TXNL4B
protein-codingthioredoxin like 4B
Gene summary
Predicted to be involved in spliceosomal tri-snRNP complex assembly and spliceosome conformational change to release U4 (or U4atac) and U1 (or U11). Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~9.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TXNL4B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_017853.3. 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 | 0 | |||||
| missense | 23 | 23 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 23 | 0 | 0 | 23 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060323.1 | 3 | MANE Select | |
| Ensembl | ENSP00000268483.3 | 3 | MANE Select | |
| RefSeq | NP_001135789.1 | 3 | Standard | |
| RefSeq | NP_001135790.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- mRNA splicing, via spliceosome
- cell cycle
Molecular Function
- protein binding
Cellular Component
- nucleoplasm
- U5 snRNP
- cytosol
- U4/U6 x U5 tri-snRNP complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000268483
- Coding exons
- 3
- Length
- 50143
- Individuals with no LoFs
- 125720
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 21
- Defined
- 125741
- p
- 0.0000835
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.794 | 96 | 76.5 | 1.26 | 0.00000337 | 993 |
| Missense (PolyPhen) | 34 | 33.268 | 1.022 | 441 | ||
| Synonymous | 0.743 | 22 | 26.9 | 0.818 | 0.00000122 | 272 |
| Loss of Function | 0.649 | 4 | 5.67 | 0.706 | 3.03e-7 | 70 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000030 | 0.000029 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00015 | 0.00015 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Essential role in pre-mRNA splicing. Required in cell cycle progression for S/G(2) transition. {ECO:0000269|PubMed:15161931}.;
Recessive Scores
- pRec
- 0.173
Intolerance Scores
- LoFtool
- 0.380
- RVIS EVS
- 0.21
- RVIS percentile EVS
- 67.72
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- E
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.799
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |