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BANF2

gene
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Also known as dJ803K15.1BAF-LBAFLBAF2

Summary

BANF2 (BANF family member 2, HGNC:16172) is a protein-coding gene on chromosome 20p12.1, encoding Barrier-to-autointegration factor-like protein (Q9H503). May play a role in BANF1 regulation and influence tissue-specific roles of BANF1.

Enables identical protein binding activity. Predicted to be involved in chromosome organization. Located in nucleus.

Source: NCBI Gene 140836 — RefSeq curated summary.

At a glance

  • GWAS associations: 14
  • Clinical variants (ClinVar): 13 total — 2 pathogenic
  • MANE Select transcript: NM_178477

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16172
Approved symbolBANF2
NameBANF family member 2
Location20p12.1
Locus typegene with protein product
StatusApproved
AliasesdJ803K15.1, BAF-L, BAFL, BAF2
Ensembl geneENSG00000125888
Ensembl biotypeprotein_coding
Entrez140836

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000246090, ENST00000377805, ENST00000427254, ENST00000467330, ENST00000545418

RefSeq mRNA: 3 — MANE Select: NM_178477 NM_001014977, NM_001159495, NM_178477

CCDS: CCDS13129, CCDS54449

Canonical transcript exons

ENST00000246090 — 4 exons

ExonStartEnd
ENSE000013598111772271617722878
ENSE000014098871769996617700055
ENSE000018191871773566517735871
ENSE000038002481772502317725151

Expression profiles

Bgee: expression breadth ubiquitous, 108 present calls, max score 95.88.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1443 / max 130.8146, expressed in 3 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1836620.11603
1836610.01503
1836630.01333

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left testisUBERON:000453395.88gold quality
right testisUBERON:000453495.48gold quality
spermCL:000001994.72gold quality
testisUBERON:000047392.48gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047382.18silver quality
adult organismUBERON:000702377.40gold quality
body of pancreasUBERON:000115074.29gold quality
kidney epitheliumUBERON:000481965.28gold quality
cardiac muscle of right atriumUBERON:000337964.78gold quality
left ventricle myocardiumUBERON:000656664.40gold quality
ileal mucosaUBERON:000033163.48silver quality
myocardiumUBERON:000234963.03gold quality
tibialis anteriorUBERON:000138562.83silver quality
pancreasUBERON:000126460.80gold quality
pancreatic ductal cellCL:000207959.06silver quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099156.89gold quality
deltoidUBERON:000147656.58gold quality
epithelial cell of pancreasCL:000008354.54gold quality
upper arm skinUBERON:000426353.52gold quality
quadriceps femorisUBERON:000137751.52gold quality
vastus lateralisUBERON:000137949.53gold quality
tendon of biceps brachiiUBERON:000818848.73gold quality
nasal cavity epitheliumUBERON:000538447.03gold quality
apex of heartUBERON:000209846.42gold quality
skin of hipUBERON:000155445.20silver quality
thyroid glandUBERON:000204644.86gold quality
muscle tissueUBERON:000238544.55gold quality
left lobe of thyroid glandUBERON:000112044.30gold quality
ventral tegmental areaUBERON:000269144.30gold quality
amniotic fluidUBERON:000017344.28gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.70

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

  • BAF and BAF-L might contribute to the shaping of the spermatozoon nucleus and, after fertilisation, its transition to the male pronucleus. (PMID:28684548)
  • BAF-L Modulates Histone-to-Protamine Transition during Spermiogenesis. (PMID:35216101)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusBanf2ENSMUSG00000037307
rattus_norvegicusBanf2ENSRNOG00000006032

Paralogs (1): BANF1 (ENSG00000175334)

Protein

Protein identifiers

Barrier-to-autointegration factor-like protein — Q9H503 (reviewed: Q9H503)

Alternative names: Barrier-to-autointegration factor 2

All UniProt accessions (3): Q9H503, A0A140VK85, B1AM15

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in BANF1 regulation and influence tissue-specific roles of BANF1.

Subunit / interactions. Homodimer. Heterodimerizes with BANF1.

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. Expressed strongly in testis and pancreas. Also detected in brain, colon, liver, lung, ovary, placenta, prostate, small intestine, spleen and thymus. Not detected in heart, kidney and skeletal muscle.

Similarity. Belongs to the BAF family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9H503-11yes
Q9H503-22

RefSeq proteins (3): NP_001014977, NP_001152967, NP_848572* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004122BAF_protFamily
IPR036617BAF_sfHomologous_superfamily
IPR051387BAFFamily

Pfam: PF02961

UniProt features (4 total): sequence variant 2, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H503-F195.990.96

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 22 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_DN, GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, GOBP_CHROMOSOME_ORGANIZATION, TAL1ALPHAE47_01, TAL1BETAE47_01, WGTTNNNNNAAA_UNKNOWN, TAL1BETAITF2_01, MYC_UP.V1_DN, ZNF184_TARGET_GENES, GSE14000_TRANSLATED_RNA_VS_MRNA_16H_LPS_DC_UP, GSE15750_WT_VS_TRAF6KO_DAY6_EFF_CD8_TCELL_DN, DESCARTES_MAIN_FETAL_THYMIC_EPITHELIAL_CELLS, FRANCO_BLOOD_SANOFI_PASTEUR_SA_INACTIVATED_INFLUENZA_VACCINE_CORRELATED_WITH_ANTIBODY_RESPONSE_AGE_18_40YO_14DY_NEGATIVE, ANDERSON_BLOOD_CN54GP140_ADJUVANTED_WITH_GLA_AF_AGE_18_45YO_1DY_UP, GSE17974_0H_VS_0.5H_IN_VITRO_ACT_CD4_TCELL_UP

GO Biological Process (1): chromosome organization (GO:0051276)

GO Molecular Function (3): DNA binding (GO:0003677), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (3): condensed chromosome (GO:0000793), nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
organelle organization1
nucleic acid binding1
protein binding1
binding1
chromosome1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

933 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
BANF2EMDP50402996
BANF2LEMD3Q9Y2U8957
BANF2LEMD2Q8NC56848
BANF2H3-3AP06351831
BANF2H3C14Q71DI3831
BANF2H3-5Q6NXT2831
BANF2H3C1P02295831
BANF2H3-4Q16695831
BANF2H3-7Q5TEC6831
BANF2LBRQ14739821
BANF2LMNAP02545811
BANF2TMPOP08918808
BANF2LMNB1P20700782
BANF2VRK1Q99986742
BANF2PSIP1O75475695

IntAct

2 interactions, top by confidence:

ABTypeScore
BANF2APAF1psi-mi:“MI:0914”(association)0.350

BioGRID (23): BANF2 (Two-hybrid), BANF2 (Two-hybrid), BANF2 (Two-hybrid), BANF2 (Two-hybrid), CFP (Two-hybrid), PSMA1 (Two-hybrid), MTUS2 (Two-hybrid), ADAMTSL4 (Two-hybrid), DDIT4L (Two-hybrid), WDYHV1 (Two-hybrid), DUSP23 (Two-hybrid), BEND7 (Two-hybrid), BANF1 (Two-hybrid), INCA1 (Two-hybrid), TCF4 (Two-hybrid)

ESM2 similar proteins: A1KXW8, A3KMX7, A4IIA7, A6QL50, A8MYZ0, E1BGQ2, F4I933, F4IVI0, H0Y354, O14772, O35099, O81916, Q08326, Q0VCL9, Q149N8, Q1JQA1, Q29RL0, Q32PE7, Q3T1H6, Q3TTL0, Q4R9C4, Q5F4A1, Q5I0G3, Q5R6Y2, Q5RBW0, Q5RFG8, Q5RJY2, Q5TYM5, Q5U515, Q66J91, Q6DCD7, Q6L9T8, Q6P338, Q7L622, Q866F4, Q86X60, Q8BFZ8, Q8BKW4, Q8BX13, Q8CEL2

Diamond homologs: A8XAC6, O54962, O75531, P61283, Q03565, Q32PE7, Q5HZM3, Q5RBU9, Q66KV4, Q6NTS2, Q6P026, Q8BVR0, Q9H503, Q9R1T1, Q9VLU0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic2
Likely pathogenic0
Uncertain significance9
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
2427149NC_000020.10:g.(?17587682)(18168103_?)delPathogenic
625735GRCh37/hg19 20p12.2-11.23(chr20:11716825-19331055)Pathogenic

SpliceAI

731 predictions. Top by Δscore:

VariantEffectΔscore
20:17725012:T:Aacceptor_gain1.0000
20:17725015:T:Aacceptor_gain1.0000
20:17725153:T:Adonor_loss1.0000
20:17710877:GGC:Gdonor_gain0.9900
20:17725010:A:AGacceptor_gain0.9900
20:17725010:ACT:Aacceptor_gain0.9900
20:17725011:C:Gacceptor_gain0.9900
20:17725020:CAGG:Cacceptor_gain0.9900
20:17725021:A:AGacceptor_gain0.9900
20:17725021:A:Gacceptor_loss0.9900
20:17725021:AG:Aacceptor_gain0.9900
20:17725021:AGGA:Aacceptor_gain0.9900
20:17725022:G:GGacceptor_gain0.9900
20:17725022:G:GTacceptor_loss0.9900
20:17725022:GG:Gacceptor_gain0.9900
20:17725022:GGA:Gacceptor_gain0.9900
20:17725022:GGAG:Gacceptor_gain0.9900
20:17734371:G:GGdonor_gain0.9900
20:17734382:G:GTdonor_gain0.9900
20:17735661:CCAG:Cacceptor_loss0.9900
20:17735662:CA:Cacceptor_loss0.9900
20:17735663:A:ACacceptor_loss0.9900
20:17735663:A:AGacceptor_gain0.9900
20:17735664:G:GAacceptor_loss0.9900
20:17735664:G:GGacceptor_gain0.9900
20:17700052:CCTGG:Cdonor_loss0.9800
20:17700054:TGG:Tdonor_loss0.9800
20:17700055:GGTGA:Gdonor_loss0.9800
20:17700056:GTGAG:Gdonor_loss0.9800
20:17700057:T:Adonor_loss0.9800

AlphaMissense

600 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
20:17735686:T:CF50L0.982
20:17735688:C:AF50L0.982
20:17735688:C:GF50L0.982
20:17735716:T:CF60L0.971
20:17735718:T:AF60L0.971
20:17735718:T:GF60L0.971
20:17735803:T:CF89L0.970
20:17735805:C:AF89L0.970
20:17735805:C:GF89L0.970
20:17735761:G:CA75P0.961
20:17735687:T:CF50S0.960
20:17735717:T:CF60S0.959
20:17735791:T:AW85R0.959
20:17735791:T:CW85R0.959
20:17725056:T:CF11L0.950
20:17725058:C:AF11L0.950
20:17725058:C:GF11L0.950
20:17735783:T:CL82P0.939
20:17735793:G:CW85C0.939
20:17735793:G:TW85C0.939
20:17725082:G:CK19N0.936
20:17725082:G:TK19N0.936
20:17735729:T:CL64P0.936
20:17725057:T:CF11S0.931
20:17735675:T:AL46Q0.931
20:17735675:T:GL46R0.931
20:17735703:G:CK55N0.931
20:17735703:G:TK55N0.931
20:17725129:T:CL35S0.930
20:17735681:G:AG48E0.927

dbSNP variants (sampled 300 via entrez): RS1000073854 (20:17716334 T>C), RS1000164618 (20:17692663 C>A,G,T), RS1000232907 (20:17695025 A>T), RS1000328598 (20:17723356 C>T), RS1000418175 (20:17704133 G>A,C), RS1000447702 (20:17700916 G>A,T), RS1000448562 (20:17721367 AT>A), RS1000509363 (20:17707166 G>A), RS1000565312 (20:17721027 T>C), RS1000677286 (20:17726658 C>A), RS1000822035 (20:17719194 G>A), RS1000873284 (20:17702544 A>T), RS1000896298 (20:17724797 C>G,T), RS1000993220 (20:17730545 G>A), RS1001027846 (20:17714871 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

14 associations (top):

StudyTraitp-value
GCST006979_536Heel bone mineral density2.000000e-10
GCST008077_84LDL cholesterol levels1.000000e-06
GCST008078_119LDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)8.000000e-11
GCST008078_15LDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)9.000000e-13
GCST008079_109LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)3.000000e-85
GCST008079_38LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)7.000000e-77
GCST008086_42LDL cholesterol levels in current drinkers1.000000e-09
GCST008086_61LDL cholesterol levels in current drinkers2.000000e-10
GCST009365_36LDL cholesterol levels x short total sleep time interaction (2df test)4.000000e-08
GCST010243_94Apolipoprotein B levels3.000000e-10
GCST010245_101LDL cholesterol levels3.000000e-08
GCST010396_166Gut microbiota (bacterial taxa, hurdle binary method)2.000000e-06
GCST011347_62Low density lipoprotein cholesterol levels9.000000e-11
GCST012490_11Femur bone mineral density x serum urate levels interaction1.000000e-13

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0009270heel bone mineral density
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0004329alcohol drinking
EFO:0004615apolipoprotein B measurement
EFO:0007874gut microbiome measurement
EFO:0004531urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

ChemicalActions (top 5)PubMed papers
Resveratrolaffects cotreatment, decreases expression1
Benzo(a)pyreneaffects methylation, decreases methylation1
Pesticidesaffects methylation1
Plant Extractsaffects cotreatment, decreases expression1
Copper Sulfatedecreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot