TCEAL7

transcription elongation factor A like 7, the group of Transcription elongation factor A like family

Basic information

Region (hg38): X:103330229-103332326

Links

ENSG00000182916 ∙ NCBI:56849 ∙ OMIM:300771 ∙ HGNC:28336 ∙ Uniprot:Q9BRU2 ∙ 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 TCEAL7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCEAL7 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			4			4
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	0	0

Variants in TCEAL7

This is a list of pathogenic ClinVar variants found in the TCEAL7 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-103331414-C-G		not specified	Uncertain significance (Jan 04, 2022)
X-103331459-G-A		not specified	Uncertain significance (Jan 26, 2023)
X-103331615-G-A		not specified	Uncertain significance (May 24, 2024)
X-103331628-G-T		not specified	Uncertain significance (Jul 27, 2022)
X-103331636-G-A		not specified	Uncertain significance (Jun 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCEAL7	protein_coding	protein_coding	ENST00000332431	1	2131

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.485	0.442	123679	2	1	123682	0.0000121

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.383	33	39.8	0.829	0.00000312	675
Missense in Polyphen		4	6.6497	0.60153		150
Synonymous	0.412	11	12.9	0.854	9.53e-7	169
Loss of Function	1.24	0	1.80	0.00	1.12e-7	42

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)	0.0000377	0.0000272
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the negative regulation of NF-kappa-B signaling at the basal level by modulating transcriptional activity of NF-kappa-B on its target gene promoters. Associates with cyclin D1 promoter containing Myc E-box sequence and transcriptionally represses cyclin D1 expression. Regulates telomerase reverse transcriptase expression and telomerase activity in both ALT (alternative lengthening of telomeres)and telomerase-positive cell lines. {ECO:0000269|PubMed:18806825, ECO:0000269|PubMed:19966855, ECO:0000269|PubMed:20454512}.

Intolerance Scores

• rvis_EVS: 0.12
• rvis_percentile_EVS: 62.38

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.164
• ghis: 0.656

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tceal7

Gene ontology

• Biological process: negative regulation of NF-kappaB transcription factor activity;negative regulation of transcription, DNA-templated
• Cellular component: nucleus
• Molecular function: WW domain binding