TANGO2

transport and golgi organization 2 homolog, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 22:20017014-20067164

Previous symbols: [ "C22orf25" ]

Links

ENSG00000183597 ∙ NCBI:128989 ∙ OMIM:616830 ∙ HGNC:25439 ∙ Uniprot:Q6ICL3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• recurrent metabolic encephalomyopathic crises-rhabdomyolysis-cardiac arrhythmia-intellectual disability syndrome (Strong), mode of inheritance: AR
• metabolic encephalomyopathic crises, recurrent, with rhabdomyolysis, cardiac arrhythmias, and neurodegeneration (Moderate), mode of inheritance: AR
• recurrent metabolic encephalomyopathic crises-rhabdomyolysis-cardiac arrhythmia-intellectual disability syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Metabolic crises, recurrent, with rhabdomyolysis, cardiac arrhythmias, and neurodegeneration	AR	Biochemical; Cardiovascular; Musculoskeletal	Individuals may have cardiac arrhythmias and acute episodes of rhabdomyolysis, as well as hypoglycemia and lactic acidemia, and awareness may allow prompt management	Biochemical; Cardiovascular; Endocrine; Musculoskeletal; Neurologic	26805781; 26805782

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TANGO2 gene.

• not_provided (393 variants)
• Inborn_genetic_diseases (44 variants)
• Recurrent_metabolic_encephalomyopathic_crises-rhabdomyolysis-cardiac_arrhythmia-intellectual_disability_syndrome (35 variants)
• TANGO2-related_disorder (20 variants)
• Episodic_flaccid_weakness (5 variants)
• Intellectual_disability (5 variants)
• Cardiac_arrhythmia (5 variants)
• Seizure (5 variants)
• Acute_rhabdomyolysis (5 variants)
• not_specified (3 variants)
• See_cases (2 variants)
• Abnormality_of_metabolism/homeostasis (1 variants)
• Autism (1 variants)
• Metabolic_crises_with_rhabdomyolysis,_cardiac_arrhythmias,_and_neurodegeneration (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TANGO2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152906.7. 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				106	2	108
missense		5	125	7	1	138
nonsense	11	4	1			16
start loss			1			1
frameshift	5	2	1			8
splice donor/acceptor (+/-2bp)	1	10				11
Total	17	21	128	113	3

Highest pathogenic variant AF is 0.0000355107

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TANGO2	protein_coding	protein_coding	ENST00000327374	8	48913

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000148	0.968	125723	0	22	125745	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.448	152	168	0.903	0.0000103	1789
Missense in Polyphen		60	65.752	0.91252		767
Synonymous	1.18	59	71.7	0.823	0.00000505	523
Loss of Function	1.92	9	17.7	0.507	0.00000117	162

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000887	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.000295	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Metabolic encephalomyopathic crises, recurrent, with rhabdomyolysis, cardiac arrhythmias, and neurodegeneration (MECRCN) [MIM:616878]: An autosomal recessive disorder characterized by metabolic encephalomyopathic crises, hypoglycemia, hyperammonemia, episodic rhabdomyolysis, susceptibility to life-threatening cardiac tachyarrhythmias, developmental delay, mental retardation, and mild diffuse cerebral atrophy. {ECO:0000269|PubMed:26805781, ECO:0000269|PubMed:26805782}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.0980

Intolerance Scores

• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.73

Haploinsufficiency Scores

• pHI: 0.0809
• hipred: N
• hipred_score: 0.238
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tango2

Gene ontology

• Biological process: Golgi organization;protein secretion
• Cellular component: Golgi apparatus