BIVM

gene
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Also known as FLJ20159

Summary

BIVM (basic, immunoglobulin-like variable motif containing, HGNC:16034) is a protein-coding gene on chromosome 13q33.1, encoding Basic immunoglobulin-like variable motif-containing protein (Q86UB2).

Predicted to enable DNA endonuclease activity and single-stranded DNA binding activity. Predicted to be involved in DNA metabolic process. Located in extracellular space.

Source: NCBI Gene 54841 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 29 total — 4 pathogenic, 1 likely-pathogenic
  • MANE Select transcript: NM_017693

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16034
Approved symbolBIVM
Namebasic, immunoglobulin-like variable motif containing
Location13q33.1
Locus typegene with protein product
StatusApproved
AliasesFLJ20159
Ensembl geneENSG00000134897
Ensembl biotypeprotein_coding
OMIM619006
Entrez54841

Gene structure

Transcript identifiers

Ensembl transcripts: 70 — 60 protein_coding, 5 nonsense_mediated_decay, 4 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000257336, ENST00000448849, ENST00000474443, ENST00000481069, ENST00000490317, ENST00000491929, ENST00000651008, ENST00000651048, ENST00000651228, ENST00000651808, ENST00000651855, ENST00000651949, ENST00000652006, ENST00000652084, ENST00000652643, ENST00000652766, ENST00000909441, ENST00000909442, ENST00000909443, ENST00000909444, ENST00000909445, ENST00000909446, ENST00000909447, ENST00000909448, ENST00000909449, ENST00000909450, ENST00000909451, ENST00000909452, ENST00000909453, ENST00000909454, ENST00000909455, ENST00000909456, ENST00000909457, ENST00000909458, ENST00000909459, ENST00000909460, ENST00000909461, ENST00000909462, ENST00000909463, ENST00000909464, ENST00000909465, ENST00000909466, ENST00000909467, ENST00000909468, ENST00000909469, ENST00000909470, ENST00000909471, ENST00000918727, ENST00000918728, ENST00000918729, ENST00000918730, ENST00000918731, ENST00000918732, ENST00000918733, ENST00000962128, ENST00000962129, ENST00000962130, ENST00000962131, ENST00000962132, ENST00000962133, ENST00000962134, ENST00000962135, ENST00000962136, ENST00000962137, ENST00000962138, ENST00000962139, ENST00000962140, ENST00000962141, ENST00000962142, ENST00000962143

RefSeq mRNA: 2 — MANE Select: NM_017693 NM_001159596, NM_017693

CCDS: CCDS53879, CCDS9505

Canonical transcript exons

ENST00000257336 — 11 exons

ExonStartEnd
ENSE00001224347102839572102841533
ENSE00001370952102799119102799521
ENSE00001381074102805307102805390
ENSE00002316723102807146102807745
ENSE00003471807102838643102838739
ENSE00003480959102822065102822159
ENSE00003516453102821743102821847
ENSE00003550235102821037102821132
ENSE00003588928102834466102834552
ENSE00003605795102816428102816554
ENSE00003638954102831565102831697

Expression profiles

Bgee: expression breadth ubiquitous, 257 present calls, max score 93.65.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3107 / max 9.9242, expressed in 134 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1359286.08951591
1359290.3107134

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left ventricle myocardiumUBERON:000656693.65gold quality
tibialis anteriorUBERON:000138592.51gold quality
cardiac muscle of right atriumUBERON:000337992.44gold quality
tendon of biceps brachiiUBERON:000818891.64gold quality
ileal mucosaUBERON:000033191.28gold quality
cerebellar hemisphereUBERON:000224591.17gold quality
cerebellar cortexUBERON:000212991.15gold quality
right hemisphere of cerebellumUBERON:001489090.82gold quality
metanephros cortexUBERON:001053390.74gold quality
cortical plateUBERON:000534390.66gold quality
cerebellumUBERON:000203790.47gold quality
kidney epitheliumUBERON:000481989.84gold quality
tendonUBERON:000004388.89gold quality
stromal cell of endometriumCL:000225588.74gold quality
cortex of kidneyUBERON:000122588.70gold quality
body of pancreasUBERON:000115088.47gold quality
cardiac atriumUBERON:000208187.86gold quality
right atrium auricular regionUBERON:000663187.72gold quality
muscle of legUBERON:000138387.67gold quality
ganglionic eminenceUBERON:000402387.56gold quality
embryoUBERON:000092287.55gold quality
deltoidUBERON:000147687.53silver quality
gastrocnemiusUBERON:000138887.48gold quality
endometriumUBERON:000129587.10gold quality
muscle organUBERON:000163087.04gold quality
skeletal muscle organUBERON:001489287.04gold quality
heart left ventricleUBERON:000208487.00gold quality
calcaneal tendonUBERON:000370187.00gold quality
right lobe of liverUBERON:000111486.91gold quality
smooth muscle tissueUBERON:000113586.84gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.33

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

98 targeting BIVM, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3163100.0077.238605
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-366299.9973.825684
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-453199.9969.703181
HSA-MIR-428299.9975.366408
HSA-MIR-548N99.9871.944170
HSA-MIR-477599.9875.006394
HSA-MIR-548P99.9872.253784
HSA-MIR-60799.9773.625593
HSA-MIR-590-3P99.9674.346478
HSA-MIR-146A-5P99.9668.93988
HSA-MIR-146B-5P99.9669.13977
HSA-MIR-570-3P99.9672.414910
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-767-5P99.9570.85993
HSA-MIR-7153-5P99.9468.891006
HSA-MIR-218-5P99.9372.222103
HSA-MIR-381-3P99.9371.872854
HSA-MIR-30099.9271.762856
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-6809-3P99.9171.453814
HSA-MIR-806399.9169.763146
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-367199.9073.043897
HSA-MIR-3065-3P99.8770.251407

Literature-anchored findings (GeneRIF, showing 1)

  • Identification of genetic susceptibility in preterm newborns with bronchopulmonary dysplasia by whole-exome sequencing: BIVM gene may play a role. (PMID:36757497)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriobivmENSDARG00000061409
mus_musculusErcc5ENSMUSG00000026048
mus_musculusBivmENSMUSG00000041684
rattus_norvegicusErcc5ENSRNOG00000022812
rattus_norvegicusBivmENSRNOG00000022894

Paralogs (1): ERCC5 (ENSG00000134899)

Protein

Protein identifiers

Basic immunoglobulin-like variable motif-containing proteinQ86UB2 (reviewed: Q86UB2)

All UniProt accessions (8): A0A494BZX4, A0A494C000, A0A494C0D0, A0A494C0F9, A0A494C0L8, A0A494C1A7, A0A494C1S8, Q86UB2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Widely expressed. Expressed at higher level in spleen, ovary, small intestine, colon, peripheral blood leukocytes and liver. Also expressed in testis, ovary, aorta, appendix, trachea, pituitary gland, bladder, uterus, spinal cord, salivary gland, stomach, mammary gland and bone marrow. Weakly or not expressed in fetal spleen, adult thymus and certain cancer cell lines.

Similarity. Belongs to the BIVM family.

Isoforms (2)

UniProt IDNamesCanonical?
Q86UB2-11yes
Q86UB2-22

RefSeq proteins (2): NP_001153068, NP_060163* (*=MANE)

Domains & families (InterPro)

UniProt features (10 total): region of interest 3, compositionally biased region 3, splice variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q86UB2-F166.500.43

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 120 (showing top): GOMF_ENDONUCLEASE_ACTIVITY, GOMF_NUCLEASE_ACTIVITY, TTTGTAG_MIR520D, MODULE_239, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, AGCTCCT_MIR28, GOMF_DNA_ENDONUCLEASE_ACTIVITY, GOMF_SINGLE_STRANDED_DNA_BINDING, SANSOM_APC_MYC_TARGETS, SANSOM_APC_TARGETS_REQUIRE_MYC, GOBP_DNA_METABOLIC_PROCESS, GEORGES_TARGETS_OF_MIR192_AND_MIR215, MODULE_533, HORIUCHI_WTAP_TARGETS_UP, MIKKELSEN_ES_ICP_WITH_H3K4ME3

GO Biological Process (1): DNA metabolic process (GO:0006259)

GO Molecular Function (3): single-stranded DNA binding (GO:0003697), DNA endonuclease activity (GO:0004520), protein binding (GO:0005515)

GO Cellular Component (3): obsolete extracellular space (GO:0005615), nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
nucleic acid metabolic process1
DNA binding1
endonuclease activity1
DNA nuclease activity1
binding1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

1956 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
BIVMPOGLUT2Q6UW63541
BIVMFAM199XQ6PEV8507
BIVMTEX9Q8N6V9424
BIVMLRRC23Q53EV4409
BIVMWDR27A2RRH5408
BIVMRGPD1P0C839394
BIVMLRRC74AQ0VAA2393
BIVMNAXDQ8IW45384
BIVMLRRC34Q8IZ02374
BIVMDEF8Q6ZN54369
BIVMTMTC3Q6ZXV5356
BIVMERCC4Q92889356
BIVMCRYBB3P26998353
BIVMNALCNQ8IZF0353
BIVMA0A2R8YFG2A0A2R8YFG2353
BIVMEXOSC10Q01780353
BIVMCOL9A3Q14050353

IntAct

33 interactions, top by confidence:

ABTypeScore
TRIM26BIVMpsi-mi:“MI:0915”(physical association)0.560
TRAF3BIVMpsi-mi:“MI:0915”(physical association)0.560
SPANXN2BIVMpsi-mi:“MI:0915”(physical association)0.560
BIVMpsi-mi:“MI:0915”(physical association)0.560
BIVML3MBTL2psi-mi:“MI:0915”(physical association)0.560
BIVMTRIM41psi-mi:“MI:0915”(physical association)0.560
BIVMPPIL6psi-mi:“MI:0915”(physical association)0.560
BAZ2BBIVMpsi-mi:“MI:0915”(physical association)0.560
LMO1BIVMpsi-mi:“MI:0915”(physical association)0.560
BIVMTRAF3psi-mi:“MI:0915”(physical association)0.000
SPANXN2BIVMpsi-mi:“MI:0915”(physical association)0.000
BIVMpsi-mi:“MI:0915”(physical association)0.000
TRIM41BIVMpsi-mi:“MI:0915”(physical association)0.000
PPIL6BIVMpsi-mi:“MI:0915”(physical association)0.000
BAZ2BBIVMpsi-mi:“MI:0915”(physical association)0.000
LMO1BIVMpsi-mi:“MI:0915”(physical association)0.000
L3MBTL2BIVMpsi-mi:“MI:0915”(physical association)0.000
TRAF3BIVMpsi-mi:“MI:0915”(physical association)0.000

BioGRID (14): BIVM (Two-hybrid), BIVM (Two-hybrid), BIVM (Two-hybrid), TRIM41 (Two-hybrid), LMO1 (Two-hybrid), PPIL6 (Two-hybrid), HOMEZ (Two-hybrid), TRIM26 (Two-hybrid), SPANXN2 (Two-hybrid), BIVM (Affinity Capture-MS), BIVM (Cross-Linking-MS (XL-MS)), BIVM (Cross-Linking-MS (XL-MS)), BIVM (Cross-Linking-MS (XL-MS)), BIVM (Affinity Capture-RNA)

ESM2 similar proteins: A0A2R6W1B1, A0FKI7, A2XC52, A2XTW9, A2Y0Q2, B8AMA8, B8B8I3, F4I9G2, O94972, P07106, P20067, P41135, P85828, Q5EAE9, Q5EAH9, Q5R7V3, Q5T8D3, Q5XEM9, Q5XG73, Q5XI67, Q6EPZ2, Q6GPE9, Q6IE24, Q6PCX9, Q70EL1, Q75IR6, Q76N89, Q7XUW3, Q84TV4, Q86UB2, Q8BJL1, Q8BL06, Q8CBX9, Q8H383, Q8H8C6, Q8K3A6, Q8K4P8, Q8LA16, Q8TB52, Q96S38

Diamond homologs: Q0V9T8, Q3KPR5, Q86UB2, Q8CBX9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic4
Likely pathogenic1
Uncertain significance18
Likely benign3
Benign2

Top pathogenic / likely-pathogenic (5)

Variant IDHGVSClassification
144504GRCh38/hg38 13q32.2-33.1(chr13:98008015-103697232)x3Pathogenic
150092GRCh38/hg38 13q32.3-33.2(chr13:101095590-105074548)x1Pathogenic
2424668NC_000013.10:g.(?102521055)(103718599_?)delPathogenic
815612GRCh37/hg19 13q32.1-33.2(chr13:96240346-106103782)x1Pathogenic
443022GRCh37/hg19 13q32.2-33.1(chr13:98607855-104370539)x3Likely pathogenic

SpliceAI

2323 predictions. Top by Δscore:

VariantEffectΔscore
13:102807745:GGTA:Gdonor_loss1.0000
13:102807746:G:Tdonor_loss1.0000
13:102807747:T:Adonor_loss1.0000
13:102816532:A:Tdonor_gain1.0000
13:102821128:GGAAA:Gdonor_gain1.0000
13:102821129:GAAA:Gdonor_gain1.0000
13:102821129:GAAAG:Gdonor_gain1.0000
13:102821130:A:Tdonor_gain1.0000
13:102821133:G:GGdonor_gain1.0000
13:102834547:TAAA:Tdonor_gain1.0000
13:102834548:AAAA:Adonor_gain1.0000
13:102834549:AAAA:Adonor_gain1.0000
13:102834553:G:GGdonor_gain1.0000
13:102816422:TTCTA:Tacceptor_loss0.9900
13:102816423:TCTA:Tacceptor_loss0.9900
13:102816423:TCTAG:Tacceptor_loss0.9900
13:102816425:TAG:Tacceptor_loss0.9900
13:102816425:TAGGC:Tacceptor_loss0.9900
13:102816426:A:AGacceptor_gain0.9900
13:102816426:A:Tacceptor_loss0.9900
13:102816427:G:GAacceptor_loss0.9900
13:102816427:G:GGacceptor_gain0.9900
13:102816427:G:GTacceptor_loss0.9900
13:102816427:GGC:Gacceptor_gain0.9900
13:102816427:GGCA:Gacceptor_gain0.9900
13:102816476:G:Tdonor_gain0.9900
13:102816561:T:Gdonor_gain0.9900
13:102821130:AAAGT:Adonor_loss0.9900
13:102821131:AA:Adonor_gain0.9900
13:102821131:AAG:Adonor_loss0.9900

AlphaMissense

3299 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
13:102821813:T:CF258L1.000
13:102821815:T:AF258L1.000
13:102821815:T:GF258L1.000
13:102822066:T:AW270R1.000
13:102822066:T:CW270R1.000
13:102831627:C:GH322D1.000
13:102831639:C:GH326D1.000
13:102838644:T:AW375R1.000
13:102838644:T:CW375R1.000
13:102807688:T:AW141R0.999
13:102807688:T:CW141R0.999
13:102821047:A:CS206R0.999
13:102821049:C:AS206R0.999
13:102821049:C:GS206R0.999
13:102821075:G:AG215D0.999
13:102821098:T:AW223R0.999
13:102821098:T:CW223R0.999
13:102821786:T:CF249L0.999
13:102821787:T:CF249S0.999
13:102821788:T:AF249L0.999
13:102821788:T:GF249L0.999
13:102821814:T:CF258S0.999
13:102821817:G:AG259D0.999
13:102821822:T:CF261L0.999
13:102821824:C:AF261L0.999
13:102821824:C:GF261L0.999
13:102821828:G:TG263W0.999
13:102821829:G:AG263E0.999
13:102821829:G:TG263V0.999
13:102821833:T:AN264K0.999

dbSNP variants (sampled 300 via entrez): RS1000029057 (13:102820969 G>A), RS1000041867 (13:102826495 CCTAA>C), RS1000055182 (13:102833537 G>C), RS1000108280 (13:102840564 G>T), RS1000152944 (13:102797996 A>G), RS1000173440 (13:102800346 G>C), RS1000209682 (13:102803685 A>G), RS1000240691 (13:102803373 C>T), RS1000271456 (13:102834403 A>G), RS1000289572 (13:102800108 G>A), RS1000292440 (13:102819956 C>A), RS1000390431 (13:102809396 C>G), RS1000414147 (13:102815822 G>C), RS1000472297 (13:102805818 T>C), RS1000519559 (13:102815588 T>A)

Disease associations

OMIM: gene MIM:619006 | disease phenotypes: MIM:606054, MIM:609637

GenCC curated gene-disease

Mondo (2): propionic acidemia (MONDO:0011628), holoprosencephaly 5 (MONDO:0012322)

Orphanet (2): Holoprosencephaly (Orphanet:2162), Propionic acidemia (Orphanet:35)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (2)

DescriptorNameTree numbers
D056693Propionic AcidemiaC16.320.565.100.823; C18.452.648.100.823
C566464Holoprosencephaly 5 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

45 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression3
trichostatin Aaffects cotreatment, increases expression2
Acetaminophendecreases expression2
Cyclosporinedecreases expression2
GSK-J4decreases expression1
triphenyl phosphateaffects expression1
alpha-pinenedecreases expression, increases abundance, affects cotreatment1
sodium arsenitedecreases expression1
butyraldehydedecreases expression1
methacrylaldehydeaffects cotreatment, decreases expression, increases abundance1
diallyl trisulfideincreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
ICG 001increases expression1
abrinedecreases expression1
dorsomorphinincreases expression, affects cotreatment1
bisphenol Saffects cotreatment, decreases expression1
NSC 689534decreases expression, affects binding1
(+)-JQ1 compounddecreases expression1
Temozolomidedecreases expression1
Zoledronic Aciddecreases expression1
Acroleinincreases abundance, affects cotreatment, decreases expression1
Air Pollutantsaffects cotreatment, decreases expression, increases abundance1
Ethanoldecreases expression1
Arsenicincreases methylation1
Carbamazepineaffects expression1
Copperaffects binding, decreases expression1
Dexamethasoneaffects cotreatment, decreases expression1
Doxorubicinincreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT02426775PHASE3COMPLETEDCarglumic Acid in Methylmalonic Acidemia and Propionic Acidemia
NCT01341379PHASE2WITHDRAWNIncreasing Ureagenesis in Inborn Errors of Metabolism With N-Carbamylglutamate
NCT01597440PHASE2TERMINATEDLong-term Outcome of N-Carbamylglutamate Treatment in Propionic Acidemia and Methylmalonic Acidemia
NCT04732429PHASE2TERMINATEDStudy of HST5040 in Subjects With Propionic or Methylmalonic Acidemia
NCT00645879PHASE1COMPLETEDAnaplerotic Therapy in Propionic Acidemia
NCT04836494PHASE1TERMINATEDA First in Human, Dose Escalation Study to Evaluate the Safety and Tolerability of BBP-671 in Healthy Volunteers and Patients With Propionic Acidemia or Methylmalonic Acidemia
NCT04159103PHASE1/PHASE2RECRUITINGOpen-Label Study of mRNA-3927 in Participants With Propionic Acidemia
NCT05130437PHASE1/PHASE2RECRUITINGA Study to Assess the Long-term Safety and Clinical Activity of mRNA-3927 in Participants Previously Enrolled in the mRNA-3927-P101 Study
NCT02890342Not specifiedRECRUITINGNatural History, Physiology, Microbiome and Biochemistry Studies of Propionic Acidemia
NCT03159026Not specifiedCOMPLETEDReview of Charts From Amish/Mennonite Variant PA Patients
NCT03484767Not specifiedCOMPLETEDThe MaP Study: Mapping the Patient Journey in MMA and PA
NCT03655223Not specifiedENROLLING_BY_INVITATIONEarly Check: Expanded Screening in Newborns
NCT04176523Not specifiedRECRUITINGUnderstanding the Long-Term Management of Organic Acidemia Patients With CARBAGLU®: A Mixed Methods Approach
NCT05040178Not specifiedRECRUITINGAn Observational Study of Carbaglu® for the Treatment of MMA and PA in Adults and Pediatrics
NCT05330039Not specifiedCOMPLETEDCharacterization of Intestinal Microbiota in Children With Inborn Errors of Metabolism (IEM)
NCT05438485Not specifiedTERMINATEDNatural History Study of Patients With Methylmalonic Acidemia and Propionic Acidemia
NCT05687474Not specifiedCOMPLETEDBaby Detect : Genomic Newborn Screening
NCT05769621Not specifiedRECRUITINGA Retrospective Study to Characterize Participants With Propionic Acidemia
NCT06664840Not specifiedNOT_YET_RECRUITINGMyRareDiet A Novel Diet Tracking Tool
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): holoprosencephaly 5, propionic acidemia