SANBR

Summary

SANBR (SANT and BTB domain regulator of CSR, HGNC:29387) is a protein-coding gene on chromosome 2p15, encoding SANT and BTB domain regulator of class switch recombination (Q6NSI8). Negatively regulates class switch recombination or isotype switching in splenic B-cells.

Predicted to enable identical protein binding activity. Predicted to be involved in isotype switching.

Source: NCBI Gene 84542 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 124 total
• MANE Select transcript: NM_001129993

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29387
Approved symbol	SANBR
Name	SANT and BTB domain regulator of CSR
Location	2p15
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000162929
Ensembl biotype	protein_coding
OMIM	620213
Entrez	84542

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 12 protein_coding, 4 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000295031, ENST00000356719, ENST00000402291, ENST00000453186, ENST00000453873, ENST00000471625, ENST00000482513, ENST00000483509, ENST00000483700, ENST00000488322, ENST00000895613, ENST00000926248, ENST00000926249, ENST00000926250, ENST00000926251, ENST00000962436, ENST00000962437, ENST00000962438

RefSeq mRNA: 7 — MANE Select: NM_001129993 NM_001129993, NM_001330432, NM_001330433, NM_001330434, NM_001330435, NM_001330436, NM_032506

CCDS: CCDS1867, CCDS46296

Canonical transcript exons

ENST00000402291 — 22 exons

Exon	Start	End
ENSE00001518571	61068849	61068985
ENSE00001560072	61122126	61124280
ENSE00001852708	61065871	61066027
ENSE00003470382	61109197	61109296
ENSE00003481859	61108317	61108349
ENSE00003501449	61097700	61097852
ENSE00003536056	61081452	61081510
ENSE00003536203	61117357	61117385
ENSE00003565725	61117467	61117540
ENSE00003568603	61118028	61118116
ENSE00003572671	61073458	61073551
ENSE00003575330	61076920	61077158
ENSE00003583838	61088358	61088468
ENSE00003585028	61070342	61070500
ENSE00003586097	61103853	61103998
ENSE00003588303	61121185	61121276
ENSE00003595779	61092464	61092587
ENSE00003603382	61115979	61116070
ENSE00003651482	61083154	61083314
ENSE00003655471	61106563	61106662
ENSE00003677688	61088159	61088245
ENSE00003685469	61071606	61071792

Expression profiles

Bgee: expression breadth ubiquitous, 231 present calls, max score 97.75.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.2198 / max 117.1167, expressed in 1719 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
20470	5.0428	1602
20469	2.8140	1269
20471	0.3631	185

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	97.75	gold quality
bronchial epithelial cell	CL:0002328	96.63	gold quality
bronchus	UBERON:0002185	95.60	gold quality
Brodmann (1909) area 23	UBERON:0013554	93.38	gold quality
primary visual cortex	UBERON:0002436	89.32	gold quality
calcaneal tendon	UBERON:0003701	89.30	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.01	gold quality
oviduct epithelium	UBERON:0004804	87.26	gold quality
occipital lobe	UBERON:0002021	87.14	gold quality
mucosa of paranasal sinus	UBERON:0005030	87.14	gold quality
corpus callosum	UBERON:0002336	86.15	gold quality
middle temporal gyrus	UBERON:0002771	85.93	silver quality
cortical plate	UBERON:0005343	85.84	gold quality
ganglionic eminence	UBERON:0004023	85.69	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	85.27	gold quality
ventricular zone	UBERON:0003053	84.92	gold quality
spinal cord	UBERON:0002240	84.78	gold quality
cerebellar vermis	UBERON:0004720	84.75	gold quality
right uterine tube	UBERON:0001302	84.58	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.38	gold quality
entorhinal cortex	UBERON:0002728	83.26	silver quality
lateral nuclear group of thalamus	UBERON:0002736	83.16	gold quality
medulla oblongata	UBERON:0001896	82.91	gold quality
pons	UBERON:0000988	82.78	gold quality
superior frontal gyrus	UBERON:0002661	82.75	gold quality
superior vestibular nucleus	UBERON:0007227	82.72	gold quality
postcentral gyrus	UBERON:0002581	82.47	silver quality
parietal lobe	UBERON:0001872	82.38	silver quality
tendon	UBERON:0000043	82.29	gold quality
cerebellar cortex	UBERON:0002129	82.24	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.54

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

76 targeting SANBR, 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-1277-5P	100.00	73.95	5056
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3163	100.00	77.23	8605
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-190A-3P	100.00	80.35	5520
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
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

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	sanbr	ENSDARG00000079857
mus_musculus	Sanbr	ENSMUSG00000042208
rattus_norvegicus	Sanbr	ENSRNOG00000054669
drosophila_melanogaster	CG6761	FBGN0036031

Protein

Protein identifiers

SANT and BTB domain regulator of class switch recombination — Q6NSI8 (reviewed: Q6NSI8)

All UniProt accessions (2): Q6NSI8, F8VWD7

UniProt curated annotations — full annotation on UniProt →

Function. Negatively regulates class switch recombination or isotype switching in splenic B-cells.

Subunit / interactions. Homodimer. Interacts (via the BTB domain) with HDAC1 and NCOR2.

Domain organisation. The BTB domain is important for homodimerization and for its function in negative regulation of class switch recombination.

Similarity. Belongs to the KIAA1841 family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q6NSI8-1	1	yes
Q6NSI8-2	2
Q6NSI8-3	3
Q6NSI8-4	4

RefSeq proteins (7): NP_001123465, NP_001317361, NP_001317362, NP_001317363, NP_001317364, NP_001317365, NP_115895 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001005	SANT/Myb	Domain
IPR011333	SKP1/BTB/POZ_sf	Homologous_superfamily
IPR021777	SANBR_BTB	Domain
IPR045902	SANBR-like	Family

Pfam: PF11822

UniProt features (19 total): splice variant 4, sequence conflict 4, compositionally biased region 4, region of interest 3, domain 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6NSI8-F1	68.60	0.31

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 139 (showing top): GOBP_B_CELL_ACTIVATION, GOBP_LEUKOCYTE_MEDIATED_IMMUNITY, GOBP_B_CELL_MEDIATED_IMMUNITY, GOBP_CELL_ACTIVATION_INVOLVED_IN_IMMUNE_RESPONSE, MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_DN, GOBP_LYMPHOCYTE_MEDIATED_IMMUNITY, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOBP_IMMUNOGLOBULIN_PRODUCTION, GOBP_SOMATIC_DIVERSIFICATION_OF_IMMUNE_RECEPTORS, GOBP_ADAPTIVE_IMMUNE_RESPONSE, GOBP_IMMUNOGLOBULIN_PRODUCTION_INVOLVED_IN_IMMUNOGLOBULIN_MEDIATED_IMMUNE_RESPONSE, GOBP_IMMUNE_EFFECTOR_PROCESS, MODULE_48, MODULE_95, GOBP_LYMPHOCYTE_ACTIVATION_INVOLVED_IN_IMMUNE_RESPONSE

GO Biological Process (1): isotype switching (GO:0045190)

GO Molecular Function (1): identical protein binding (GO:0042802)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
somatic recombination of immunoglobulin genes involved in immune response	1
B cell activation involved in immune response	1
protein binding	1

Protein interactions and networks

STRING

326 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SANBR	C2orf74	A8MZ97	668
SANBR	SIRPD	Q9H106	507
SANBR	FAM162B	Q5T6X4	448
SANBR	PUS10	Q3MIT2	446
SANBR	PABIR2	Q7Z309	431
SANBR	MINDY4	Q4G0A6	418
SANBR	NKAPD1	Q6ZUT1	418
SANBR	TTC13	Q8NBP0	412
SANBR	TMEM174	Q8WUU8	400
SANBR	KRCC1	Q9NPI7	397
SANBR	CCDC85A	Q96PX6	390
SANBR	PREPL	Q4J6C6	390
SANBR	LETM2	Q2VYF4	378
SANBR	PEX13	Q92968	372
SANBR	ZNF680	Q8NEM1	356

IntAct

17 interactions, top by confidence:

A	B	Type	Score
NICN1	TTLL1	psi-mi:“MI:0914”(association)	0.640
TTLL1	CDC27	psi-mi:“MI:0914”(association)	0.640
LRRC49	EIF3F	psi-mi:“MI:0914”(association)	0.640
LRRC49	SNAP29	psi-mi:“MI:0914”(association)	0.530
SANBR	SRPK1	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
SANBR	H1-2	psi-mi:“MI:0915”(physical association)	0.400
LRRC49	PCM1	psi-mi:“MI:0914”(association)	0.350
ROS1	ODAD3	psi-mi:“MI:0914”(association)	0.350
TPGS1	PPFIA3	psi-mi:“MI:0914”(association)	0.350
CSTPP1	CRYGS	psi-mi:“MI:0914”(association)	0.350
CSTPP1	KRBA1	psi-mi:“MI:0914”(association)	0.350
NICN1	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
TTLL1	RGS12	psi-mi:“MI:0914”(association)	0.350
CAT	PSMD12	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (22): KIAA1841 (Affinity Capture-MS), KIAA1841 (Affinity Capture-MS), KIAA1841 (Affinity Capture-MS), KIAA1841 (Proximity Label-MS), KIAA1841 (Affinity Capture-RNA), KIAA1841 (Proximity Label-MS), KIAA1841 (Affinity Capture-MS), KIAA1841 (Affinity Capture-MS), KIAA1841 (Affinity Capture-MS), KIAA1841 (Affinity Capture-MS), KIAA1841 (Affinity Capture-MS), KIAA1841 (Affinity Capture-MS), KIAA1841 (Proximity Label-MS), DDX21 (Cross-Linking-MS (XL-MS)), KIAA1841 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A0R4IXF6, A1A5R8, A9ZLX4, D3YXJ0, E9PUQ8, G3UZ78, O00750, O15164, O54828, P30052, P40818, P48984, P52963, P59997, P97496, Q02225, Q08AX9, Q08BR4, Q08D35, Q16760, Q1LUC3, Q2I6J1, Q3UWM4, Q498F0, Q5JSH3, Q5JTW2, Q5RHD1, Q60665, Q64398, Q68FF0, Q6INA9, Q6NSI8, Q6NVE8, Q6PDG5, Q6ZMT4, Q7ZVP1, Q80U87, Q86XP1, Q8C5W4, Q8N7X0

Diamond homologs: A1A5R8, Q08AX9, Q68FF0, Q6NSI8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	90
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3979 predictions. Top by Δscore:

Variant	Effect	Δscore
2:61068848:GAT:G	acceptor_gain	1.0000
2:61068981:ACAAG:A	donor_loss	1.0000
2:61068982:CAAG:C	donor_loss	1.0000
2:61068983:AAG:A	donor_loss	1.0000
2:61068984:AG:A	donor_loss	1.0000
2:61068985:GG:G	donor_loss	1.0000
2:61070340:A:AG	acceptor_gain	1.0000
2:61070341:G:A	acceptor_loss	1.0000
2:61070341:G:GT	acceptor_gain	1.0000
2:61070341:GT:G	acceptor_gain	1.0000
2:61070341:GTT:G	acceptor_gain	1.0000
2:61070341:GTTC:G	acceptor_gain	1.0000
2:61070341:GTTCC:G	acceptor_gain	1.0000
2:61070498:GAG:G	donor_gain	1.0000
2:61071595:T:G	acceptor_gain	1.0000
2:61071604:A:AG	acceptor_gain	1.0000
2:61071605:G:GG	acceptor_gain	1.0000
2:61071605:GT:G	acceptor_gain	1.0000
2:61073550:GG:G	donor_gain	1.0000
2:61073551:GG:G	donor_gain	1.0000
2:61081511:G:GG	donor_gain	1.0000
2:61083310:AAAAG:A	donor_loss	1.0000
2:61083311:AAAG:A	donor_loss	1.0000
2:61083312:AAG:A	donor_loss	1.0000
2:61083313:AGG:A	donor_loss	1.0000
2:61083314:GG:G	donor_loss	1.0000
2:61083315:GTA:G	donor_loss	1.0000
2:61083316:T:G	donor_loss	1.0000
2:61088157:A:AG	acceptor_gain	1.0000
2:61088158:G:GA	acceptor_gain	1.0000

AlphaMissense

4761 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:61077069:T:A	V194D	1.000
2:61081490:T:C	F237L	1.000
2:61081492:T:A	F237L	1.000
2:61081492:T:G	F237L	1.000
2:61081494:T:C	L238S	1.000
2:61117489:T:A	W630R	1.000
2:61117489:T:C	W630R	1.000
2:61076934:T:A	I149N	0.999
2:61076934:T:C	I149T	0.999
2:61076934:T:G	I149S	0.999
2:61076940:T:A	V151E	0.999
2:61076994:T:C	L169S	0.999
2:61077014:T:C	F176L	0.999
2:61077015:T:C	F176S	0.999
2:61077016:T:A	F176L	0.999
2:61077016:T:G	F176L	0.999
2:61077099:T:C	L204S	0.999
2:61081476:T:C	L232P	0.999
2:61081491:T:C	F237S	0.999
2:61081491:T:G	F237C	0.999
2:61092474:T:A	W367R	0.999
2:61092474:T:C	W367R	0.999
2:61117491:G:C	W630C	0.999
2:61117491:G:T	W630C	0.999
2:61117525:G:C	A642P	0.999
2:61117532:G:C	R644T	0.999
2:61117533:A:C	R644S	0.999
2:61117533:A:T	R644S	0.999
2:61118061:T:C	L658P	0.999
2:61076936:C:G	H150D	0.998

dbSNP variants (sampled 300 via entrez): RS1000034833 (2:61130038 G>T), RS1000068444 (2:61105594 G>A,C,T), RS1000071810 (2:61096151 C>G,T), RS1000072732 (2:61112279 G>A,C), RS1000128425 (2:61084019 C>G,T), RS1000149736 (2:61071376 C>T), RS1000198866 (2:61118795 C>T), RS1000243327 (2:61130314 G>A), RS1000283173 (2:61078484 C>T), RS1000299007 (2:61096786 A>G), RS1000333876 (2:61066458 G>A), RS1000355034 (2:61089187 C>G,T), RS1000364911 (2:61089403 G>A), RS1000367793 (2:61117855 A>C), RS1000416859 (2:61084180 C>G)

Disease associations

OMIM: gene MIM:620213 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST001438_15	Crohn’s disease	5.000000e-09
GCST001725_44	Inflammatory bowel disease	9.000000e-32
GCST006956_8	Erectile dysfunction	8.000000e-06
GCST010989_201	Body size at age 10	2.000000e-08
GCST90002386_248	High light scatter reticulocyte percentage of red cells	2.000000e-10
GCST90002388_71	Lymphocyte count	7.000000e-13

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0009819	comparative body size at age 10, self-reported
EFO:0004587	lymphocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tobacco Smoke Pollution	decreases expression, increases methylation	2
aristolochic acid I	decreases expression	1
bisphenol A	affects cotreatment, decreases methylation, increases methylation	1
sodium arsenite	affects cotreatment, decreases expression, increases abundance	1
manganese chloride	decreases expression, increases abundance, affects cotreatment	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
abrine	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Benzo(a)pyrene	decreases methylation	1
Cisplatin	increases expression	1
Estradiol	affects cotreatment, increases expression	1
Lead	affects expression	1
Manganese	affects cotreatment, decreases expression, increases abundance	1
Plant Extracts	affects cotreatment, increases expression	1
Tretinoin	decreases expression	1
Antirheumatic Agents	increases expression	1
Okadaic Acid	increases expression	1
Lactic Acid	increases expression	1

Clinical trials (associated diseases)

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