TCEAL2

transcription elongation factor A like 2, the group of Transcription elongation factor A like family

Basic information

Region (hg38): X:102125678-102140426

Links

ENSG00000184905 ∙ NCBI:140597 ∙ ∙ HGNC:29818 ∙ Uniprot:Q9H3H9 ∙ 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 TCEAL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCEAL2 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			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	3	0

Variants in TCEAL2

This is a list of pathogenic ClinVar variants found in the TCEAL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-102126839-A-T		not specified	Uncertain significance (Aug 08, 2022)
X-102126841-T-C		not specified	Uncertain significance (Jan 19, 2024)
X-102126844-T-A		not specified	Uncertain significance (Feb 28, 2023)
X-102126847-A-G		not specified	Uncertain significance (Feb 28, 2023)
X-102126883-T-C		not specified	Uncertain significance (Apr 06, 2023)
X-102126903-C-T		not specified	Uncertain significance (Jun 11, 2024)
X-102126930-T-C		not specified	Uncertain significance (Feb 07, 2023)
X-102126943-A-G		not specified	Uncertain significance (Feb 21, 2024)
X-102126953-A-G			Likely benign (Jul 01, 2022)
X-102126990-G-A		not specified	Uncertain significance (Dec 15, 2023)
X-102127041-A-G		not specified	Uncertain significance (Mar 17, 2023)
X-102127186-A-G		not specified	Uncertain significance (Aug 16, 2022)
X-102127230-A-G		not specified	Likely benign (Jan 26, 2022)
X-102127304-T-C			Likely benign (Nov 01, 2022)
X-102127492-C-T		not specified	Uncertain significance (Oct 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCEAL2	protein_coding	protein_coding	ENST00000372780	1	2024

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.351	0.495	120000	0	1	120001	0.00000417

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.115	80	83.0	0.964	0.00000588	1500
Missense in Polyphen		9	11.155	0.80681		175
Synonymous	-1.71	43	30.9	1.39	0.00000247	391
Loss of Function	0.737	0	0.632	0.00	3.90e-8	17

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000128	0.00000939
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.

Recessive Scores

• pRec: 0.0656

Intolerance Scores

• loftool: 0.212
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.57

Haploinsufficiency Scores

• pHI: 0.0591
• hipred: N
• hipred_score: 0.229
• ghis: 0.418

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.888

Gene Damage Prediction

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

Gene ontology

• Cellular component: nucleus
• Molecular function: WW domain binding