TBCE

tubulin folding cofactor E

Basic information

Region (hg38): 1:235367360-235452443

Previous symbols: [ "KCS", "HRD" ]

Links

ENSG00000284770 ∙ NCBI:6905 ∙ OMIM:604934 ∙ HGNC:11582 ∙ Uniprot:Q15813 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 53.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_003193.5	NP_003184.1	16	yes	-
ENST00000642610.2	ENSP00000494796.1	16	yes	-
NM_001079515.3	NP_001072983.1	16	-	-
NM_001287801.2	NP_001274730.1	17	-	-

Phenotypes

GenCC

Source: genCC

• autosomal recessive Kenny-Caffey syndrome (Moderate), mode of inheritance: AR
• encephalopathy, progressive, with amyotrophy and optic atrophy (Limited), mode of inheritance: AR
• encephalopathy, progressive, with amyotrophy and optic atrophy (Moderate), mode of inheritance: AR
• hypoparathyroidism-retardation-dysmorphism syndrome (Strong), mode of inheritance: AR
• early-onset progressive diffuse brain atrophy-microcephaly-muscle weakness-optic atrophy syndrome (Strong), mode of inheritance: AR
• hypoparathyroidism-retardation-dysmorphism syndrome (Supportive), mode of inheritance: AR
• autosomal recessive Kenny-Caffey syndrome (Supportive), mode of inheritance: AR
• encephalopathy, progressive, with amyotrophy and optic atrophy (Strong), mode of inheritance: AR
• hypoparathyroidism-retardation-dysmorphism syndrome (Strong), mode of inheritance: AR
• encephalopathy, progressive, with amyotrophy and optic atrophy (Strong), mode of inheritance: AR
• hypoparathyroidism-retardation-dysmorphism syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Kenny-Caffey syndrome, type 1; Hypoparathyroidism-retardation-dysmorphism syndrome	AR	Endocrine	Individuals can present with sequelae of neonatal hypocalcemia, and prompt diagnosis and treatment can lead to correction of electrolyte abnormalities; Some individuals with multiple pituitary anomalies (eg, affecting GH, cortisol, and including features of hypogonadotropic hypogonadism have been described), and surveillance may allow early diagnosis and treatment	Endocrine; Musculoskeletal; Neurologic; Ophthalmologic	2843457; 1701077; 2001103; 1308349; 7538982; 9056548; 12389028; 19491227; 19554981; 27666369

ClinVar

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

• not_provided (478 variants)
• Inborn_genetic_diseases (73 variants)
• Hypoparathyroidism-retardation-dysmorphism_syndrome (59 variants)
• Encephalopathy,_progressive,_with_amyotrophy_and_optic_atrophy (29 variants)
• Autosomal_recessive_Kenny-Caffey_syndrome (23 variants)
• TBCE-related_disorder (23 variants)
• not_specified (17 variants)
• Disorder_of_sexual_differentiation (1 variants)
• Pituitary_stalk_interruption_syndrome (1 variants)
• Microcephaly (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 TBCE gene is commonly pathogenic or not. These statistics are base on transcript: NM_003193.5. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			7	141	2	150
missense		3	128	15	2	148
nonsense	16	3				19
start loss			1			1
frameshift	24	5	5			34
splice donor/acceptor (+/-2bp)		11	5	1		17
Total	40	22	146	157	4

Highest pathogenic variant AF is 0.0000685139

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Tubulin-folding protein; involved in the second step of the tubulin folding pathway and in the regulation of tubulin heterodimer dissociation. Required for correct organization of microtubule cytoskeleton and mitotic splindle, and maintenance of the neuronal microtubule network. {ECO:0000269|PubMed:11847227, ECO:0000269|PubMed:27666369}.
• Disease: DISEASE: Hypoparathyroidism-retardation-dysmorphism syndrome (HRDS) [MIM:241410]: An autosomal recessive multisystem disorder characterized by hypoparathyroidism, intrauterine and postnatal growth retardation, psychomotor retardation, epilepsy, microcephaly, and facial dysmorphism. {ECO:0000269|PubMed:12389028}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Kenny-Caffey syndrome 1 (KCS1) [MIM:244460]: An autosomal recessive form of Kenny-Caffey syndrome, a disorder characterized by impaired skeletal development with small and dense bones, short stature, and primary hypoparathyroidism with hypocalcemia. Clinical features include cortical thickening and medullary stenosis of the tubular bones, delayed closure of fontanels, defective dentition, small eyes with hypermetropia, and frontal bossing with a triangular face. {ECO:0000269|PubMed:12389028}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Encephalopathy, progressive, with amyotrophy and optic atrophy (PEAMO) [MIM:617207]: An autosomal recessive, progressive, neurodegenerative encephalopathy with onset in infancy. Affected individuals manifest delayed psychomotor development, severe hypotonia, motor regression, spinal muscular atrophy, distal amyotrophy and weakness of all limbs, and intellectual disability of variable severity. Additional features include optic atrophy, thin corpus callosum, and cerebellar atrophy. {ECO:0000269|PubMed:27666369}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Metabolism of proteins;Protein folding;Post-chaperonin tubulin folding pathway (Consensus)

Recessive Scores

• pRec: 0.348

Intolerance Scores

• loftool: 0.901
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.66

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.281

Gene Damage Prediction

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

Gene ontology

• Biological process: microtubule cytoskeleton organization;protein folding;post-chaperonin tubulin folding pathway;mitotic spindle organization
• Cellular component: cytoplasm;microtubule
• Molecular function: protein binding;chaperone binding