GTF2IRD2

gene
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Also known as FLJ37938GTF2IRD2A

Summary

GTF2IRD2 (GTF2I repeat domain containing 2, HGNC:30775) is a protein-coding gene on chromosome 7q11.23, encoding General transcription factor II-I repeat domain-containing protein 2A (Q86UP8).

This gene is one of several closely related genes on chromosome 7 encoding proteins containing helix-loop-helix motifs. These proteins may function as regulators of transcription. The encoded protein is unique in that its C-terminus is derived from CHARLIE8 transposable element sequence. This gene is located in a region of chromosome 7 that is deleted in Williams-Beuren syndrome, and loss of this locus may contribute to the cognitive phenotypes observed in this disease. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 84163 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 33 total
  • Phenotypes (HPO): 186
  • Dosage sensitivity (ClinGen): haploinsufficiency no evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_173537

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30775
Approved symbolGTF2IRD2
NameGTF2I repeat domain containing 2
Location7q11.23
Locus typegene with protein product
StatusApproved
AliasesFLJ37938, GTF2IRD2A
Ensembl geneENSG00000196275
Ensembl biotypeprotein_coding
OMIM608899
Entrez84163

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 22 protein_coding, 3 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000451013, ENST00000478628, ENST00000484624, ENST00000610955, ENST00000614386, ENST00000619775, ENST00000651129, ENST00000652362, ENST00000907793, ENST00000907794, ENST00000907795, ENST00000907796, ENST00000907797, ENST00000907798, ENST00000907799, ENST00000907800, ENST00000907801, ENST00000907802, ENST00000907803, ENST00000966521, ENST00000966522, ENST00000966523, ENST00000966524, ENST00000966525, ENST00000966526, ENST00000966527, ENST00000966528

RefSeq mRNA: 15 — MANE Select: NM_173537 NM_001281447, NM_001368300, NM_001388079, NM_001388080, NM_001388081, NM_001388082, NM_001388083, NM_001388084, NM_001388085, NM_001388086, NM_001388087, NM_001388088, NM_001388089, NM_001388460, NM_173537

CCDS: CCDS5576, CCDS64682, CCDS94122

Canonical transcript exons

ENST00000451013 — 16 exons

ExonStartEnd
ENSE000022073127479615174798265
ENSE000037387567485136774851605
ENSE000039257147481273974812816
ENSE000039258917480477774804860
ENSE000039272957480910874809173
ENSE000039278167483280574832943
ENSE000039297907481996974820023
ENSE000039317827483628074836383
ENSE000039326837481089674810952
ENSE000039330437482262474822807
ENSE000039354957480329874803481
ENSE000039363767482493374825052
ENSE000039366317482242774822455
ENSE000039370547481955474819597
ENSE000039381877480198574802013
ENSE000039385967480693474807011

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 93.69.

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right uterine tubeUBERON:000130293.69gold quality
left ovaryUBERON:000211991.49gold quality
skeletal muscle tissueUBERON:000113490.76gold quality
ovaryUBERON:000099290.73gold quality
mucosa of stomachUBERON:000119990.46gold quality
muscle of legUBERON:000138390.46gold quality
endocervixUBERON:000045890.38gold quality
apex of heartUBERON:000209890.34gold quality
gastrocnemiusUBERON:000138890.33gold quality
right ovaryUBERON:000211889.95gold quality
prostate glandUBERON:000236789.68gold quality
calcaneal tendonUBERON:000370189.54gold quality
sural nerveUBERON:001548889.51gold quality
fundus of stomachUBERON:000116089.33gold quality
muscle tissueUBERON:000238589.23gold quality
body of pancreasUBERON:000115089.22gold quality
left lobe of thyroid glandUBERON:000112089.21gold quality
right lobe of thyroid glandUBERON:000111989.20gold quality
thyroid glandUBERON:000204689.14gold quality
muscle layer of sigmoid colonUBERON:003580589.02gold quality
hindlimb stylopod muscleUBERON:000425288.99gold quality
body of uterusUBERON:000985388.88gold quality
esophagogastric junction muscularis propriaUBERON:003584188.88gold quality
lower esophagus muscularis layerUBERON:003583388.83gold quality
lower esophagusUBERON:001347388.80gold quality
body of stomachUBERON:000116188.56gold quality
metanephros cortexUBERON:001053388.54gold quality
uterine cervixUBERON:000000288.49gold quality
minor salivary glandUBERON:000183088.24gold quality
thoracic mammary glandUBERON:000520088.21gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes8.85

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

35 targeting GTF2IRD2, 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-371B-5P99.9975.344759
HSA-MIR-150-5P99.9966.691976
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-314899.9775.066478
HSA-MIR-4760-3P99.9370.502385
HSA-MIR-380-3P99.8970.181978
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-548AR-3P99.8571.263889
HSA-MIR-548AZ-3P99.8270.563549
HSA-MIR-548BC99.8270.613524
HSA-MIR-548E-3P99.8270.593514
HSA-MIR-548F-3P99.8270.593540
HSA-MIR-548A-3P99.7670.583524
HSA-MIR-3158-5P99.6567.511763
HSA-MIR-182799.6368.573265
HSA-MIR-1260A99.6166.671098
HSA-MIR-1260B99.6166.671098
HSA-MIR-1211799.5067.57868
HSA-MIR-568999.5071.261154
HSA-MIR-4762-3P99.4369.722363
HSA-MIR-431699.3765.751360
HSA-MIR-205499.2068.891699
HSA-MIR-129498.9169.261030
HSA-MIR-998698.9169.281024
HSA-MIR-520G-3P98.9167.381914
HSA-MIR-520H98.9167.381914
HSA-MIR-4755-3P98.7765.591915
HSA-MIR-797798.6566.182590
HSA-MIR-4768-3P98.1666.022330

Functional genomics

ClinGen dosage: haploinsufficiency 0 (no evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 5)

  • Williams-Beuren syndrome patients are hemizygous for the GTF2IRD2 gene. (PMID:15100712)
  • GTF2IRD2 genes in mice and humans allows refinement of the centromeric breakpoint position of the primate-specific inversion within the Williams-Beuren syndrome critical region. (PMID:15243160)
  • There is high indentity between CTF2IRD2 and CTF2I, which suggests that heterodimers as well as homodimers are possible, and indicates overlapping functions between their respective short isoforms. (PMID:15388857)
  • We provide the first evidence for a role for GTF2IRD2 in higher-level (executive functioning) abilities and highlight the importance of integrating detailed molecular characterisation of patients with comprehensive neuropsychological profiling (PMID:23118870)
  • atypical Williams Syndrome patients with GTF2IRD2 deletion had more impaired visuospatial abilities and more significant behavioral problems, mainly related to the construct of social cognition (PMID:30375319)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusGtf2ird2ENSMUSG00000015942
rattus_norvegicusGtf2ird2ENSRNOG00000001482

Paralogs (18): GTF2IRD1 (ENSG00000006704), ZMYM2 (ENSG00000121741), ZMYM5 (ENSG00000132950), THAP12 (ENSG00000137492), ZMYM4 (ENSG00000146463), ZMYM3 (ENSG00000147130), ZMYM6 (ENSG00000163867), KIAA1958 (ENSG00000165185), GTF2IRD2B (ENSG00000174428), EPM2AIP1 (ENSG00000178567), ZMYM1 (ENSG00000197056), QRICH1 (ENSG00000198218), FAM200C (ENSG00000221886), FAM200A (ENSG00000221909), SCAND3 (ENSG00000232040), ZBED5 (ENSG00000236287), FAM200B (ENSG00000237765), GTF2I (ENSG00000263001)

Protein

Protein identifiers

General transcription factor II-I repeat domain-containing protein 2AQ86UP8 (reviewed: Q86UP8)

Alternative names: Transcription factor GTF2IRD2-alpha

All UniProt accessions (2): A0A494C0I1, Q86UP8

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

Tissue specificity. Ubiquitous.

Disease relevance. GTF2IRD2 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region.

Similarity. Belongs to the TFII-I family.

Isoforms (6)

UniProt IDNamesCanonical?
Q86UP8-11yes
Q86UP8-22
Q86UP8-33
Q86UP8-44
Q86UP8-55
Q86UP8-66

RefSeq proteins (15): NP_001268376, NP_001355229, NP_001375008, NP_001375009, NP_001375010, NP_001375011, NP_001375012, NP_001375013, NP_001375014, NP_001375015, NP_001375016, NP_001375017, NP_001375018, NP_001375389, NP_775808* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004212GTF2IRepeat
IPR012337RNaseH-like_sfHomologous_superfamily
IPR036647GTF2I-like_rpt_sfHomologous_superfamily
IPR042224GTF2IRD2Family

Pfam: PF02946

UniProt features (17 total): splice variant 8, sequence conflict 5, repeat 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q86UP8-F173.240.33

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 495 (showing top): chr7q11, ACEVEDO_LIVER_CANCER_UP, YAGI_AML_SURVIVAL, WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_UP, KOINUMA_TARGETS_OF_SMAD2_OR_SMAD3, PEDRIOLI_MIR31_TARGETS_DN, ZWANG_DOWN_BY_2ND_EGF_PULSE, GSE5503_MLN_DC_VS_SPLEEN_DC_ACTIVATED_ALLOGENIC_TCELL_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, MIR616_5P, MIR371B_5P, MIR373_5P, MIR548AR_3P, MIR548F_3P, MIR548BC

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition (GO:0006617)

GO Molecular Function (3): DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), signal recognition particle, endoplasmic reticulum targeting (GO:0005786)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of DNA-templated transcription1
transcription by RNA polymerase II1
SRP-dependent cotranslational protein targeting to membrane1
protein-containing complex assembly1
chromatin1
RNA polymerase II transcription regulatory region sequence-specific DNA binding1
DNA-binding transcription factor activity1
regulation of transcription by RNA polymerase II1
nucleic acid binding1
binding1
intracellular membrane-bounded organelle1
signal recognition particle1

Protein interactions and networks

STRING

548 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GTF2IRD2NCF1P14598787
GTF2IRD2ELNP15502641
GTF2IRD2TBL2Q9Y4P3637
GTF2IRD2TRIM50Q86XT4618
GTF2IRD2NSUN5Q96P11579
GTF2IRD2BCL7BQ9BQE9547
GTF2IRD2CLIP2Q9UDT6539
GTF2IRD2EIF4HQ15056530
GTF2IRD2FKBP6O75344502
GTF2IRD2FKBP10Q96AY3482
GTF2IRD2AGTP01019469
GTF2IRD2ZNF805Q5CZA5432
GTF2IRD2DNAJC30Q96LL9419
GTF2IRD2FZD9O00144418
GTF2IRD2SRGAP2CP0DJJ0417

IntAct

16 interactions, top by confidence:

ABTypeScore
GTF2IRD2TRIM54psi-mi:“MI:0915”(physical association)0.560
TRIM54GTF2IRD2psi-mi:“MI:0915”(physical association)0.560
GTF2IRD2HSP90AB1psi-mi:“MI:0915”(physical association)0.400
GTF2IRD2MLF1psi-mi:“MI:0915”(physical association)0.400
Hacd3GTF2IRD2psi-mi:“MI:0915”(physical association)0.400
GTF2IRD2psi-mi:“MI:0915”(physical association)0.400
PSMD2GTF2IRD2psi-mi:“MI:0915”(physical association)0.400
GTF2IRD2psi-mi:“MI:0915”(physical association)0.400
GTF2IRD2CDC37psi-mi:“MI:0915”(physical association)0.400
AARSD1GTF2IRD2psi-mi:“MI:0915”(physical association)0.400
Ppsi-mi:“MI:0914”(association)0.350
GTF2IRD2GTF2Ipsi-mi:“MI:0914”(association)0.350
GPC3PXDNLpsi-mi:“MI:0914”(association)0.350

BioGRID (15): GTF2IRD2 (Two-hybrid), GTF2IRD2 (Affinity Capture-MS), GTF2IRD2 (Affinity Capture-MS), GTF2IRD2 (Affinity Capture-MS), GTF2IRD2 (Affinity Capture-MS), GTF2IRD1 (Affinity Capture-MS), GTF2I (Affinity Capture-MS), UBE2Z (Affinity Capture-MS), GTF2IRD2B (Affinity Capture-MS), GTF2IRD2 (Cross-Linking-MS (XL-MS)), GTF2IRD2 (Cross-Linking-MS (XL-MS)), GTF2IRD2 (Affinity Capture-MS), GTF2IRD2 (Two-hybrid), GTF2IRD2 (Affinity Capture-Luminescence), GTF2IRD2 (Two-hybrid)

ESM2 similar proteins: A3KMX0, A4IFA3, A4IGY9, A4Z943, A4Z944, B8QB46, D2EAC2, E1C2V1, O43422, O60290, P10911, P35125, P86452, Q13075, Q2NKX8, Q3UPF5, Q49AG3, Q5FWF4, Q5SVZ6, Q5T890, Q5TKR9, Q6DJS0, Q6EKJ0, Q6R2W3, Q6YI93, Q7Z2W4, Q80WE4, Q86UP8, Q86VD1, Q8BZ21, Q8N8K9, Q8QMP8, Q8TDB6, Q8WML3, Q92794, Q96JM7, Q96JS3, Q99388, Q99NI3, Q9CUX1

Diamond homologs: A4IFA3, A7MB80, B7ZQJ9, P78347, Q5U2Y1, Q6EKJ0, Q86UP8, Q99NI3, Q9ESZ8, Q9JI57, Q9UHL9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance22
Likely benign7
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

2419 predictions. Top by Δscore:

VariantEffectΔscore
7:74803293:CTTA:Cdonor_gain1.0000
7:74803297:C:CGdonor_loss1.0000
7:74804770:AACTT:Adonor_loss1.0000
7:74804771:ACTT:Adonor_loss1.0000
7:74804772:CTT:Cdonor_loss1.0000
7:74804773:TTA:Tdonor_loss1.0000
7:74804774:TA:Tdonor_loss1.0000
7:74804775:A:ACdonor_gain1.0000
7:74804775:AC:Adonor_gain1.0000
7:74804776:C:CGdonor_gain1.0000
7:74804776:CC:Cdonor_gain1.0000
7:74804776:CCA:Cdonor_gain1.0000
7:74804776:CCAA:Cdonor_gain1.0000
7:74804776:CCAAA:Cdonor_gain1.0000
7:74804856:ATTAT:Aacceptor_gain1.0000
7:74804857:TTAT:Tacceptor_gain1.0000
7:74804858:TAT:Tacceptor_gain1.0000
7:74804859:AT:Aacceptor_gain1.0000
7:74804859:ATC:Aacceptor_loss1.0000
7:74804860:TCTAA:Tacceptor_loss1.0000
7:74804861:C:CCacceptor_gain1.0000
7:74804867:A:ACacceptor_gain1.0000
7:74804867:A:Cacceptor_gain1.0000
7:74804870:A:ACacceptor_gain1.0000
7:74804871:T:Cacceptor_gain1.0000
7:74804871:T:TCacceptor_gain1.0000
7:74807012:C:CCacceptor_gain1.0000
7:74807013:T:Cacceptor_gain1.0000
7:74812733:TATTA:Tdonor_loss1.0000
7:74812735:TTA:Tdonor_loss1.0000

AlphaMissense

6294 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:74798218:A:GW432R1.000
7:74798218:A:TW432R1.000
7:74798216:C:AW432C0.999
7:74798216:C:GW432C0.999
7:74798228:A:CF428L0.998
7:74798228:A:TF428L0.998
7:74798229:A:GF428S0.998
7:74798230:A:GF428L0.998
7:74798257:G:TR419S0.998
7:74803310:A:GF402S0.998
7:74804794:A:GL339P0.998
7:74804803:A:TV336D0.998
7:74798121:C:GR464P0.997
7:74798138:T:AK458N0.997
7:74798138:T:GK458N0.997
7:74798139:T:AK458I0.997
7:74798173:A:GC447R0.997
7:74798229:A:CF428C0.997
7:74803361:A:GL385P0.997
7:74803379:A:GF379S0.997
7:74804791:A:GF340S0.997
7:74797667:G:CS615R0.996
7:74797667:G:TS615R0.996
7:74797669:T:GS615R0.996
7:74798116:A:CY466D0.996
7:74798127:A:GL462P0.996
7:74798217:C:GW432S0.996
7:74803412:A:TV368E0.996
7:74803433:A:CI361S0.996
7:74803433:A:GI361T0.996

dbSNP variants (sampled 300 via entrez): RS10225848 (7:74805436 G>A), RS111340667 (7:74833721 A>T), RS111449690 (7:74807855 T>C), RS111471245 (7:74835922 T>C,G), RS111757525 (7:74805881 G>A,T), RS112022464 (7:74800203 T>C), RS112148398 (7:74834767 T>G), RS112446134 (7:74813441 G>C,T), RS113157837 (7:74831058 T>A), RS113191694 (7:74801769 G>C), RS113533859 (7:74813400 A>G), RS1137618 (7:74796434 C>G,T), RS1137619 (7:74796419 A>G), RS113815546 (7:74800705 T>C,G), RS115501971 (7:74830053 G>C)

Disease associations

OMIM: gene MIM:608899 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

186 total (30 of 186 shown, HPO-id order):

HPOTerm
HP:0000010Recurrent urinary tract infections
HP:0000014Abnormality of the bladder
HP:0000015Bladder diverticulum
HP:0000023Inguinal hernia
HP:0000025Functional abnormality of male internal genitalia
HP:0000028Cryptorchidism
HP:0000044Hypogonadotropic hypogonadism
HP:0000075Renal duplication
HP:0000076Vesicoureteral reflux
HP:0000083Renal insufficiency
HP:0000089Renal hypoplasia
HP:0000093Proteinuria
HP:0000121Nephrocalcinosis
HP:0000125Pelvic kidney
HP:0000147Polycystic ovaries
HP:0000154Wide mouth
HP:0000158Macroglossia
HP:0000179Thick lower lip vermilion
HP:0000212Gingival overgrowth
HP:0000232Everted lower lip vermilion
HP:0000252Microcephaly
HP:0000275Narrow face
HP:0000280Coarse facial features
HP:0000286Epicanthus
HP:0000307Pointed chin
HP:0000337Broad forehead
HP:0000343Long philtrum
HP:0000347Micrognathia
HP:0000348High forehead
HP:0000358Posteriorly rotated ears

GWAS associations

5 associations (top):

StudyTraitp-value
GCST004621_113Red cell distribution width5.000000e-18
GCST006414_123Atrial fibrillation3.000000e-10
GCST006804_68Red cell distribution width2.000000e-12
GCST010988_158Adult body size2.000000e-08
GCST90002404_289Red cell distribution width2.000000e-25

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0009188Red cell distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression6
bisphenol Aaffects cotreatment, increases expression, decreases expression2
trichostatin Aaffects cotreatment, decreases expression2
aristolochic acid Iincreases expression1
bisphenol Faffects cotreatment, increases expression1
sotorasibincreases expression, affects cotreatment1
propionaldehydedecreases expression1
butyraldehydedecreases expression1
pentanaldecreases expression1
15-acetyldeoxynivalenolincreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
entinostatdecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
NSC 689534affects binding, increases expression1
trametinibincreases expression, affects cotreatment1
NVP-BKM120affects cotreatment, increases expression1
Resveratrolaffects cotreatment, increases expression1
Vorinostatdecreases expression1
Air Pollutantsdecreases expression1
Aldehydesdecreases expression1
Benzo(a)pyrenedecreases expression1
Copperaffects binding, increases expression1
Dexamethasoneaffects cotreatment, increases expression1
Indomethacinaffects cotreatment, increases expression1
Plant Extractsaffects cotreatment, increases expression1
Rifampinincreases expression1
Silicon Dioxidedecreases 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.