TBX10

T-box transcription factor 10, the group of T-box transcription factors

Basic information

Region (hg38): 11:67631303-67639763

Previous symbols: [ "TBX7" ]

Links

ENSG00000167800

∙ NCBI:347853 ∙ OMIM:604648 ∙ HGNC:11593 ∙ Uniprot:O75333 ∙ 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 TBX10 gene.

not_specified (60 variants)
TBX10-related_disorder (15 variants)
not_provided (1 variants)
Mendelian_syndromes_with_cleft_lip/palate (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBX10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005995.5. 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				7 clinvar		7
missense			58 clinvar	7 clinvar	1 clinvar	66
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	59	14	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBX10	protein_coding	protein_coding	ENST00000335385	8	8258

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.07e-8	0.260	125643	0	105	125748	0.000418

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0686	224	221	1.01	0.0000127	2467
Missense in Polyphen		53	58.981	0.89859		722
Synonymous	0.0567	93	93.7	0.993	0.00000549	816
Loss of Function	0.515	13	15.2	0.857	7.57e-7	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000355	0.000354
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000594	0.0000462
European (Non-Finnish)	0.000583	0.000580
Middle Eastern	0.000272	0.000272
South Asian	0.000653	0.000653
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

Function: FUNCTION: Probable transcriptional regulator involved in developmental processes.;

Recessive Scores

pRec: 0.129

Intolerance Scores

loftool: 0.257
rvis_EVS: -0.09
rvis_percentile_EVS: 46.92

Haploinsufficiency Scores

pHI: 0.117
hipred: N
hipred_score: 0.170
ghis: 0.439

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.403

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tbx10
Phenotype: growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); craniofacial phenotype; vision/eye phenotype; normal 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); pigmentation phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); digestive/alimentary phenotype; hearing/vestibular/ear 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);

Gene ontology

Biological process: regulation of transcription by RNA polymerase II;anatomical structure morphogenesis
Cellular component: nucleus
Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding