TCEA3

transcription elongation factor A3

Basic information

Region (hg38): 1:23380909-23424748

Links

ENSG00000204219 ∙ NCBI:6920 ∙ OMIM:604128 ∙ HGNC:11615 ∙ Uniprot:O75764 ∙ 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 TCEA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCEA3 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						0
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in TCEA3

This is a list of pathogenic ClinVar variants found in the TCEA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-23384354-G-A		not specified	Uncertain significance (Jun 11, 2021)
1-23387286-C-T		not specified	Uncertain significance (Jan 11, 2023)
1-23393887-T-G		not specified	Uncertain significance (Aug 17, 2022)
1-23393889-A-G		not specified	Uncertain significance (Jan 20, 2023)
1-23393908-C-T		not specified	Uncertain significance (Nov 18, 2022)
1-23393929-C-T		not specified	Uncertain significance (Oct 06, 2021)
1-23393935-G-A		not specified	Uncertain significance (Aug 28, 2023)
1-23393938-G-A		not specified	Uncertain significance (Aug 21, 2023)
1-23393944-C-T		not specified	Uncertain significance (Oct 12, 2022)
1-23393994-C-T		not specified	Uncertain significance (Dec 19, 2022)
1-23394009-G-A		not specified	Uncertain significance (Sep 21, 2021)
1-23397797-G-A		not specified	Uncertain significance (Jul 14, 2022)
1-23408707-T-G		not specified	Uncertain significance (Jul 19, 2023)
1-23417267-C-T		not specified	Uncertain significance (Jan 03, 2022)
1-23417340-T-C		not specified	Uncertain significance (Dec 20, 2021)
1-23417343-C-T		not specified	Uncertain significance (Apr 19, 2023)
1-23417347-T-G		not specified	Uncertain significance (Jul 12, 2022)
1-23417369-C-T		not specified	Uncertain significance (Feb 22, 2023)
1-23417387-G-T		not specified	Uncertain significance (Dec 06, 2022)
1-23417990-G-C		not specified	Uncertain significance (Mar 19, 2024)
1-23419112-G-T		not specified	Uncertain significance (Mar 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCEA3	protein_coding	protein_coding	ENST00000450454	11	43680

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00451	0.989	124600	0	57	124657	0.000229

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.955	168	207	0.813	0.0000121	2282
Missense in Polyphen		37	50.051	0.73924		565
Synonymous	-0.0410	76	75.5	1.01	0.00000428	646
Loss of Function	2.40	7	18.0	0.389	8.55e-7	236

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00123	0.00123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000559	0.000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000191	0.000186
Middle Eastern	0.000559	0.000556
South Asian	0.0000656	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.

Recessive Scores

• pRec: 0.0852

Intolerance Scores

• loftool: 0.636
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.557
• hipred: N
• hipred_score: 0.250
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tcea3

Gene ontology

• Biological process: transcription, DNA-templated;regulation of transcription, DNA-templated
• Cellular component: nucleus
• Molecular function: DNA binding;zinc ion binding