TXNL4A

thioredoxin like 4A, the group of U5 small nuclear ribonucleoprotein

Basic information

Region (hg38): 18:79970813-80033949

Previous symbols: [ "TXNL4" ]

Links

ENSG00000141759

∙ NCBI:10907 ∙ OMIM:611595 ∙ HGNC:30551 ∙ Uniprot:P83876 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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: CGD

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 ClinVar and linked to the TXNL4A gene.

Choanal_atresia-hearing_loss-cardiac_defects-craniofacial_dysmorphism_syndrome (13 variants)
Inborn_genetic_diseases (5 variants)
not_provided (4 variants)
TXNL4A-related_disorder (4 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. These statistics are base on transcript: NM_000006701.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar		3
missense			8 clinvar			8
nonsense	1 clinvar	1 clinvar				2
start loss			1			1
frameshift	2 clinvar	2 clinvar				4
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	3	3	11	3	0

Highest pathogenic variant AF is 0.00000342372

Loading clinvar variants...

GnomAD

Source: gnomAD

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: dbNSFP

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