HIRIP3

gene
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Summary

HIRIP3 (HIRA interacting protein 3, HGNC:4917) is a protein-coding gene on chromosome 16p11.2, encoding HIRA-interacting protein 3 (Q9BW71). Histone chaperone that carries a H2A-H2B histone complex and facilitates its deposition onto chromatin.

The HIRA protein shares sequence similarity with Hir1p and Hir2p, the two corepressors of histone gene transcription characterized in the yeast, Saccharomyces cerevisiae. The structural features of the HIRA protein suggest that it may function as part of a multiprotein complex. Several cDNAs encoding HIRA-interacting proteins, or HIRIPs, have been identified. In vitro, the protein encoded by this gene binds HIRA, as well as H2B and H3 core histones, indicating that a complex containing HIRA-HIRIP3 could function in some aspects of chromatin and histone metabolism. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene.

Source: NCBI Gene 8479 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 108 total — 1 likely-pathogenic
  • Druggable target: yes — 1 molecules with ChEMBL bioactivity
  • MANE Select transcript: NM_003609

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:4917
Approved symbolHIRIP3
NameHIRA interacting protein 3
Location16p11.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000149929
Ensembl biotypeprotein_coding
OMIM603365
Entrez8479

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 12 protein_coding, 4 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000279392, ENST00000563053, ENST00000563680, ENST00000564026, ENST00000565996, ENST00000566471, ENST00000568880, ENST00000873668, ENST00000873669, ENST00000873670, ENST00000873671, ENST00000873672, ENST00000873673, ENST00000918288, ENST00000948388, ENST00000948389, ENST00000948390

RefSeq mRNA: 2 — MANE Select: NM_003609 NM_001197323, NM_003609

CCDS: CCDS10664, CCDS58449

Canonical transcript exons

ENST00000279392 — 7 exons

ExonStartEnd
ENSE000009930262999390629994843
ENSE000026088322999554129995617
ENSE000026285772999233029993370
ENSE000035461762999510329995217
ENSE000036031992999534329995463
ENSE000036262502999364029993808
ENSE000036685542999345929993557

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 94.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.3504 / max 315.7795, expressed in 1718 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
1569814.56721375
1569834.55101537
1569820.5175316
1569840.4923219
1569800.222486

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
oocyteCL:000002394.25gold quality
left testisUBERON:000453393.77gold quality
right testisUBERON:000453493.58gold quality
testisUBERON:000047391.64gold quality
ganglionic eminenceUBERON:000402391.61gold quality
ventricular zoneUBERON:000305391.47gold quality
apex of heartUBERON:000209891.10gold quality
C1 segment of cervical spinal cordUBERON:000646990.82gold quality
spinal cordUBERON:000224090.07gold quality
secondary oocyteCL:000065589.67gold quality
gastrocnemiusUBERON:000138889.59gold quality
hindlimb stylopod muscleUBERON:000425289.47gold quality
embryoUBERON:000092289.42gold quality
muscle of legUBERON:000138389.06gold quality
type B pancreatic cellCL:000016988.90gold quality
gluteal muscleUBERON:000200088.43gold quality
cerebellar hemisphereUBERON:000224588.39gold quality
prefrontal cortexUBERON:000045188.33gold quality
cerebellar cortexUBERON:000212988.33gold quality
right hemisphere of cerebellumUBERON:001489088.32gold quality
lateral globus pallidusUBERON:000247688.20silver quality
amygdalaUBERON:000187688.01gold quality
lower esophagus muscularis layerUBERON:003583387.73gold quality
lower esophagusUBERON:001347387.69gold quality
cerebellumUBERON:000203787.68gold quality
putamenUBERON:000187487.63gold quality
muscle organUBERON:000163087.60gold quality
esophagogastric junction muscularis propriaUBERON:003584187.46gold quality
heart left ventricleUBERON:000208487.40gold quality
triceps brachiiUBERON:000150987.39gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes6.67

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

40 targeting HIRIP3, 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-340-5P100.0072.504437
HSA-MIR-493-5P99.9672.472382
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-6744-5P99.9366.82748
HSA-MIR-515-5P99.9269.822343
HSA-MIR-519E-5P99.9269.622358
HSA-MIR-1251-3P99.6467.211408
HSA-MIR-397599.6265.97697
HSA-MIR-3136-3P99.5766.59781
HSA-MIR-7155-3P99.5766.48794
HSA-MIR-427699.5667.662514
HSA-MIR-4687-3P99.4866.41968
HSA-MIR-312399.4767.152693
HSA-MIR-942-5P99.4168.401977
HSA-MIR-431199.3170.473041
HSA-MIR-4667-3P99.2665.451608
HSA-MIR-797499.2465.481137
HSA-MIR-7854-3P99.0866.261117
HSA-MIR-625-5P99.0268.642031
HSA-MIR-361-5P98.9570.161340
HSA-MIR-3928-5P98.5067.48980
HSA-MIR-6806-3P98.5067.31980
HSA-MIR-58198.3967.42835
HSA-MIR-4664-5P98.1765.071020
HSA-MIR-444398.0266.251928
HSA-MIR-92497.7866.21681
HSA-MIR-483-3P97.7764.95731
HSA-MIR-467597.6964.82774
HSA-MIR-474197.6964.14883

Literature-anchored findings (GeneRIF, showing 2)

  • HIRIP3 can be phosphorylated in vitro by a recombinant form of the serine-threonine kinase CK2. Moreover, HIRIP3 protein was found to co-purify with a CK2 activity. (PMID:17391060)
  • Identification and Characterization of HIRIP3 as a Histone H2A Chaperone. (PMID:38334665)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriohirip3ENSDARG00000027749
mus_musculusHirip3ENSMUSG00000042606
rattus_norvegicusHirip3ENSRNOG00000029061

Protein

Protein identifiers

HIRA-interacting protein 3Q9BW71 (reviewed: Q9BW71)

All UniProt accessions (1): Q9BW71

UniProt curated annotations — full annotation on UniProt →

Function. Histone chaperone that carries a H2A-H2B histone complex and facilitates its deposition onto chromatin.

Subunit / interactions. Interacts (via C-terminus) with histone H2A-H2B dimers; the interaction is direct. Interacts with HIRA. Interacts with CK2.

Subcellular location. Nucleus.

Tissue specificity. Widely expressed. Isoform 1 is predominant in skeletal muscle. Isoform 2 is predominant in liver and heart.

Post-translational modifications. Phosphorylated by CK2.

Isoforms (3)

UniProt IDNamesCanonical?
Q9BW71-11yes
Q9BW71-22
Q9BW71-33

RefSeq proteins (2): NP_001184252, NP_003600* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR019098Histone_chaperone_domain_CHZDomain
IPR037647HIRIP3Family

Pfam: PF09649

UniProt features (50 total): modified residue 30, compositionally biased region 10, region of interest 3, splice variant 3, sequence variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BW71-F160.040.21

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 (30): 27, 84, 87, 98, 100, 125, 142, 143, 159, 160, 196, 199, 223, 227, 289, 291, 330, 332, 333, 357 …

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 143 (showing top): GGAMTNNNNNTCCY_UNKNOWN, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, chr16p11, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, IVANOVA_HEMATOPOIESIS_STEM_CELL_SHORT_TERM, FISCHER_DREAM_TARGETS, ACTWSNACTNY_UNKNOWN, GOCC_NUCLEOLUS, SCGGAAGY_ELK1_02, MULLIGHAN_MLL_SIGNATURE_1_UP, MGGAAGTG_GABP_B, NAKAMURA_METASTASIS_MODEL_UP, CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_DN, GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_UP, PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7

GO Biological Process (1): chromatin organization (GO:0006325)

GO Molecular Function (2): H2A-H2B histone complex chaperone activity (GO:0000511), protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
nuclear lumen2
cellular component organization1
histone chaperone activity1
binding1
intracellular membrane-bounded organelle1
cellular anatomical structure1
intracellular membraneless organelle1

Protein interactions and networks

STRING

614 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
HIRIP3HIRAP54198816
HIRIP3H2BC21Q16778760
HIRIP3SEZ6L2Q6UXD5703
HIRIP3DOC2AQ14183696
HIRIP3ASPHD1Q5U4P2688
HIRIP3KIF22Q14807679
HIRIP3PAGR1Q9BTK6676
HIRIP3C16orf54Q6UWD8664
HIRIP3KCTD13Q8WZ19643
HIRIP3YPEL3P61236640
HIRIP3INO80EQ8NBZ0627
HIRIP3TMEM219Q86XT9605
HIRIP3FIMP1Q96LL3602
HIRIP3TAOK2Q9UL54602
HIRIP3PPP4CP33172601

IntAct

47 interactions, top by confidence:

ABTypeScore
CSNK2A2EIF3Jpsi-mi:“MI:0914”(association)0.790
HIRIP3CSNK2Bpsi-mi:“MI:0914”(association)0.730
HIRIP3AMPD2psi-mi:“MI:0915”(physical association)0.710
ASF1BHAT1psi-mi:“MI:0914”(association)0.640
AMPD2SDC2psi-mi:“MI:0914”(association)0.640
CSNK2A2PES1psi-mi:“MI:0914”(association)0.640
HIRIP3SGK2psi-mi:“MI:0915”(physical association)0.560
HTTHIRIP3psi-mi:“MI:0915”(physical association)0.560
ENGHIRIP3psi-mi:“MI:0407”(direct interaction)0.440
HIRIP3SRPK2psi-mi:“MI:0217”(phosphorylation reaction)0.440
SRPK1HIRIP3psi-mi:“MI:0217”(phosphorylation reaction)0.440
HIRIP3VDAC3psi-mi:“MI:0915”(physical association)0.400
HIRIP3H2BC9psi-mi:“MI:0915”(physical association)0.400
HIRIP3H2BC12Lpsi-mi:“MI:0915”(physical association)0.400
HIRIP3H1-4psi-mi:“MI:0915”(physical association)0.400
HIRIP3PDIA3psi-mi:“MI:0915”(physical association)0.400
CSNK2A1MYO1Bpsi-mi:“MI:0914”(association)0.350
TMPOpsi-mi:“MI:0914”(association)0.350
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
HIRIP3H2AXpsi-mi:“MI:0914”(association)0.350
RYBPPIPSLpsi-mi:“MI:0914”(association)0.350
CSNK2A2CNOT1psi-mi:“MI:0914”(association)0.350
CSNK2A1EIF3Fpsi-mi:“MI:0914”(association)0.350
IQCB1PCP4L1psi-mi:“MI:0914”(association)0.350

BioGRID (117): HIRIP3 (Affinity Capture-MS), HIRIP3 (Affinity Capture-MS), HIRIP3 (Co-fractionation), RPL8 (Co-fractionation), HIRIP3 (Proximity Label-MS), HIRIP3 (Affinity Capture-MS), HIRIP3 (Affinity Capture-MS), HIRIP3 (Affinity Capture-MS), HIRIP3 (Affinity Capture-MS), HIRIP3 (Affinity Capture-MS), HIRA (Reconstituted Complex), HIRIP3 (Affinity Capture-MS), HIRIP3 (Two-hybrid), HIRIP3 (Affinity Capture-MS), HIRIP3 (Proximity Label-MS)

ESM2 similar proteins: A0P8Z5, A2AJT4, A6NNA2, A7MD48, F1LR10, O88573, P0CB65, P51825, P51826, P51827, Q14241, Q2KJH5, Q2T9Y0, Q569Z6, Q5BJ39, Q5M7V8, Q5PPJ2, Q5RD75, Q5T6C5, Q5VUA4, Q63187, Q6QZN6, Q6ZPR1, Q80WV7, Q80Z37, Q8BKA3, Q8BM65, Q8BTI8, Q8BZX4, Q8CB77, Q8K019, Q8TF01, Q93075, Q96B23, Q96IZ7, Q96RL1, Q99PP2, Q9BW71, Q9DBU6, Q9ERQ3

Diamond homologs: Q8BLH7, Q9BW71

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 49 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.

Reactome pathways:

PathwayPartnersFoldFDR
Replacement of protamines by nucleosomes in the male pronucleus534.9×5e-05
Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks518.8×4e-04
CHD1 and CHD2 subfamily513.9×9e-04
NoRC negatively regulates rRNA expression513.4×9e-04
Activation of anterior HOX genes in hindbrain development during early embryogenesis511.7×1e-03

GO biological processes:

GO termPartnersFoldFDR
nucleosome assembly721.9×1e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic1
Uncertain significance89
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
1330157GRCh37/hg19 16p11.2(chr16:29974415-30596982)x1Likely pathogenic

SpliceAI

1096 predictions. Top by Δscore:

VariantEffectΔscore
16:29993366:CCGGC:Cacceptor_gain1.0000
16:29993367:CGGC:Cacceptor_gain1.0000
16:29993367:CGGCC:Cacceptor_gain1.0000
16:29993368:GGC:Gacceptor_gain1.0000
16:29993369:GC:Gacceptor_gain1.0000
16:29993370:CC:Cacceptor_gain1.0000
16:29993371:C:CCacceptor_gain1.0000
16:29993372:T:Cacceptor_loss1.0000
16:29993453:CCTTA:Cdonor_loss1.0000
16:29993454:CTTA:Cdonor_loss1.0000
16:29993455:TTACC:Tdonor_loss1.0000
16:29993456:TA:Tdonor_loss1.0000
16:29993457:A:ACdonor_gain1.0000
16:29993457:AC:Adonor_gain1.0000
16:29993457:ACCCG:Adonor_loss1.0000
16:29993458:C:CCdonor_gain1.0000
16:29993458:CC:Cdonor_gain1.0000
16:29993638:AC:Adonor_gain1.0000
16:29993639:CC:Cdonor_gain1.0000
16:29993639:CCCTT:Cdonor_gain1.0000
16:29993652:G:Cdonor_gain1.0000
16:29993657:T:TAdonor_gain1.0000
16:29993681:A:ACdonor_gain1.0000
16:29993681:AGG:Adonor_gain1.0000
16:29993681:AGGCG:Adonor_gain1.0000
16:29993682:G:Cdonor_gain1.0000
16:29993804:CCAGC:Cacceptor_gain1.0000
16:29993805:CAGC:Cacceptor_gain1.0000
16:29993805:CAGCC:Cacceptor_gain1.0000
16:29993807:GC:Gacceptor_gain1.0000

AlphaMissense

3652 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:29993660:A:GL463P0.998
16:29993672:A:TL459H0.998
16:29993758:C:AK430N0.998
16:29993758:C:GK430N0.998
16:29995576:G:CF10L0.997
16:29995576:G:TF10L0.997
16:29995578:A:GF10L0.997
16:29993672:A:GL459P0.996
16:29993750:A:TI433N0.996
16:29993762:A:GL429P0.995
16:29993254:A:GW542R0.994
16:29993254:A:TW542R0.994
16:29993660:A:TL463Q0.994
16:29993750:A:GI433T0.994
16:29993228:G:CS550R0.993
16:29993228:G:TS550R0.993
16:29993230:T:GS550R0.993
16:29993750:A:CI433S0.993
16:29993745:C:GA435P0.992
16:29993252:C:AW542C0.991
16:29993252:C:GW542C0.991
16:29995577:A:GF10S0.991
16:29993232:A:TI549N0.990
16:29993523:C:AK481N0.990
16:29993523:C:GK481N0.990
16:29993741:C:TC436Y0.990
16:29995356:A:GL58P0.990
16:29993473:A:GI498T0.989
16:29993488:A:GL493S0.989
16:29993645:A:GM468T0.989

dbSNP variants (sampled 300 via entrez): RS1000638423 (16:29994476 A>G), RS1001278787 (16:29998006 A>G), RS1001640977 (16:29995506 G>A), RS1002589261 (16:29991940 C>G), RS1003059588 (16:29995361 C>T), RS1003113623 (16:29995654 T>C), RS1003367469 (16:29996125 T>A,G), RS1004591487 (16:29996288 T>C), RS1005078146 (16:29995915 G>C), RS1005673423 (16:29997093 C>T), RS1006344812 (16:29992551 G>C), RS1006397241 (16:29992198 C>G,T), RS1006591970 (16:29994094 T>C), RS1006950842 (16:29994424 C>T), RS1007271169 (16:29997702 C>T)

Disease associations

OMIM: gene MIM:603365 | disease phenotypes: MIM:613444

GenCC curated gene-disease

Mondo (1): distal 16p11.2 microdeletion syndrome (MONDO:0013267)

Orphanet (1): Distal 16p11.2 microdeletion syndrome (Orphanet:261222)

HPO phenotypes

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

GWAS associations

7 associations (top):

StudyTraitp-value
GCST002539_82Schizophrenia5.000000e-11
GCST004521_236Autism spectrum disorder or schizophrenia4.000000e-10
GCST006803_23Schizophrenia6.000000e-13
GCST007293_15Body fat distribution (arm fat ratio)6.000000e-06
GCST007293_81Body fat distribution (arm fat ratio)4.000000e-08
GCST007611_22Chronic obstructive pulmonary disease or high blood pressure (pleiotropy)7.000000e-09
GCST010703_269Brain morphology (MOSTest)4.000000e-13

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004341body fat distribution
EFO:0004346neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5724673 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 1,538 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL1232461MOLIBRESIB21,538

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
7.12Kd75nMMOLIBRESIB
7.05IC5090nMMOLIBRESIB

PubChem BioAssay actives

2 with measured affinity, of 7 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide2179241: Binding affinity against HIRIP3 (unknown origin) assessed as apparent dissociation constant incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysiskd0.0750uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases expression, decreases expression, increases abundance3
bisphenol Aaffects cotreatment, increases expression, decreases expression2
Valproic Aciddecreases expression, increases methylation2
aristolochic acid Idecreases expression1
GSK-J4decreases expression1
FR900359affects phosphorylation1
methylmercuric chloridedecreases expression1
propionaldehydedecreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, increases expression1
coumarinaffects phosphorylation1
isobutyl alcoholaffects cotreatment, decreases expression, increases abundance1
di-n-butylphosphoric acidaffects expression1
trans-10,cis-12-conjugated linoleic aciddecreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibdecreases expression1
Arsenicincreases abundance, increases expression1
Atrazinedecreases expression1
Benzo(a)pyreneincreases methylation1
Caffeinedecreases phosphorylation1
Calcitrioldecreases expression, affects cotreatment1
Coumestrolaffects cotreatment, increases expression1
Dexamethasoneaffects cotreatment, increases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Estradiolincreases expression1
Gasolineaffects cotreatment, decreases expression, increases abundance1
Indomethacinaffects cotreatment, increases expression1
Ivermectindecreases expression1
Methyl Methanesulfonateincreases expression1
Polycyclic Aromatic Hydrocarbonsaffects cotreatment, decreases expression, increases abundance1
Potassium Dichromateincreases expression1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5697735BindingInhibition of HIRIP3 (unknown origin) assessed as fold change at 10 uM incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysisInhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia. — Nature

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): distal 16p11.2 microdeletion syndrome