	1.000
11:124767676:A:G	W394R	1.000
11:124767676:A:T	W394R	1.000
11:124767693:A:G	L388P	1.000
11:124767701:G:C	C385W	1.000
11:124767703:A:G	C385R	1.000
11:124767709:C:G	A383P	1.000
11:124767713:G:C	S381R	1.000
11:124767713:G:T	S381R	1.000
11:124767715:T:G	S381R	1.000
11:124767752:C:A	W368C	1.000
11:124767752:C:G	W368C	1.000
11:124767754:A:G	W368R	1.000
11:124767754:A:T	W368R	1.000
11:124767822:A:G	L345P	1.000
11:124767848:G:C	S336R	1.000
11:124767848:G:T	S336R	1.000
11:124767850:T:G	S336R	1.000
11:124767858:G:T	A333D	1.000
11:124767886:A:G	W324R	1.000
11:124767886:A:T	W324R	1.000

dbSNP variants (sampled 300 via entrez): RS1000085280 (11:124796254 C>G), RS1000173968 (11:124770149 A>G), RS1000347955 (11:124769861 C>T), RS1000367977 (11:124790037 T>C), RS1000436402 (11:124783882 G>A), RS1000510607 (11:124775299 G>A), RS1000734860 (11:124800937 C>T), RS1000857657 (11:124775024 C>G,T), RS1000944973 (11:124795556 A>G), RS1000966264 (11:124801173 T>G), RS1001001003 (11:124782315 G>A), RS1001033247 (11:124800626 C>A,G,T), RS1001095008 (11:124788625 G>A), RS1001136035 (11:124768443 T>C,G), RS1001246786 (11:124789114 T>C)

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

3 associations (top):

Study	Trait	p-value
GCST002539_10	Schizophrenia	3.000000e-12
GCST004521_214	Autism spectrum disorder or schizophrenia	5.000000e-13
GCST006803_11	Schizophrenia	2.000000e-15

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
FR900359	affects phosphorylation	1
bisphenol F	affects cotreatment, decreases methylation	1
coumarin	decreases phosphorylation	1
di-n-butylphosphoric acid	affects expression	1
2-palmitoylglycerol	increases expression	1
K 7174	increases expression	1
bisphenol S	increases expression	1
bisphenol AF	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Air Pollutants	decreases expression, increases abundance	1
Doxorubicin	decreases expression	1
Lead	affects expression	1
Phthalic Acids	decreases methylation	1
Plant Extracts	affects cotreatment, increases expression	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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