TXNL4B

thioredoxin like 4B

Basic information

Region (hg38): 16:72084857-72094431

Links

ENSG00000140830 ∙ NCBI:54957 ∙ OMIM:617722 ∙ HGNC:26041 ∙ Uniprot:Q9NX01 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TXNL4B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TXNL4B 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						0
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in TXNL4B

This is a list of pathogenic ClinVar variants found in the TXNL4B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-72086755-T-C		not specified	Uncertain significance (Aug 26, 2022)
16-72086774-T-C		not specified	Uncertain significance (Jun 29, 2022)
16-72089002-A-T		not specified	Uncertain significance (Dec 21, 2023)
16-72089003-T-C		not specified	Uncertain significance (Apr 17, 2024)
16-72089059-T-C		not specified	Uncertain significance (Jun 29, 2023)
16-72089075-T-C		not specified	Uncertain significance (Jun 01, 2023)
16-72090619-A-G		not specified	Uncertain significance (Mar 17, 2023)
16-72090641-C-A		not specified	Uncertain significance (Feb 06, 2023)
16-72090641-C-T		not specified	Uncertain significance (Apr 12, 2022)
16-72090670-A-G		not specified	Uncertain significance (May 01, 2024)
16-72090676-A-G		not specified	Uncertain significance (Sep 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TXNL4B	protein_coding	protein_coding	ENST00000268483	3	50143

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00435	0.684	125720	0	21	125741	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.794	96	76.5	1.26	0.00000337	993
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000305	0.0000305
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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

Haploinsufficiency Scores

• pHI: 0.152
• hipred: N
• hipred_score: 0.403
• ghis: 0.439

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.799

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Txnl4b

Gene ontology

• Biological process: mRNA splicing, via spliceosome;cell cycle
• Cellular component: nucleoplasm;U5 snRNP;cytosol;U4/U6 x U5 tri-snRNP complex
• Molecular function: protein binding