TBX15

T-box transcription factor 15, the group of T-box transcription factors

Basic information

Region (hg38): 1:118883045-118989556

Previous symbols: [ "TBX14" ]

Links

ENSG00000092607 ∙ NCBI:6913 ∙ OMIM:604127 ∙ HGNC:11594 ∙ Uniprot:Q96SF7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• pelviscapular dysplasia (Definitive), mode of inheritance: AR
• pelviscapular dysplasia (Strong), mode of inheritance: AR
• pelviscapular dysplasia (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cousin syndrome	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal	7103674; 19068278

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TBX15 gene.

• not provided (155 variants)
• Inborn genetic diseases (22 variants)
• Pelviscapular dysplasia (19 variants)
• not specified (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBX15 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				29	2	31
missense			65	2	3	70
nonsense	1		2			3
start loss						0
frameshift		1	2			3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			4	3	3	10
non coding				19	32	51
Total	1	1	69	50	37

Variants in TBX15

This is a list of pathogenic ClinVar variants found in the TBX15 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-118884605-GA-G			Benign (Nov 22, 2019)
1-118884605-GAAA-G			Benign (Sep 13, 2019)
1-118884605-GAAAA-G			Likely benign (Dec 19, 2019)
1-118884605-G-GA			Benign (Aug 15, 2019)
1-118884605-G-GAA			Benign (Aug 18, 2019)
1-118884636-G-A			Likely benign (Sep 08, 2019)
1-118884740-T-G			Uncertain significance (Oct 22, 2023)
1-118884746-C-T		Inborn genetic diseases	Uncertain significance (Dec 30, 2023)
1-118884748-G-A			Likely benign (Jun 28, 2023)
1-118884763-G-A			Uncertain significance (Jun 13, 2022)
1-118884783-C-T			Likely benign (Dec 08, 2020)
1-118884798-A-G			Likely benign (Aug 08, 2023)
1-118884799-G-A			Uncertain significance (Jun 07, 2022)
1-118884813-T-C			Conflicting classifications of pathogenicity (Oct 03, 2023)
1-118884820-T-C		Inborn genetic diseases • Pelviscapular dysplasia	Uncertain significance (Apr 11, 2023)
1-118884831-G-A		Pelviscapular dysplasia	Benign (Jan 31, 2024)
1-118884844-A-C		not specified • Pelviscapular dysplasia	Benign (Jan 29, 2024)
1-118884858-C-T			Likely benign (Jun 02, 2022)
1-118884864-C-T			Likely benign (Feb 26, 2023)
1-118884871-T-A			Uncertain significance (Aug 08, 2022)
1-118884871-T-C			Uncertain significance (Oct 24, 2022)
1-118884889-G-A			Uncertain significance (Aug 01, 2022)
1-118884894-G-A			Likely benign (Aug 09, 2022)
1-118884918-A-C			Likely benign (Aug 29, 2022)
1-118884921-G-A			Likely benign (Sep 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBX15	protein_coding	protein_coding	ENST00000207157	7	106511

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.658	0.342	125721	0	14	125735	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.993	218	263	0.828	0.0000133	3264
Missense in Polyphen		80	118.58	0.67463		1540
Synonymous	1.04	85	98.1	0.867	0.00000536	979
Loss of Function	3.43	4	20.9	0.191	0.00000122	230

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000973	0.0000967
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable transcriptional regulator involved in the development of the skeleton of the limb, vertebral column and head. Acts by controlling the number of mesenchymal precursor cells and chondrocytes (By similarity). {ECO:0000250}.
• Disease: DISEASE: Cousin syndrome (COUSS) [MIM:260660]: Defined as pelviscapular dysplasia with epiphyseal abnormalities, congenital dwarfism and facial dysmorphy (frontal bossing, hypertelorism, narrow palpebral fissures, deep set globes, strabismus, low-set posteriory rotated and unusually formed external ears, dysplasia of conchae, small chin, short neck with redundant skin folds, and a low hairline). Intelligence may vary from normal to moderately impaired. Radiographic features comprise aplasia of the body of the scapula, hypoplasia of the iliac bone, humeroradial synosthosis, dislocation of the femoral heads, and moderate brachydactyly. {ECO:0000269|PubMed:19068278}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.143
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.96

Haploinsufficiency Scores

• pHI: 0.727
• hipred: Y
• hipred_score: 0.698
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.635

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbx15
• Phenotype: vision/eye phenotype; limbs/digits/tail phenotype; hearing/vestibular/ear phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; pigmentation 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); 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); reproductive system phenotype; craniofacial phenotype; muscle phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;embryonic cranial skeleton morphogenesis
• Cellular component: Tle3-Aes complex
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;protein binding;protein homodimerization activity;protein heterodimerization activity