TBX10

protein-coding

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

Gene summary

This gene encodes a member of the T-box family of transcription factors. These transcription factors share a DNA-binding domain called the T-box, and play a role in several developmental processes including early embryonic cell fate and organogenesis. The encoded protein is a member of the T-box 1 subfamily. Mutations in this gene are thought to be a cause of isolated cleft lip with or without cleft palate. [provided by RefSeq, Nov 2010]

Previous symbols:

TBX7

MANE transcript

NM_005995.5

Inheritance

—

ClinVar variants

U:65B:15

Top phenotype

TBX10-related disorder

gnomAD constraint

pLI —, LoF o/e 0.86

Max pathogenic AF

—

Genomic locus

chr11:67,631,303-67,639,763

External References & Databases

Ensembl (ENSG00000167800)

Transcript & Mutation Effects

hg38 • Region Span ~8.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TBX10 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 66

TBX10-related disorderTotal: 15

not providedTotal: 1

Mendelian syndromes with cleft lip/palateTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005995.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				7 clinvar		7
missense			64 clinvar	7 clinvar	1 clinvar	72
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	65	14	1	80

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005995.5	RefSeq	NP_005986.2	8	MANE Select
ENST00000335385.4	Ensembl	ENSP00000335191.3	8	MANE Select
ENST00001143439.1	Ensembl	ENSP00000807546.1	8	Standard
XM_047426879.1	RefSeq	XP_047282835.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
anatomical structure morphogenesis

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000335385
Coding exons: 8
Length: 8258
Individuals with no LoFs: 125643
Homozygous LoFs: 0
Heterozygous LoFs: 105
Defined: 125748
p: 0.000418

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0686	224	221	1.01	0.0000127	2467
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0.000059	0.000046	rare
European (Non-Finnish)	0.00058	0.00058	rare
South Asian	0.00065	0.00065	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.403

Gene Damage Prediction

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