TEDC1

tubulin epsilon and delta complex 1

Basic information

Region (hg38): 14:105489854-105499575

Previous symbols: [ "C14orf80" ]

Links

ENSG00000185347 ∙ NCBI:283643 ∙ ∙ HGNC:20127 ∙ Uniprot:Q86SX3 ∙ 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 TEDC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TEDC1 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				2		2
missense			4	1		5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	3	0

Variants in TEDC1

This is a list of pathogenic ClinVar variants found in the TEDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-105491396-G-T			Likely benign (Feb 01, 2023)
14-105492192-G-A			Likely benign (Jun 01, 2021)
14-105492640-A-C		not specified	Uncertain significance (Nov 12, 2021)
14-105492675-C-T		not specified	Uncertain significance (Sep 17, 2021)
14-105492687-C-T		not specified	Uncertain significance (Jul 15, 2021)
14-105498930-C-T		not specified	Likely benign (Oct 29, 2021)
14-105498932-C-A		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TEDC1	protein_coding	protein_coding	ENST00000392522	8	9721

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0149	0.980	125265	0	29	125294	0.000116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.331	267	252	1.06	0.0000169	2588
Missense in Polyphen		78	79.853	0.97679		934
Synonymous	-0.574	118	110	1.07	0.00000653	981
Loss of Function	2.44	6	16.8	0.357	9.07e-7	172

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000215	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.000491	0.000490
Finnish	0.0000565	0.0000463
European (Non-Finnish)	0.000116	0.000115
Middle Eastern	0.000491	0.000490
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in counteracting perturbation of actin filaments, such as after treatment with the actin depolymerizing microbial metabolite Chivosazole F. {ECO:0000269|PubMed:28796488}.

Intolerance Scores

• rvis_EVS: 0.93
• rvis_percentile_EVS: 89.83

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.123
• ghis: 0.468

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Tedc1

Gene ontology

• Molecular function: protein binding