TXNL4A
thioredoxin like 4A, the group of U5 small nuclear ribonucleoprotein
Basic information
Region (hg38): 18:79970812-80033949
Previous symbols: [ "TXNL4" ]
Links
Phenotypes
GenCC
Source:
- choanal atresia-hearing loss-cardiac defects-craniofacial dysmorphism syndrome (Definitive), mode of inheritance: AR
- choanal atresia-hearing loss-cardiac defects-craniofacial dysmorphism syndrome (Supportive), mode of inheritance: AR
- choanal atresia-hearing loss-cardiac defects-craniofacial dysmorphism syndrome (Strong), mode of inheritance: AR
- choanal atresia-hearing loss-cardiac defects-craniofacial dysmorphism syndrome (Limited), mode of inheritance: Unknown
- choanal atresia-hearing loss-cardiac defects-craniofacial dysmorphism syndrome (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Burn-McKeown syndrome | AR | Audiologic/Otolaryngologic; Cardiovascular | As the condition can include prelingual deafness, early recognition and treatment of hearing impairment may improve outcomes, including speech and language development; The condition can involve congenital cardiac anomalies, and awareness may allow early management | Audiologic/Otolaryngologic; Cardiovascular; Craniofacial | 1342861; 14564154; 25434003 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (14 variants)
- Choanal atresia-hearing loss-cardiac defects-craniofacial dysmorphism syndrome (8 variants)
- TXNL4A-related condition (3 variants)
- Inborn genetic diseases (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TXNL4A 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 | |||||
| missense | 3 | |||||
| nonsense | 1 | |||||
| start loss | 1 | |||||
| frameshift | 2 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 0 | |||||
| non coding ? | 11 | 12 | ||||
| Total | 0 | 4 | 4 | 1 | 11 |
Variants in TXNL4A
This is a list of pathogenic ClinVar variants found in the TXNL4A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TXNL4A | protein_coding | protein_coding | ENST00000269601 | 3 | 61083 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000723 | 0.314 | 125740 | 0 | 8 | 125748 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.77 | 15 | 88.2 | 0.170 | 0.00000487 | 962 |
| Missense in Polyphen | 8 | 30.904 | 0.25887 | 337 | ||
| Synonymous | -0.888 | 39 | 32.6 | 1.20 | 0.00000189 | 241 |
| Loss of Function | -0.151 | 6 | 5.61 | 1.07 | 2.38e-7 | 68 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000152 | 0.000151 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000273 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000335 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays role in pre-mRNA splicing as component of the U5 snRNP and U4/U6-U5 tri-snRNP complexes that are involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex). {ECO:0000269|PubMed:28781166, ECO:0000305|PubMed:10610776, ECO:0000305|PubMed:26912367}.;
- Disease
- DISEASE: Burn-McKeown syndrome (BMKS) [MIM:608572]: A disease characterized by choanal atresia, sensorineural deafness, cardiac defects, and typical craniofacial dysmorphism consisting of narrow palpebral fissures, coloboma of the lower eyelids, prominent nose with high nasal bridge, short philtrum, cleft lip and/or palate, and large and protruding ears. Intellectual development is normal. {ECO:0000269|PubMed:25434003}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Spliceosome - Homo sapiens (human);mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.130
Intolerance Scores
- loftool
- 0.447
- rvis_EVS
- -0.08
- rvis_percentile_EVS
- 47.79
Haploinsufficiency Scores
- pHI
- 0.354
- hipred
- Y
- hipred_score
- 0.786
- ghis
- 0.649
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.988
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Low | Medium |
Mouse Genome Informatics
- Gene name
- Txnl4a
- Phenotype
Gene ontology
- Biological process
- spliceosomal complex assembly;RNA splicing, via transesterification reactions;mRNA splicing, via spliceosome;cell cycle;cell division
- Cellular component
- nucleus;nucleoplasm;spliceosomal complex;U5 snRNP;cytosol;nuclear membrane;U4/U6 x U5 tri-snRNP complex;U2-type precatalytic spliceosome
- Molecular function
- protein binding