GeneBe

TGIF2

TGFB induced factor homeobox 2, the group of TALE class homeoboxes and pseudogenes

Basic information

Region (hg38): 20:36573488-36593950

Links

ENSG00000118707 ∙ NCBI:60436 ∙ OMIM:607294 ∙ HGNC:15764 ∙ Uniprot:Q9GZN2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TGIF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TGIF2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
0
missense
10
clinvar
 10
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 10 0 0

Variants in TGIF2

This is a list of pathogenic ClinVar variants found in the TGIF2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
20-36578802-G-A not specified Uncertain significance (Mar 06, 2023)2494520
20-36590980-C-A not specified Uncertain significance (Mar 28, 2023)2530805
20-36591004-G-A not specified Uncertain significance (Dec 06, 2022)2400407
20-36591028-C-T not specified Uncertain significance (Sep 01, 2021)2248199
20-36591054-G-A not specified Uncertain significance (Mar 01, 2023)2457286
20-36591097-T-A not specified Uncertain significance (Apr 15, 2024)3325738
20-36591177-C-T not specified Uncertain significance (Nov 14, 2023)3176691
20-36591349-A-C not specified Uncertain significance (Mar 15, 2024)3325737
20-36591351-A-G not specified Uncertain significance (Dec 28, 2023)3176692
20-36591390-C-G not specified Uncertain significance (Mar 03, 2025)2312347

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TGIF2protein_codingprotein_codingENST00000373874 220463
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.1360.787125742061257480.0000239
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.071071430.7480.000008501503
Missense in Polyphen2749.250.54823483
Synonymous0.6115662.10.9010.00000348537
Loss of Function1.4325.680.3522.39e-772

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002890.0000289
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.00002660.0000264
Middle Eastern0.0001090.000109
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Transcriptional repressor, which probably repress transcription by binding directly the 5'-CTGTCAA-3' DNA sequence or by interacting with TGF-beta activated SMAD proteins. Probably represses transcription via the recruitment of histone deacetylase proteins. {ECO:0000269|PubMed:11427533}.;
Pathway
TGF-beta signaling pathway - Homo sapiens (human);mir34a and TGIF2 in osteoclastogenesis;Tgif disruption of Shh signaling;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Downregulation of SMAD2/3:SMAD4 transcriptional activity;Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;Regulation of nuclear SMAD2/3 signaling (Consensus)

Recessive Scores

pRec
0.106

Intolerance Scores

loftool
0.421
rvis_EVS
-0.21
rvis_percentile_EVS
38.28

Haploinsufficiency Scores

pHI
0.709
hipred
Y
hipred_score
0.703
ghis
0.568

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.903

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumLowLow
Primary ImmunodeficiencyMediumLowMedium
CancerLowLowLow

Mouse Genome Informatics

Gene name
Tgif2
Phenotype
nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; embryo phenotype; respiratory system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; reproductive system phenotype; taste/olfaction phenotype; craniofacial phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype;

Gene ontology

Biological process
negative regulation of transcription by RNA polymerase II;regulation of transcription, DNA-templated;regulation of gastrulation;nodal signaling pathway;positive regulation of neuron differentiation;retina development in camera-type eye
Cellular component
nucleus;nucleoplasm
Molecular function
DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity