Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	10907
Gene name	Thioredoxin like 4A
Gene symbol	TXNL4A
Synonyms (NCBI Gene)	BMKSDIB1DIM1SNRNP15TXNL4U5-15kD
Chromosome	18
Chromosome location	18q23
Summary	The protein encoded by this gene is a member of the U5 small ribonucleoprotein particle (snRNP), and is involved in pre-mRNA splicing. This protein contains a thioredoxin-like fold and it is expected to interact with multiple proteins. Protein-protein int

Show/Hide all (7)

SNP ID	Visualize variation	Clinical significance	Consequence
rs535089924	CGCGCGCGCTAGCGCCGTGCGTGCTGACGGCATG>-,CGCGCGCGCTAGCGCCGTGCGTGCTGACGGCATGCGCGCGCGCTAGCGCCGTGCGTGCTGACGGCATG,CGCGCGCGCTAGCGCCGTGCGTGCTGACGGCATGCGCGCGCGCTAGCGCCGTGCGTGCTGACGGCATGCGCGCGCGCTAGCGCCGTGCGTGCTGACGGCATG	Pathogenic	Intron variant, upstream transcript variant, genic upstream transcript variant
rs727502793	C>A,T	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant, missense variant
rs727502794	G>A	Pathogenic	Stop gained, coding sequence variant, non coding transcript variant, intron variant, 5 prime UTR variant
rs727502795	A>-	Pathogenic	Coding sequence variant, non coding transcript variant, intron variant, splice donor variant, frameshift variant, 5 prime UTR variant
rs786205699	CGCGCTAGCGCCGTGCGTGCTGACGGCATGTGCG>-	Pathogenic	Genic upstream transcript variant, intron variant, upstream transcript variant
rs879255559	T>C	Pathogenic	Intron variant
rs1555719172	TAGGATCCCAGTCGTGGCCGAAG>-	Likely-pathogenic	5 prime UTR variant, non coding transcript variant, coding sequence variant, intron variant, frameshift variant

Show/Hide all (60)

miRTarBase ID	miRNA	Experiments	Reference
MIRT052139	hsa-let-7b-5p	CLASH	23622248
MIRT050419	hsa-miR-23a-3p	CLASH	23622248
MIRT041224	hsa-miR-193b-3p	CLASH	23622248
MIRT036005	hsa-miR-1301-3p	CLASH	23622248
MIRT712648	hsa-miR-6752-3p	HITS-CLIP	19536157
MIRT712647	hsa-miR-3667-3p	HITS-CLIP	19536157
MIRT712646	hsa-miR-18a-3p	HITS-CLIP	19536157
MIRT712645	hsa-miR-938	HITS-CLIP	19536157
MIRT712644	hsa-miR-6886-3p	HITS-CLIP	19536157
MIRT712643	hsa-miR-670-3p	HITS-CLIP	19536157
MIRT712648	hsa-miR-6752-3p	HITS-CLIP	19536157
MIRT712647	hsa-miR-3667-3p	HITS-CLIP	19536157
MIRT712646	hsa-miR-18a-3p	HITS-CLIP	19536157
MIRT712645	hsa-miR-938	HITS-CLIP	19536157
MIRT712644	hsa-miR-6886-3p	HITS-CLIP	19536157
MIRT712643	hsa-miR-670-3p	HITS-CLIP	19536157
MIRT712648	hsa-miR-6752-3p	HITS-CLIP	19536157
MIRT712647	hsa-miR-3667-3p	HITS-CLIP	19536157
MIRT712646	hsa-miR-18a-3p	HITS-CLIP	19536157
MIRT712645	hsa-miR-938	HITS-CLIP	19536157
MIRT712644	hsa-miR-6886-3p	HITS-CLIP	19536157
MIRT712643	hsa-miR-670-3p	HITS-CLIP	19536157
MIRT712648	hsa-miR-6752-3p	HITS-CLIP	19536157
MIRT712647	hsa-miR-3667-3p	HITS-CLIP	19536157
MIRT712646	hsa-miR-18a-3p	HITS-CLIP	19536157
MIRT712645	hsa-miR-938	HITS-CLIP	19536157
MIRT712644	hsa-miR-6886-3p	HITS-CLIP	19536157
MIRT712643	hsa-miR-670-3p	HITS-CLIP	19536157
MIRT1465386	hsa-miR-1197	CLIP-seq
MIRT1465387	hsa-miR-125a-3p	CLIP-seq
MIRT1465388	hsa-miR-1273f	CLIP-seq
MIRT1465389	hsa-miR-3180	CLIP-seq
MIRT1465390	hsa-miR-3180-3p	CLIP-seq
MIRT1465391	hsa-miR-3196	CLIP-seq
MIRT1465392	hsa-miR-329	CLIP-seq
MIRT1465393	hsa-miR-362-3p	CLIP-seq
MIRT1465394	hsa-miR-3647-3p	CLIP-seq
MIRT1465395	hsa-miR-3675-5p	CLIP-seq
MIRT1465396	hsa-miR-3714	CLIP-seq
MIRT1465397	hsa-miR-4493	CLIP-seq
MIRT1465398	hsa-miR-4756-3p	CLIP-seq
MIRT1465399	hsa-miR-552	CLIP-seq
MIRT2360593	hsa-miR-3121-3p	CLIP-seq
MIRT2360594	hsa-miR-320a	CLIP-seq
MIRT2360595	hsa-miR-320b	CLIP-seq
MIRT2360596	hsa-miR-320c	CLIP-seq
MIRT2360597	hsa-miR-320d	CLIP-seq
MIRT2360598	hsa-miR-361-3p	CLIP-seq
MIRT2360599	hsa-miR-3907	CLIP-seq
MIRT2360600	hsa-miR-4429	CLIP-seq
MIRT2360601	hsa-miR-4677-3p	CLIP-seq
MIRT2360602	hsa-miR-4742-3p	CLIP-seq
MIRT2360603	hsa-miR-518a-5p	CLIP-seq
MIRT2360604	hsa-miR-527	CLIP-seq
MIRT2360605	hsa-miR-664	CLIP-seq
MIRT2360606	hsa-miR-766	CLIP-seq
MIRT2360598	hsa-miR-361-3p	CLIP-seq
MIRT2462695	hsa-miR-4786-3p	CLIP-seq
MIRT2360593	hsa-miR-3121-3p	CLIP-seq
MIRT2360602	hsa-miR-4742-3p	CLIP-seq

Show/Hide all (25)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000245	Process	Spliceosomal complex assembly	TAS	10610776
GO:0000375	Process	RNA splicing, via transesterification reactions	TAS	10610776
GO:0000398	Process	MRNA splicing, via spliceosome	IDA	28781166
GO:0000398	Process	MRNA splicing, via spliceosome	IEA
GO:0000398	Process	MRNA splicing, via spliceosome	NAS	30975767
GO:0005515	Function	Protein binding	IPI	15840814, 16723661, 20858735, 25416956, 28514442, 32296183, 33961781, 35271311
GO:0005634	Component	Nucleus	IDA	26912367
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	30975767
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005681	Component	Spliceosomal complex	IBA
GO:0005681	Component	Spliceosomal complex	IEA
GO:0005681	Component	Spliceosomal complex	IPI	30975767
GO:0005681	Component	Spliceosomal complex	TAS	10610776
GO:0005682	Component	U5 snRNP	IBA
GO:0005829	Component	Cytosol	IDA
GO:0006397	Process	MRNA processing	IEA
GO:0008380	Process	RNA splicing	IEA
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IBA
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IDA	26912367
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IEA
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IPI	30975767
GO:0051301	Process	Cell division	IEA
GO:0071005	Component	U2-type precatalytic spliceosome	IDA	28781166

MIM	HGNC	e!Ensembl
611595	30551	ENSG00000141759

P83876

Protein name

Thioredoxin-like protein 4A (DIM1 protein homolog) (Spliceosomal U5 snRNP-specific 15 kDa protein) (Thioredoxin-like U5 snRNP protein U5-15kD)

Protein function

Plays a 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, EC

PDB

1PQN , 1QGV , 1SYX , 3JCR , 4BWQ , 4BWS , 4CDO , 5O9Z , 6AH0 , 6AHD , 6QW6 , 6QX9 , 8H6E , 8H6J , 8H6K , 8H6L , 8Q7N , 8QO9 , 8QOZ , 8QP8 , 8QP9 , 8QPA , 8QPB , 8QPE , 8QPK , 8QXD , 8QZS , 8R08 , 8R09 , 8R0A , 8R0B , 8RM5

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF02966	DIM1	4 → 136	Mitosis protein DIM1	Domain

Sequence

MSYMLPHLHNGWQVDQAILSEEDRVVVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYL
VDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVY
RGARKGRGLVVSPKDYSTKYRY

Sequence length

142

Interactions

View interactions

	KEGG		Reactome
	Spliceosome		mRNA Splicing - Major Pathway mRNA Splicing - Minor Pathway

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Choanal atresia-hearing loss-cardiac defects-craniofacial dysmorphism syndrome	Likely pathogenic; Pathogenic	rs1568360069, rs2145089648, rs2145048234, rs535089924, rs727502793, rs727502794, rs727502795, rs786205699, rs1555719172	RCV002226967 RCV002273877 RCV002273878 RCV000149583 RCV000149584 View all (4 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
TXNL4A-related disorder	Likely pathogenic; Pathogenic	rs727502793, rs786205699	RCV003422037 RCV003407632	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (4)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
BURN-MCKEOWN SYNDROME	—	CTD, Disgenet, HPO, Orphanet CTD, Disgenet, HPO, Orphanet CTD, Disgenet, HPO, Orphanet CTD, Disgenet, HPO, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (23)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
2-3 toe syndactyly	Syndactyly Of The Toes	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Acrofacial Dysostosis	Acrofacial Dysostosis	BEFREE	25865758		★★★★★ ★☆☆☆☆ Found in Text Mining only
Atrial Septal Defects	Atrial Septal Defect	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Bilateral choanal atresia/stenosis	Choanal Atresia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Blepharophimosis	Blepharophimosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Burn-Mckeown syndrome	Burn-Mckeown Syndrome	BEFREE	25434003, 25865758, 28905882		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Burn-Mckeown syndrome	Burn-Mckeown Syndrome	ORPHANET_DG	25434003		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Burn-Mckeown syndrome	Burn-Mckeown Syndrome	CLINVAR_DG	25434003		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Burn-Mckeown syndrome	Burn-Mckeown Syndrome	GENOMICS_ENGLAND_DG	25434003		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Burn-McKeown syndrome	Burn-Mckeown Syndrome	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Burn-Mckeown syndrome	Burn-Mckeown Syndrome	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Choanal Atresia	Choanal Atresia	BEFREE	28905882		★★★★★ ★☆☆☆☆ Found in Text Mining only
Choanal Atresia	Choanal atresia syndrome	Pubtator	28905882	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Class III malocclusion	Malocclusion	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Conductive hearing loss	Hearing Loss	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital hypoplasia of kidney	Renal hypoplasia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	32735620	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Heart Septal Defects	Heart Septal Defects	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	32041777	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Microstomia	Microstomia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Ventricular Septal Defects	Ventricular septal defect	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only

TXNL4A (thioredoxin like 4A)