TCEA2

transcription elongation factor A2

Basic information

Region (hg38): 20:64049835-64072347

Links

ENSG00000171703 ∙ NCBI:6919 ∙ OMIM:604784 ∙ HGNC:11614 ∙ Uniprot:Q15560 ∙ 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 TCEA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCEA2 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			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in TCEA2

This is a list of pathogenic ClinVar variants found in the TCEA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-64066497-C-T		not specified	Uncertain significance (Sep 14, 2023)
20-64066510-C-G		not specified	Uncertain significance (Jul 09, 2021)
20-64068074-G-A		not specified	Likely benign (Nov 06, 2023)
20-64068098-C-T		not specified	Uncertain significance (Apr 19, 2024)
20-64068112-G-A		not specified	Uncertain significance (Mar 14, 2023)
20-64069363-G-T		not specified	Uncertain significance (Aug 12, 2022)
20-64069367-G-T		not specified	Uncertain significance (Nov 09, 2023)
20-64069420-C-T		not specified	Uncertain significance (May 30, 2023)
20-64069473-G-A		not specified	Uncertain significance (Mar 29, 2023)
20-64069771-A-G		not specified	Uncertain significance (Jun 12, 2023)
20-64069773-G-A		not specified	Uncertain significance (Jul 06, 2021)
20-64069814-C-G		not specified	Uncertain significance (Dec 15, 2023)
20-64070567-A-G		not specified	Uncertain significance (May 25, 2022)
20-64070568-C-A		not specified	Uncertain significance (May 26, 2024)
20-64071907-T-A		not specified	Uncertain significance (Mar 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCEA2	protein_coding	protein_coding	ENST00000343484	10	22512

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000568	0.976	125704	0	7	125711	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.67	139	206	0.673	0.0000141	1943
Missense in Polyphen		43	86.384	0.49778		839
Synonymous	-1.58	98	80.0	1.22	0.00000530	593
Loss of Function	2.01	8	16.9	0.473	9.88e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000355	0.0000352
Middle Eastern	0.000112	0.000109
South Asian	0.00	0.00
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. {ECO:0000269|PubMed:12034815}.

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.444
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.542
• hipred: Y
• hipred_score: 0.750
• ghis: 0.696

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.998

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tcea2

Gene ontology

• Biological process: DNA-templated transcription, elongation;regulation of DNA-templated transcription, elongation;positive regulation of transcription by RNA polymerase II
• Cellular component: transcription elongation factor complex
• Molecular function: DNA binding;protein binding;zinc ion binding