TRIP11

thyroid hormone receptor interactor 11, the group of Golgins

Basic information

Region (hg38): 14:91965990-92040896

Links

ENSG00000100815 ∙ NCBI:9321 ∙ OMIM:604505 ∙ HGNC:12305 ∙ Uniprot:Q15643 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• achondrogenesis type IA (Definitive), mode of inheritance: AR
• achondrogenesis type IA (Strong), mode of inheritance: AR
• achondrogenesis type IA (Supportive), mode of inheritance: AR
• achondrogenesis type IA (Moderate), mode of inheritance: AR
• achondrogenesis type IA (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Achondrogenesis, type IA; Odontochondrodysplasia	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	Dental; Musculoskeletal; Pulmonary; Renal	4885523; 7460382; 3275766; 18241073; 20089971; 30728324

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRIP11 gene.

• Achondrogenesis, type IA (540 variants)
• not provided (232 variants)
• Inborn genetic diseases (60 variants)
• Connective tissue disorder (47 variants)
• not specified (44 variants)
• Goldblatt syndrome (12 variants)
• Achondrogenesis (6 variants)
• Goldblatt syndrome;Achondrogenesis, type IA (3 variants)
• Achondrogenesis, type IA;Goldblatt syndrome (2 variants)
• TRIP11-related condition (2 variants)
• Autism spectrum disorder (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIP11 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			9	94	9	112
missense		2	263	15	14	294
nonsense	16	5				21
start loss						0
frameshift	19	5				24
inframe indel			5	1		6
splice donor/acceptor (+/-2bp)	1	4	1			6
splice region			9	9	2	20
non coding	1		43	98	81	223
Total	37	16	321	208	104

Highest pathogenic variant AF is 0.0000854

Variants in TRIP11

This is a list of pathogenic ClinVar variants found in the TRIP11 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-91967929-C-T		Achondrogenesis, type IA	Benign (Jan 12, 2018)
14-91968082-C-A		Achondrogenesis, type IA	Uncertain significance (Jan 12, 2018)
14-91968119-A-T		Achondrogenesis, type IA	Benign (Jan 13, 2018)
14-91968152-C-T		Achondrogenesis, type IA	Uncertain significance (Jan 13, 2018)
14-91968299-T-G		Achondrogenesis, type IA	Benign (Jan 12, 2018)
14-91968333-AT-A		Achondrogenesis	Uncertain significance (Jun 14, 2016)
14-91968333-A-AT		Achondrogenesis	Likely benign (Jun 14, 2016)
14-91968379-T-C		Achondrogenesis, type IA	Uncertain significance (Jan 12, 2018)
14-91968461-G-A		Achondrogenesis, type IA	Uncertain significance (Jan 12, 2018)
14-91968479-T-C		Achondrogenesis, type IA	Uncertain significance (Jan 13, 2018)
14-91968488-C-T		Achondrogenesis, type IA	Uncertain significance (Jan 12, 2018)
14-91968498-G-C		Achondrogenesis, type IA	Uncertain significance (Jan 13, 2018)
14-91968613-G-A		Achondrogenesis, type IA	Benign (Jan 13, 2018)
14-91968721-T-A		Achondrogenesis, type IA	Benign (Jan 13, 2018)
14-91968735-T-C		Achondrogenesis, type IA	Uncertain significance (Jan 13, 2018)
14-91968743-G-A		Achondrogenesis, type IA	Benign (Jan 13, 2018)
14-91968769-T-C		Achondrogenesis, type IA	Uncertain significance (Jan 12, 2018)
14-91968782-T-C		Achondrogenesis, type IA	Uncertain significance (Jan 12, 2018)
14-91968833-T-C		Achondrogenesis, type IA	Uncertain significance (Jan 12, 2018)
14-91968924-C-T		Achondrogenesis, type IA	Benign (Jan 13, 2018)
14-91969009-G-A		Achondrogenesis, type IA	Benign (Jan 13, 2018)
14-91969045-G-A		Achondrogenesis, type IA	Uncertain significance (Jan 13, 2018)
14-91969063-T-G		Achondrogenesis, type IA	Benign (Jan 13, 2018)
14-91969129-G-A		Achondrogenesis, type IA	Uncertain significance (Jan 13, 2018)
14-91969182-T-G		Achondrogenesis, type IA	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIP11	protein_coding	protein_coding	ENST00000267622	21	74906

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.71e-12	1.00	125562	0	186	125748	0.000740

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.515	903	948	0.953	0.0000464	13129
Missense in Polyphen		230	270.47	0.85036		4021
Synonymous	-0.886	367	346	1.06	0.0000175	3506
Loss of Function	5.72	39	101	0.386	0.00000554	1259

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000870	0.000869
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000436	0.000435
Finnish	0.00157	0.00157
European (Non-Finnish)	0.000901	0.000888
Middle Eastern	0.000436	0.000435
South Asian	0.000532	0.000523
Other	0.000819	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds the ligand binding domain of the thyroid receptor (THRB) in the presence of triiodothyronine and enhances THRB- modulated transcription. Golgi auto-antigen; probably involved in maintaining cis-Golgi structure. {ECO:0000269|PubMed:10189370, ECO:0000269|PubMed:9256431}.
• Disease: DISEASE: Note=A chromosomal aberration involving TRIP11 may be a cause of acute myelogenous leukemia. Translocation t(5;14)(q33;q32) with PDGFRB. The fusion protein may be involved in clonal evolution of leukemia and eosinophilia. {ECO:0000269|PubMed:9373237}.; DISEASE: Achondrogenesis 1A (ACG1A) [MIM:200600]: A form of achondrogenesis type 1, a lethal form of chondrodysplasia characterized by deficient ossification in the lumbar vertebrae and absent ossification in the sacral, pubic and ischial bones and clinically by stillbirth or early death. In addition to severe micromelia, there is a disproportionately large cranium due to marked edema of soft tissues. {ECO:0000269|PubMed:20089971}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Intra-Golgi traffic;Intra-Golgi and retrograde Golgi-to-ER traffic;Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.900
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.61

Haploinsufficiency Scores

• pHI: 0.194
• hipred: Y
• hipred_score: 0.590
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.805

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trip11
• Phenotype: growth/size/body region phenotype; craniofacial phenotype; cellular phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system 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); 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); limbs/digits/tail 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); digestive/alimentary phenotype; skeleton phenotype

Gene ontology

• Biological process: ventricular septum development;chondrocyte differentiation involved in endochondral bone morphogenesis;transcription by RNA polymerase II;protein glycosylation;Golgi organization;intraciliary transport involved in cilium assembly;inner ear receptor cell stereocilium organization;positive regulation of nucleic acid-templated transcription
• Cellular component: Golgi membrane;inner acrosomal membrane;outer acrosomal membrane;nucleus;Golgi apparatus;cis-Golgi network;cytoskeleton;cilium;nuclear speck;transport vesicle
• Molecular function: transcription coactivator activity;protein binding