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TGIF2LX

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Summary

TGIF2LX (TGFB induced factor homeobox 2 like X-linked, HGNC:18570) is a protein-coding gene on chromosome Xq21.31, encoding Homeobox protein TGIF2LX (Q8IUE1). May have a transcription role in testis.

This gene encodes a member of the TALE/TGIF homeobox family of transcription factors. Testis-specific expression suggests that this gene may play a role in spermatogenesis. A homolog of this gene lies within the male specific region of chromosome Y, in a block of sequence that is thought to be the result of a large X-to-Y transposition.

Source: NCBI Gene 90316 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 26 total
  • MANE Select transcript: NM_138960

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18570
Approved symbolTGIF2LX
NameTGFB induced factor homeobox 2 like X-linked
LocationXq21.31
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000153779
Ensembl biotypeprotein_coding
OMIM300411
Entrez90316

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000283891, ENST00000561129

RefSeq mRNA: 1 — MANE Select: NM_138960 NM_138960

CCDS: CCDS14459

Canonical transcript exons

ENST00000283891 — 2 exons

ExonStartEnd
ENSE000017053888992190889921968
ENSE000018964218992206589922883

Expression profiles

Bgee: expression breadth broad, 14 present calls, max score 92.20.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0105 / max 4.4804, expressed in 7 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1968750.01057

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099192.20gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047385.88gold quality
testisUBERON:000047373.05gold quality
left testisUBERON:000453372.96gold quality
right testisUBERON:000453470.60gold quality
colonic epitheliumUBERON:000039737.20gold quality
ventricular zoneUBERON:000305336.48gold quality
cortical plateUBERON:000534336.47gold quality
bone marrow cellCL:000209236.16gold quality
ganglionic eminenceUBERON:000402335.49gold quality
duodenumUBERON:000211433.53silver quality
skeletal muscle tissueUBERON:000113433.38gold quality
hindlimb stylopod muscleUBERON:000425232.15gold quality
bone marrowUBERON:000237131.74gold quality
muscle tissueUBERON:000238531.06gold quality
sural nerveUBERON:001548830.93gold quality
stromal cell of endometriumCL:000225529.87gold quality
prefrontal cortexUBERON:000045129.04gold quality
liverUBERON:000210728.81gold quality
tonsilUBERON:000237228.63gold quality
monocyteCL:000057628.26silver quality
leukocyteCL:000073828.20silver quality
primary visual cortexUBERON:000243627.78gold quality
lymph nodeUBERON:000002927.57gold quality
cortex of kidneyUBERON:000122527.28silver quality
urinary bladderUBERON:000125526.85gold quality
islet of LangerhansUBERON:000000626.55gold quality
vermiform appendixUBERON:000115426.42gold quality
gall bladderUBERON:000211025.98gold quality
olfactory segment of nasal mucosaUBERON:000538625.89gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no0.82

Regulation

Is transcription factor: yes

JASPAR motifs

MotifNameFamily
MA1571.1TGIF2LXTALE-type homeo domain factors

JASPAR matrix evidence (PMIDs): PMID:8537382

Literature-anchored findings (GeneRIF, showing 4)

  • Association of TGIFLX/Y mRNA expression with azoospermia in infertile men.( (PMID:18384077)
  • most prostate tumors (73.5%) express at least one of these genes (TGIFLX and TGIFLY), although different patterns of mRNA expression were observed. These results suggest an association of TGIFLX/Y expression with the progression of prostate cancer. (PMID:18663611)
  • To the best of our knowledge, this is the first report that proposes Nir1, Nir2, and Fhit genes might be regulated by homeodomain protein TGIF2LX in colorectal adenocarcinoma cells. (PMID:29960902)
  • Regulation of long non-coding RNAs XIST and ROR induced by homeodomain protein TGIF2LX in colorectal cancer. (PMID:36510989)

Cross-species orthologs

12 orthologs

OrganismSymbolGene ID
danio_reriopbx2ENSDARG00000019717
danio_reriopbx4ENSDARG00000052150
mus_musculusTgif2lx1ENSMUSG00000100133
mus_musculusTgif2lx2ENSMUSG00000100194
rattus_norvegicusTgif2lx2ENSRNOG00000029850
drosophila_melanogasterexdFBGN0000611
drosophila_melanogasterhthFBGN0001235
drosophila_melanogastervisFBGN0033748
drosophila_melanogasterachiFBGN0033749
caenorhabditis_elegansWBGENE00000443
caenorhabditis_elegansWBGENE00006796
caenorhabditis_elegansWBGENE00017690

Paralogs (13): MEIS3 (ENSG00000105419), PBX4 (ENSG00000105717), TGIF2 (ENSG00000118707), MEIS2 (ENSG00000134138), MEIS1 (ENSG00000143995), PKNOX1 (ENSG00000160199), PKNOX2 (ENSG00000165495), PBX3 (ENSG00000167081), TGIF2LY (ENSG00000176679), TGIF1 (ENSG00000177426), PBX1 (ENSG00000185630), MEIS3P2 (ENSG00000188013), PBX2 (ENSG00000204304)

Protein

Protein identifiers

Homeobox protein TGIF2LX — Q8IUE1 (reviewed: Q8IUE1)

Alternative names: TGF-beta-induced transcription factor 2-like protein, TGFB-induced factor 2-like protein, X-linked, TGIF-like on the X

All UniProt accessions (1): Q8IUE1

UniProt curated annotations — full annotation on UniProt →

Function. May have a transcription role in testis.

Subcellular location. Nucleus.

Tissue specificity. Specifically expressed in adult testis.

Similarity. Belongs to the TALE/TGIF homeobox family.

RefSeq proteins (1): NP_620410* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001356HDDomain
IPR008422KN_HDDomain
IPR009057Homeodomain-like_sfHomologous_superfamily
IPR050224TALE_homeoboxFamily

Pfam: PF05920

UniProt features (12 total): helix 4, region of interest 2, compositionally biased region 2, chain 1, DNA-binding region 1, sequence variant 1, turn 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2DMNSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8IUE1-F168.590.30

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 28 (showing top): ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, ZHOU_INFLAMMATORY_RESPONSE_LIVE_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, chrXq21, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, RATTENBACHER_BOUND_BY_CELF1, GOMF_DNA_BINDING_TRANSCRIPTION_REPRESSOR_ACTIVITY, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, GSE15750_WT_VS_TRAF6KO_DAY6_EFF_CD8_TCELL_DN, FOURATI_BLOOD_TWINRIX_AGE_25_83YO_RESPONDERS_VS_POOR_RESPONDERS_0DY_DN, GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY, GOMF_CIS_REGULATORY_REGION_SEQUENCE_SPECIFIC_DNA_BINDING, PULVER_FOREY_PERTURB_ACCUMULATION_LG1, PULVER_FOREY_PERTURB_ATTRITION_G2_M

GO Biological Process (2): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (4): DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677)

GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of transcription by RNA polymerase II2
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
transcription by RNA polymerase II1
negative regulation of DNA-templated transcription1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
chromatin1
DNA-binding transcription factor activity1
negative regulation of transcription by RNA polymerase II1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription repressor activity1
double-stranded DNA binding1
sequence-specific DNA binding1
nucleic acid binding1
chromosome1
cellular anatomical structure1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

676 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TGIF2LXPABPC5Q96DU9943
TGIF2LXPCDH11XQ9BZA7854
TGIF2LXTGFBIQ15582840
TGIF2LXRHOXF2Q9BQY4599
TGIF2LXCPXCR1Q8N123571
TGIF2LXC10orf120Q5SQS8512
TGIF2LXSPRY3O43610501
TGIF2LXTRIM42Q8IWZ5476
TGIF2LXRHOXF2BP0C7M4476
TGIF2LXTXLNGQ9NUQ3474
TGIF2LXA0A087WUC5A0A087WUC5458
TGIF2LXGTPBP6O43824448
TGIF2LXVCX3BQ9H321448
TGIF2LXZNF705AQ6ZN79434
TGIF2LXSATL1Q86VE3433

IntAct

23 interactions, top by confidence:

ABTypeScore
HDAC1ZNF609psi-mi:“MI:0914”(association)0.730
RBBP7HAT1psi-mi:“MI:0914”(association)0.730
TGIF2LYPGPpsi-mi:“MI:0914”(association)0.640
SINHCAFTNRC18psi-mi:“MI:0914”(association)0.640
MBL2TRMUpsi-mi:“MI:0914”(association)0.500
TGIF2LXLRRK2psi-mi:“MI:0407”(direct interaction)0.440
TGIF2LXpsi-mi:“MI:0915”(physical association)0.370
IFNA14TGIF2LXpsi-mi:“MI:0915”(physical association)0.370
PPBPTGIF2LXpsi-mi:“MI:0915”(physical association)0.370
XCL1TGIF2LXpsi-mi:“MI:0915”(physical association)0.370
TGIF2LXTNRC18psi-mi:“MI:0914”(association)0.350
DKK2ZZEF1psi-mi:“MI:0914”(association)0.350
PCGF3POTEIpsi-mi:“MI:0914”(association)0.350
DKK2LRP5psi-mi:“MI:0914”(association)0.350
PDIA5MBL2psi-mi:“MI:0914”(association)0.350
FUBP3PRSS2psi-mi:“MI:0914”(association)0.350
RBBP4PHF20L1psi-mi:“MI:0914”(association)0.350

BioGRID (38): TGIF2LX (Affinity Capture-MS), TGIF2LX (Reconstituted Complex), TGIF2LX (Affinity Capture-MS), FAM60A (Affinity Capture-MS), UBE2W (Affinity Capture-MS), SAP30L (Affinity Capture-MS), ING1 (Affinity Capture-MS), FOXK1 (Affinity Capture-MS), BAHCC1 (Affinity Capture-MS), RCHY1 (Affinity Capture-MS), ING2 (Affinity Capture-MS), HDAC1 (Affinity Capture-MS), BRMS1 (Affinity Capture-MS), SUDS3 (Affinity Capture-MS), TGIF2LX (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GTS1, A0A1B0GWH4, A1A4L6, A1YGI6, A6NDR6, B8QB46, F1MJR8, F1QDF8, O35892, O35893, P09015, P15036, P15037, P23497, P52729, P59598, Q32NH9, Q3KRF1, Q3UM89, Q4G112, Q4V7E1, Q5M7N6, Q5ND04, Q5XIV2, Q5ZHX5, Q66IG8, Q6P1R3, Q6PCX9, Q6PJQ5, Q708W2, Q76I76, Q76I79, Q76N89, Q7M6U3, Q8AXQ4, Q8BVK9, Q8IUE0, Q8IUE1, Q8IWB6, Q8IXJ9

Diamond homologs: A1YGI6, A6NDR6, A8K0S8, A8WL06, B7ZRT8, O00470, O04136, O14770, O22300, O42261, O46339, O65685, O70477, P41779, P41817, P46606, P48000, P48001, P48002, P48731, P53147, P54269, P55347, P56659, P56660, P56664, P56665, P56669, P70284, P78412, P78413, P78414, P78415, P79937, P81067, P81068, P97367, P97368, Q0E3C3, Q0J6N4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance24
Likely benign1
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

92 predictions. Top by Δscore:

VariantEffectΔscore
X:89921965:ACAGG:Adonor_loss0.9800
X:89921967:AGGTG:Adonor_loss0.9800
X:89921968:GGTGA:Gdonor_loss0.9800
X:89921969:G:GAdonor_loss0.9800
X:89921970:T:Adonor_loss0.9800
X:89922063:A:AGacceptor_gain0.9800
X:89922064:G:GAacceptor_gain0.9800
X:89922064:GTAAC:Gacceptor_gain0.9800
X:89922064:GT:Gacceptor_gain0.9700
X:89922064:GTA:Gacceptor_gain0.9600
X:89922064:GTAA:Gacceptor_gain0.9400
X:89922060:TATA:Tacceptor_loss0.9200
X:89922061:ATAG:Aacceptor_loss0.9200
X:89922062:T:Gacceptor_gain0.9200
X:89922058:A:AGacceptor_gain0.8900
X:89922059:A:Gacceptor_gain0.8600
X:89922089:G:Cacceptor_gain0.8600
X:89922289:G:GTdonor_gain0.8500
X:89922061:A:AGacceptor_gain0.8200
X:89921971:GAGAA:Gdonor_loss0.8000
X:89922087:TGG:Tacceptor_gain0.8000
X:89921969:G:GGdonor_gain0.7900
X:89922048:T:TAacceptor_loss0.7500
X:89922085:TATGG:Tacceptor_gain0.7100
X:89922086:ATGGA:Aacceptor_gain0.7100
X:89922087:T:TAacceptor_gain0.7100
X:89922060:T:Gacceptor_gain0.6600
X:89921965:ACAG:Adonor_gain0.6500
X:89922053:T:Gacceptor_loss0.6500
X:89922052:A:AGacceptor_loss0.6400

AlphaMissense

1579 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:89922383:T:AW100R0.994
X:89922383:T:CW100R0.994
X:89922385:G:CW100C0.994
X:89922385:G:TW100C0.994
X:89922386:T:CF101L0.994
X:89922388:T:AF101L0.994
X:89922388:T:GF101L0.994
X:89922289:G:CW68C0.993
X:89922289:G:TW68C0.993
X:89922317:C:TP78S0.993
X:89922279:T:AL65H0.991
X:89922287:T:AW68R0.991
X:89922287:T:CW68R0.991
X:89922360:T:CL92S0.991
X:89922387:T:CF101S0.991
X:89922403:A:CR106S0.989
X:89922403:A:TR106S0.989
X:89922279:T:CL65P0.987
X:89922404:C:AR107S0.985
X:89922405:G:CR107P0.985
X:89922282:G:CR66P0.984
X:89922318:C:AP78H0.984
X:89922334:G:CK83N0.984
X:89922334:G:TK83N0.984
X:89922395:G:CA104P0.983
X:89922398:C:AR105S0.983
X:89922288:G:CW68S0.982
X:89922755:G:CA224P0.982
X:89922317:C:AP78T0.981
X:89922384:G:CW100S0.981

dbSNP variants (sampled 300 via entrez): RS1000242752 (X:89922123 G>C), RS1001514073 (X:89921244 G>A), RS1001566618 (X:89920687 G>A,T), RS1001795653 (X:89921637 G>A), RS1008364760 (X:89920379 C>T), RS1014280095 (X:89921708 G>A), RS1014747084 (X:89921282 G>A), RS1016665127 (X:89922883 A>C,G), RS1018217388 (X:89921841 GA>G), RS1020218595 (X:89920402 A>G), RS1020406990 (X:89921323 G>A,C), RS1020773306 (X:89921762 G>A), RS1025605737 (X:89922787 G>A), RS1027282705 (X:89920625 T>C), RS1032137265 (X:89921791 G>A)

Disease associations

OMIM: gene MIM:300411 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST001613_5Antineutrophil cytoplasmic antibody-associated vasculitis9.000000e-14
GCST010298_3Metopic nonsyndromic craniosynostosis6.000000e-07

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0008511metopic craniosynostosis

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
Benzo(a)pyreneincreases expression, affects methylation, decreases methylation2
benzo(e)pyrenedecreases methylation1
aflatoxin B2decreases methylation1
CGP 52608affects binding, increases reaction1
Methapyrilenedecreases methylation1

Clinical trials (associated diseases)

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

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