TCEAL4

transcription elongation factor A like 4, the group of Transcription elongation factor A like family

Basic information

Region (hg38): X:103576231-103587729

Links

ENSG00000133142 ∙ NCBI:79921 ∙ ∙ HGNC:26121 ∙ Uniprot:Q96EI5 ∙ 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 TCEAL4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCEAL4 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			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	6	3	0

Variants in TCEAL4

This is a list of pathogenic ClinVar variants found in the TCEAL4 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-103577173-A-AG		Spinocerebellar ataxia 7	Uncertain significance (Feb 02, 2024)
X-103585645-C-T			Likely benign (Dec 01, 2022)
X-103586683-A-G		not specified	Uncertain significance (Jan 30, 2024)
X-103586764-C-T		not specified	Uncertain significance (Jul 13, 2022)
X-103586836-G-A		not specified	Likely benign (Jan 29, 2024)
X-103586879-G-A			Likely benign (Dec 01, 2022)
X-103586881-G-C		not specified	Uncertain significance (Sep 16, 2021)
X-103586923-A-G		not specified	Uncertain significance (Jul 26, 2024)
X-103586980-G-A		not specified	Uncertain significance (Aug 02, 2023)
X-103587114-G-A		not specified	Uncertain significance (Sep 29, 2023)
X-103587300-A-G		not specified	Conflicting classifications of pathogenicity (Apr 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCEAL4	protein_coding	protein_coding	ENST00000472745	1	11499

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.748	0.243	125461	0	4	125465	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.953	52	75.3	0.691	0.00000509	1429
Missense in Polyphen		1	20.047	0.049883		432
Synonymous	-0.306	28	26.0	1.08	0.00000191	359
Loss of Function	1.98	0	4.56	0.00	2.84e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000367	0.0000367
Ashkenazi Jewish	0.000135	0.0000993
East Asian	0.0000724	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000123	0.00000881
Middle Eastern	0.0000724	0.0000544
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: 0.0780

Intolerance Scores

• loftool: 0.881
• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.72

Haploinsufficiency Scores

• pHI: 0.103
• hipred: N
• hipred_score: 0.195
• ghis: 0.396

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.554

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