TEDC2

tubulin epsilon and delta complex 2, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 16:2460085-2464963

Previous symbols: [ "C16orf59" ]

Links

ENSG00000162062 ∙ NCBI:80178 ∙ ∙ HGNC:25849 ∙ Uniprot:Q7L2K0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TEDC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEDC2 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				1		1
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in TEDC2

This is a list of pathogenic ClinVar variants found in the TEDC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-2460163-T-G		not specified	Uncertain significance (Sep 16, 2021)
16-2460346-G-C		not specified	Uncertain significance (Sep 27, 2021)
16-2460370-G-A			Likely benign (Nov 01, 2022)
16-2461056-C-T		not specified	Uncertain significance (Oct 05, 2021)
16-2461124-G-C		not specified	Uncertain significance (Aug 17, 2021)
16-2462470-G-A		not specified	Uncertain significance (Jun 18, 2021)
16-2464074-G-A		not specified	Uncertain significance (Aug 12, 2021)
16-2464618-G-A		not specified	Uncertain significance (Nov 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEDC2	protein_coding	protein_coding	ENST00000361837	10	4884

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.10e-12	0.0690	124665	0	89	124754	0.000357

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.145	258	252	1.03	0.0000152	2670
Missense in Polyphen		57	62.278	0.91525		831
Synonymous	-1.39	131	112	1.17	0.00000714	958
Loss of Function	0.301	18	19.4	0.926	9.94e-7	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000346	0.000346
Ashkenazi Jewish	0.00	0.00
East Asian	0.000613	0.000612
Finnish	0.0000467	0.0000464
European (Non-Finnish)	0.000538	0.000521
Middle Eastern	0.000613	0.000612
South Asian	0.000264	0.000261
Other	0.000514	0.000495

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0793

Intolerance Scores

• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.69

Haploinsufficiency Scores

• pHI: 0.331
• hipred: N
• hipred_score: 0.146
• ghis: 0.490

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Tedc2

Gene ontology

• Molecular function: protein binding