XIRP2

gene
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Summary

XIRP2 (xin actin binding repeat containing 2, HGNC:14303) is a protein-coding gene on chromosome 2q24.3, encoding Xin actin-binding repeat-containing protein 2 (A4UGR9). Protects actin filaments from depolymerization.

Enables actin filament binding activity. Predicted to be involved in actin filament organization and regulation of actin filament organization. Predicted to act upstream of or within cardiac muscle tissue morphogenesis; cell-cell junction organization; and ventricular septum development. Located in focal adhesion and stress fiber. Implicated in depressive disorder.

Source: NCBI Gene 129446 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 724 total
  • Phenotypes (HPO): 1
  • MANE Select transcript: NM_152381

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14303
Approved symbolXIRP2
Namexin actin binding repeat containing 2
Location2q24.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000163092
Ensembl biotypeprotein_coding
OMIM609778
Entrez129446

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 8 protein_coding, 1 retained_intron

ENST00000409043, ENST00000409195, ENST00000409273, ENST00000409605, ENST00000409728, ENST00000628543, ENST00000672277, ENST00000672671, ENST00000672716

RefSeq mRNA: 5 — MANE Select: NM_152381 NM_001079810, NM_001199143, NM_001199144, NM_001199145, NM_152381

CCDS: CCDS42768, CCDS42769, CCDS56143, CCDS56144, CCDS56145

Canonical transcript exons

ENST00000409195 — 11 exons

ExonStartEnd
ENSE00000000295166888480166888557
ENSE00001276753167242569167251947
ENSE00001299302167135909167136062
ENSE00001300610167239855167239965
ENSE00001317162167241777167241910
ENSE00001320657167240664167240736
ENSE00001324449167218166167218300
ENSE00001580025166903465166903890
ENSE00003591481167210735167210895
ENSE00003607800167254032167254165
ENSE00003901999167257857167259753

Expression profiles

Bgee: expression breadth ubiquitous, 150 present calls, max score 99.92.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 5.4002 / max 2598.6808, expressed in 77 samples.

FANTOM5 promoters (45 alternative TSS)

Promoter IDTPM avgSamples expressed
234503.687255
234490.334332
234940.118918
234900.104620
234800.081517
234720.075717
234980.074518
234820.070314
234770.063811
234810.050512

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
deltoidUBERON:000147699.92gold quality
biceps brachiiUBERON:000150799.86gold quality
quadriceps femorisUBERON:000137799.85gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451199.85gold quality
vastus lateralisUBERON:000137999.84gold quality
tibialis anteriorUBERON:000138599.84gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450299.82gold quality
skeletal muscle tissueUBERON:000113499.69gold quality
left ventricle myocardiumUBERON:000656699.68gold quality
body of tongueUBERON:001187699.48gold quality
hindlimb stylopod muscleUBERON:000425299.45gold quality
heart right ventricleUBERON:000208099.27gold quality
gastrocnemiusUBERON:000138899.26gold quality
myocardiumUBERON:000234998.25gold quality
apex of heartUBERON:000209898.08gold quality
muscle organUBERON:000163097.90gold quality
skeletal muscle organUBERON:001489297.90gold quality
muscle of legUBERON:000138397.39gold quality
cardiac muscle of right atriumUBERON:000337996.30gold quality
cardiac ventricleUBERON:000208296.25gold quality
heart left ventricleUBERON:000208496.18gold quality
tongueUBERON:000172393.25gold quality
muscle tissueUBERON:000238593.25gold quality
heartUBERON:000094887.56gold quality
cardiac atriumUBERON:000208186.37gold quality
right atrium auricular regionUBERON:000663185.72gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047384.33silver quality
superior surface of tongueUBERON:000737183.95gold quality
pharyngeal mucosaUBERON:000035582.44gold quality
larynxUBERON:000173782.35gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-MTAB-11268no1929.05
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MEF2A

miRNA regulators (miRDB)

99 targeting XIRP2, 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-4795-3P100.0074.624024
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-477599.9875.006394
HSA-MIR-314899.9775.066478
HSA-MIR-570-3P99.9672.414910
HSA-MIR-590-3P99.9674.346478
HSA-MIR-3912-5P99.9566.11925
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-767-5P99.9570.85993
HSA-MIR-144-3P99.9473.982698
HSA-MIR-1236-3P99.9468.041695
HSA-MIR-335-3P99.9373.364958
HSA-MIR-4760-3P99.9370.502385
HSA-MIR-205-3P99.9269.923165
HSA-MIR-145-5P99.9271.131836
HSA-MIR-5195-3P99.9270.921877
HSA-MIR-589-3P99.9169.622088
HSA-MIR-374A-5P99.9071.342923
HSA-MIR-374B-5P99.9069.982734
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-627-3P99.9071.423316
HSA-MIR-6499-3P99.9066.381212
HSA-MIR-153-5P99.8973.866317
HSA-MIR-17-5P99.8973.832665
HSA-MIR-106B-5P99.8874.722795
HSA-MIR-20B-5P99.8874.012621
HSA-MIR-519D-3P99.8873.972607
HSA-MIR-526B-3P99.8874.062587

Literature-anchored findings (GeneRIF, showing 4)

  • Xin and XIRP2 define a novel actin-binding motif (PMID:15454575)
  • Genetic information from this patient implies that genes involved in development and maintenance of extraocular muscles can cause congenital ocular motility disorders as well. (PMID:24475916)
  • A genome-wide association study reveals 2 new susceptibility loci for atopic dermatitis, XIRP2 and DMRTA1. (PMID:25865352)
  • Report pathogenic XIRP1/2 rare variants in arrhythmogenic disorders such as sudden unexplained nocturnal death syndrome and Brugada syndrome. (PMID:29306897)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusXirp2ENSMUSG00000027022
rattus_norvegicusXirp2ENSRNOG00000034258

Paralogs (1): XIRP1 (ENSG00000168334)

Protein

Protein identifiers

Xin actin-binding repeat-containing protein 2A4UGR9 (reviewed: A4UGR9)

Alternative names: Beta-xin, Cardiomyopathy-associated protein 3, Xeplin

All UniProt accessions (3): A0A5F9ZH43, A0A5F9ZHW6, A4UGR9

UniProt curated annotations — full annotation on UniProt →

Function. Protects actin filaments from depolymerization. Required for correct morphology of cell membranes and maturation of intercalated disks of cardiomyocytes via facilitating localization of XIRP1 and CDH2 to the termini of aligned mature cardiomyocytes. Thereby required for correct postnatal heart development and growth regulation that is crucial for overall heart morphology and diastolic function. Required for normal electrical conduction in the heart including formation of the infranodal ventricular conduction system and normal action potential configuration, as a result of its interaction with the cardiac ion channel components Scn5a/Nav1.5 and Kcna5/Kv1.5. Required for regular actin filament spacing of the paracrystalline array in both inner and outer hair cells of the cochlea, thereby required for maintenance of stereocilia morphology.

Subunit / interactions. Interacts with ACTN2. Interacts with F-actin. Interacts with NEBL (via SH3 domain). Interacts with Kcna5/Kv1.5 and Scn5a/Nav1.5; the interactions are required for normal action potential configuration in the heart.

Subcellular location. Cell junction.

Tissue specificity. Expressed in skeletal muscle at areas of Z-disk disruption in a longitudinal pattern spanning one or more sarcomeres (at protein level). Weakly expressed in mature myofibrils (at protein level). Expressed in the blood.

Domain organisation. Xin repeats bind F-actin.

Miscellaneous. ‘Xin’ means ‘heart’ in Chinese.

Similarity. Belongs to the Xin family.

Isoforms (8)

UniProt IDNamesCanonical?
A4UGR9-11yes
A4UGR9-22
A4UGR9-33
A4UGR9-44
A4UGR9-55
A4UGR9-66
A4UGR9-77
A4UGR9-88

RefSeq proteins (5): NP_001073278, NP_001186072, NP_001186073, NP_001186074, NP_689594* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR012510Actin-binding_Xin_repeatRepeat
IPR030072XIRP1/XIRP2Family

Pfam: PF08043

UniProt features (123 total): sequence variant 32, repeat 28, sequence conflict 17, compositionally biased region 15, modified residue 11, region of interest 8, splice variant 7, coiled-coil region 4, chain 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
4F14X-RAY DIFFRACTION1.2

Predicted structure (AlphaFold)

No AlphaFold model available for A4UGR9 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

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 (11): 621, 868, 1265, 1629, 1989, 1994, 2222, 2276, 2318, 3059, 3297

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-9662360Sensory processing of sound by inner hair cells of the cochlea
R-HSA-9662361Sensory processing of sound by outer hair cells of the cochlea

MSigDB gene sets: 97 (showing top): GOBP_CARDIAC_CHAMBER_DEVELOPMENT, LI_CISPLATIN_RESISTANCE_DN, GOBP_MUSCLE_TISSUE_DEVELOPMENT, GOBP_CARDIAC_SEPTUM_DEVELOPMENT, GOBP_POSITIVE_REGULATION_OF_PROTEIN_LOCALIZATION, GOBP_REGULATION_OF_ACTIN_FILAMENT_BASED_PROCESS, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_CELL_JUNCTION_ORGANIZATION, GOBP_MUSCLE_STRUCTURE_DEVELOPMENT, GOBP_HEART_MORPHOGENESIS, GOBP_ACTIN_FILAMENT_ORGANIZATION, chr2q24, GOBP_CARDIAC_MUSCLE_TISSUE_MORPHOGENESIS, GOBP_MUSCLE_ORGAN_MORPHOGENESIS, GOBP_CARDIAC_VENTRICLE_DEVELOPMENT

GO Biological Process (7): ventricular septum development (GO:0003281), actin filament organization (GO:0007015), cell-cell junction organization (GO:0045216), cardiac muscle tissue morphogenesis (GO:0055008), regulation of actin filament organization (GO:0110053), positive regulation of protein localization (GO:1903829), actin cytoskeleton organization (GO:0030036)

GO Molecular Function (5): actin filament binding (GO:0051015), alpha-actinin binding (GO:0051393), actin binding (GO:0003779), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (6): cell-cell junction (GO:0005911), Z disc (GO:0030018), stress fiber (GO:0001725), focal adhesion (GO:0005925), cell junction (GO:0030054), anchoring junction (GO:0070161)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Sensory processing of sound2

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
cardiac ventricle development1
cardiac septum development1
actin cytoskeleton organization1
supramolecular fiber organization1
cell junction organization1
heart morphogenesis1
cardiac muscle tissue development1
muscle tissue morphogenesis1
actin filament organization1
regulation of actin cytoskeleton organization1
regulation of supramolecular fiber organization1
intracellular protein localization1
regulation of protein localization1
positive regulation of biological process1
cytoskeleton organization1
actin filament-based process1
actin binding1
protein-containing complex binding1
actinin binding1
cytoskeletal protein binding1
binding1
cation binding1
anchoring junction1
I band1
actomyosin1
contractile actin filament bundle1
cell-substrate junction1
cell junction1

Protein interactions and networks

STRING

1658 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
XIRP2MEF2AQ02078753
XIRP2ACTN2P35609725
XIRP2NEBLO76041631
XIRP2CSMD3Q7Z407605
XIRP2LRP1BQ9NZR2576
XIRP2USH2AO75445547
XIRP2ZFHX4Q86UP3544
XIRP2TTNQ8WZ42537
XIRP2MUC16Q8WXI7510
XIRP2RYR2Q92736491
XIRP2PKHD1L1Q86WI1486
XIRP2PCLOQ9Y6V0482
XIRP2NAV3Q8IVL0470
XIRP2CNBD1Q8NA66467
XIRP2SPTA1P02549459

IntAct

29 interactions, top by confidence:

ABTypeScore
XIRP2NEBLpsi-mi:“MI:0915”(physical association)0.670
NEBLXIRP2psi-mi:“MI:0407”(direct interaction)0.670
XIRP2NEBLpsi-mi:“MI:0407”(direct interaction)0.670
XIRP2NEBpsi-mi:“MI:0915”(physical association)0.600
XIRP2NEBpsi-mi:“MI:0407”(direct interaction)0.600
NEBXIRP2psi-mi:“MI:0407”(direct interaction)0.600
VASPXIRP2psi-mi:“MI:0407”(direct interaction)0.440
XIRP2LRRK2psi-mi:“MI:0407”(direct interaction)0.440
XIRP2PNPT1psi-mi:“MI:0915”(physical association)0.400
XIRP2H2BC9psi-mi:“MI:0915”(physical association)0.400
XIRP2H1-5psi-mi:“MI:0915”(physical association)0.400
XIRP2H1-4psi-mi:“MI:0915”(physical association)0.400
TTKXIRP2psi-mi:“MI:0915”(physical association)0.400
PCNAXIRP2psi-mi:“MI:0915”(physical association)0.370
CRY1IGKV2D-30psi-mi:“MI:0914”(association)0.350
NSMAFXIRP2psi-mi:“MI:0914”(association)0.350
DYRK1ATEX13Dpsi-mi:“MI:0914”(association)0.350
PDE3ATMEM131Lpsi-mi:“MI:0914”(association)0.350
XIRP2ATE1psi-mi:“MI:0914”(association)0.350
AKT1XIRP2psi-mi:“MI:2364”(proximity)0.270
BRAFXIRP2psi-mi:“MI:2364”(proximity)0.270
FBXW7XIRP2psi-mi:“MI:2364”(proximity)0.270
SMAD4XIRP2psi-mi:“MI:2364”(proximity)0.270
XIRP2DYSFpsi-mi:“MI:0915”(physical association)0.000

BioGRID (48): XIRP2 (Reconstituted Complex), HIST1H1E (Proximity Label-MS), PNPT1 (Proximity Label-MS), HIST1H1B (Proximity Label-MS), HIST1H2BH (Proximity Label-MS), XIRP2 (Two-hybrid), XIRP2 (Affinity Capture-MS), XIRP2 (Affinity Capture-MS), HECW2 (Affinity Capture-MS), XIRP2 (Affinity Capture-MS), ATE1 (Affinity Capture-MS), NEDD4L (Affinity Capture-MS), BAG3 (Affinity Capture-MS), XIRP2 (Affinity Capture-MS), DIS3 (Affinity Capture-MS)

ESM2 similar proteins: A0MZ66, A0MZ67, A2APB8, A4IH24, A4UGR9, A6H6Z7, A9JRM0, D4A702, E7F7X0, O35867, O60566, P13505, P14317, P49710, Q14247, Q1LVV0, Q28IH8, Q2MJV9, Q3B820, Q3MHH7, Q4KM62, Q4R6Q9, Q4U4S6, Q5E9V3, Q5NVK0, Q5PZ43, Q5R6I2, Q5RAF2, Q60598, Q66HL2, Q66KE9, Q6AYN9, Q6DDV8, Q6DFB7, Q6NUF4, Q6P0R8, Q6ZUJ8, Q71LX6, Q7T0S7, Q80ZU5

Diamond homologs: A4UGR9, Q4U4S6, Q5PZ43, Q71LX6, Q91957, O70373, Q702N8, B0KYV5, D4A1F2, E7F9T0, F1LR10, F1MF74, F1MH07, F1QH17, F1QWK4, F1RA39, F6QZ15, G3MWR8, O04193, O60952, O80839, O94851, P29675, Q0VFX8, Q1ECF5, Q1LZA7, Q4KM31, Q500W4, Q7F9R9, Q7RTP6, Q86BA1, Q8BGB5, Q8BML1, Q8CJ19, Q94JX5, Q9BIW4, Q9BT23, Q9ERG0, Q9M047, Q9UHB6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance522
Likely benign100
Benign73

Top pathogenic / likely-pathogenic (0)

SpliceAI

3387 predictions. Top by Δscore:

VariantEffectΔscore
2:167135904:AACAG:Aacceptor_gain1.0000
2:167135906:CA:Cacceptor_loss1.0000
2:167135908:GGAA:Gacceptor_gain1.0000
2:167136058:TGAAG:Tdonor_loss1.0000
2:167136059:GAAGG:Gdonor_loss1.0000
2:167136060:AAGG:Adonor_loss1.0000
2:167136061:AGGTT:Adonor_loss1.0000
2:167136063:GTTA:Gdonor_loss1.0000
2:167181606:G:GTdonor_gain1.0000
2:167183129:G:Tdonor_gain1.0000
2:167210730:TTCA:Tacceptor_loss1.0000
2:167210731:TCAG:Tacceptor_loss1.0000
2:167210733:A:AGacceptor_gain1.0000
2:167210733:AGC:Aacceptor_gain1.0000
2:167210734:G:GAacceptor_gain1.0000
2:167210734:G:GTacceptor_loss1.0000
2:167210734:GC:Gacceptor_gain1.0000
2:167210734:GCG:Gacceptor_gain1.0000
2:167210734:GCGA:Gacceptor_gain1.0000
2:167210734:GCGAC:Gacceptor_gain1.0000
2:167210894:AT:Adonor_gain1.0000
2:167210894:ATGT:Adonor_loss1.0000
2:167210896:G:GAdonor_loss1.0000
2:167210896:G:GGdonor_gain1.0000
2:167210897:TAA:Tdonor_loss1.0000
2:167218155:A:Gacceptor_gain1.0000
2:167218164:AGAT:Aacceptor_gain1.0000
2:167218165:GATG:Gacceptor_gain1.0000
2:167239927:TCCA:Tdonor_gain1.0000
2:167240656:A:AGacceptor_gain1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000008529 (2:167127251 G>C), RS1000012283 (2:167204022 G>A), RS1000030351 (2:166998021 T>G), RS1000031606 (2:166913048 G>A,T), RS1000051088 (2:167015415 C>T), RS1000062109 (2:167037312 A>C,G), RS1000063555 (2:166960159 T>C), RS1000068900 (2:167165756 C>A,T), RS1000086602 (2:166958432 C>T), RS1000095248 (2:166889160 T>C,G), RS1000119477 (2:166956746 G>A), RS1000123184 (2:167086606 A>T), RS1000126980 (2:166971637 G>A,C), RS1000128039 (2:167160491 G>A), RS1000135672 (2:167036228 C>A)

Disease associations

OMIM: gene MIM:609778 | disease phenotypes: MIM:615779

GenCC curated gene-disease

Mondo (2): blepharophimosis (MONDO:0001008), congenital heart defects, multiple types, 4 (MONDO:0014344)

Orphanet (0):

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPOTerm
HP:0000581Blepharophimosis

GWAS associations

5 associations (top):

StudyTraitp-value
GCST002844_2Atopic dermatitis4.000000e-08
GCST006043_2Plasma renin activity levels2.000000e-07
GCST008223_1Diabetic peripheral neuropathy in type 2 diabetes8.000000e-12
GCST010396_154Gut microbiota (bacterial taxa, hurdle binary method)2.000000e-06
GCST011743_84HDL cholesterol levels in HIV infection3.000000e-06

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0006828plasma renin activity measurement
EFO:0007874gut microbiome measurement
EFO:0004612high density lipoprotein cholesterol measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
D016569BlepharophimosisC11.250.090; C11.338.190; C16.131.384.190

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB clinical annotations

1 annotations.

VariantTypeLevelDrugsPhenotypes
rs7606603Efficacy3atenololHypertension

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs7606603XIRP232.251atenolol

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects cotreatment, increases methylation, decreases expression, decreases methylation2
Benzo(a)pyreneincreases expression, decreases methylation2
Doxorubicindecreases expression2
Valproic Aciddecreases methylation, increases expression2
2,4,6-tribromophenoldecreases expression1
decabromobiphenyl etherdecreases expression1
tetrabromobisphenol Adecreases expression1
coumarinincreases phosphorylation1
CGP 52608affects binding, increases reaction1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
pentabrominated diphenyl ether 100decreases expression1
hexabrominated diphenyl ether 153decreases expression1
bisphenol Sincreases expression1
Sunitinibdecreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Benztropinedecreases expression1
Ethyl Methanesulfonatedecreases expression1
Formaldehydedecreases expression1
Haloperidoldecreases expression1
Methyl Methanesulfonatedecreases expression1
Oxygenincreases expression1
Phthalic Acidsincreases methylation1
Vincristinedecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT06514612PHASE3RECRUITINGLIDRISE Study: A Phase 3 Study on the Efficacy and Safety of STN1013800 (Oxymetazoline HCl 0.1% Eye Drops, Single Dose) in the Treatment of Acquired Blepharoptosis.