TBX22

T-box transcription factor 22, the group of T-box transcription factors

Basic information

Region (hg38): X:80014753-80031774

Previous symbols: [ "CPX", "CLPA" ]

Links

ENSG00000122145

∙ NCBI:50945 ∙ OMIM:300307 ∙ HGNC:11600 ∙ Uniprot:Q9Y458 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Abruzzo-Erickson syndrome (Supportive), mode of inheritance: XL
cleft palate with or without ankyloglossia, X-linked (Supportive), mode of inheritance: XL
Abruzzo-Erickson syndrome (Limited), mode of inheritance: XL
cleft palate with or without ankyloglossia, X-linked (Strong), mode of inheritance: XL
cleft palate with or without ankyloglossia, X-linked (Definitive), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Abruzzo-Erickson syndrome	XL	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic; Craniofacial; Genitourinary; Musculoskeletal; Ophthalmologic	11559848; 12374769; 14729838; 15602089; 17846996; 17868388; 21248356; 22784330

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TBX22 gene.

not_provided (42 variants)
Inborn_genetic_diseases (33 variants)
Cleft_palate_with_or_without_ankyloglossia,_X-linked (28 variants)
TBX22-related_disorder (13 variants)
Cleft_palate_with_ankyloglossia (9 variants)
not_specified (4 variants)
Abruzzo-Erickson_syndrome (3 variants)
Mendelian_syndromes_with_cleft_lip/palate (1 variants)
Cleft_palate (1 variants)
Orofacial_cleft (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBX22 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001109878.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	12 clinvar	5 clinvar	18
missense	4 clinvar	4 clinvar	57 clinvar	3 clinvar	1 clinvar	69
nonsense	1 clinvar	1 clinvar	1 clinvar			3
start loss			1			1
frameshift	2 clinvar					2
splice donor/acceptor (+/-2bp)	2 clinvar	1 clinvar				3
Total	9	6	60	15	6

Highest pathogenic variant AF is 0.0000074480868

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBX22	protein_coding	protein_coding	ENST00000373294	8	17014

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.977	0.0230	125646	3	6	125655	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.126	204	199	1.03	0.0000145	3425
Missense in Polyphen		55	65.412	0.84083		1072
Synonymous	-0.266	80	77.0	1.04	0.00000611	997
Loss of Function	3.47	1	16.0	0.0625	0.00000117	277

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000295	0.000280
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000722	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000122	0.00000880
Middle Eastern	0.0000722	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Probable transcriptional regulator involved in developmental processes. This is major determinant crucial to palatogenesis.;
Disease: DISEASE: Abruzzo-Erickson syndrome (ABERS) [MIM:302905]: A disease characterized by cleft palate, coloboma, hypospadias, deafness, short stature, and radial synostosis. {ECO:0000269|PubMed:22784330}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec: 0.128

Intolerance Scores

loftool: 0.0586
rvis_EVS: -0.18
rvis_percentile_EVS: 40.16

Haploinsufficiency Scores

pHI: 0.0884
hipred: N
hipred_score: 0.482
ghis: 0.468

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.610

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Tbx22
Phenotype: homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; growth/size/body region phenotype; skeleton phenotype; digestive/alimentary phenotype; 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; respiratory system phenotype;

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription, DNA-templated;multicellular organism development;negative regulation of transcription, DNA-templated
Cellular component: nucleus
Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding