TCEAL1
protein-codingtranscription elongation factor A like 1, the group of Transcription elongation factor A like family
Gene summary
This gene encodes a member of the transcription elongation factor A (SII)-like (TCEAL) gene family. Members of this family may function as nuclear phosphoproteins that modulate transcription in a promoter context-dependent manner. The encoded protein is similar to transcription elongation factor A/transcription factor SII and contains a zinc finger-like motif as well as a sequence related to the transcription factor SII Pol II-binding region. It may exert its effects via protein-protein interactions with other transcriptional regulators rather than via direct binding of DNA. Multiple family members are located on the X chromosome. Alternative splicing results in multiple transcript variants encoding a single isoform. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~2.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: XL
Disease ID:MONDO:0859085
Submitter: G2P
Inheritance Pattern: XL
Disease ID:MONDO:0859085
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: XL
Disease ID:MONDO:0859085
Submitter: Ambry Genetics
Inheritance Pattern: XL
Disease ID:MONDO:0859085
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Allergy/Immunology/Infectious; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic
Intervention: Allergy/Immunology/Infectious
Rationale: In addition to other features, recurrent infections have been described (including respiratory and ear infections), and awareness may allow early and aggressive treatment of infections
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TCEAL1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004780.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | 4 | |||
| missense | 1 | 15 | 3 | 19 | ||
| nonsense | 1 | 5 | 1 | 7 | ||
| start loss | 0 | |||||
| frameshift | 5 | 2 | 7 | |||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 11 | 20 | 5 | 0 | 37 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004771.2 | 1 | MANE Select | |
| Ensembl | ENSP00000361708.3 | 1 | MANE Select | |
| RefSeq | NP_001006640.1 | 1 | Standard | |
| RefSeq | NP_001006641.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- negative regulation of transcription by RNA polymerase II
Molecular Function
- DNA-binding transcription factor activity
- WW domain binding
Cellular Component
- nucleus
- nucleoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000372625
- Coding exons
- 1
- Length
- 2250
- Individuals with no LoFs
- 122593
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 0
- Defined
- 122594
- p
- 0.00000408
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.04 | 35 | 57.3 | 0.611 | 0.00000383 | 1056 |
| Missense (PolyPhen) | 12 | 17.187 | 0.69821 | 289 | ||
| Synonymous | -0.0328 | 21 | 20.8 | 1.01 | 0.00000133 | 290 |
| Loss of Function | 1.53 | 0 | 2.73 | 0.00 | 1.72e-7 | 63 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.00013 | 0.000047 | rare |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be involved in transcriptional regulation. Modulates various viral and cellular promoters in a promoter context- dependent manner. For example, transcription from the FOS promoter is increased, while Rous sarcoma virus (RSV) long terminal repeat (LTR) promoter activity is repressed. Does not bind DNA directly.;
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- RVIS EVS
- 0.08
- RVIS percentile EVS
- 59.43
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.988
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |