TXNL1

thioredoxin like 1

Basic information

Region (hg38): 18:56597208-56651600

Previous symbols: [ "TXNL" ]

Links

ENSG00000091164 ∙ NCBI:9352 ∙ OMIM:603049 ∙ HGNC:12436 ∙ Uniprot:O43396 ∙ 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 TXNL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TXNL1 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		1
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	4	1	0

Variants in TXNL1

This is a list of pathogenic ClinVar variants found in the TXNL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-56614600-T-C			Benign (Dec 31, 2019)
18-56616312-C-G			Benign (Dec 28, 2017)
18-56624292-C-A		not specified	Uncertain significance (Feb 27, 2024)
18-56624310-T-A		not specified	Uncertain significance (Dec 19, 2022)
18-56626370-A-C		not specified	Uncertain significance (Jun 11, 2024)
18-56626373-T-A			Likely benign (Jul 30, 2018)
18-56626452-C-T		not specified	Uncertain significance (Oct 12, 2021)
18-56638350-T-C		not specified	Uncertain significance (Sep 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TXNL1	protein_coding	protein_coding	ENST00000217515	8	54393

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.889	0.111	125689	0	3	125692	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.52	101	154	0.655	0.00000708	1932
Missense in Polyphen		21	51.636	0.40669		654
Synonymous	-0.183	54	52.3	1.03	0.00000242	512
Loss of Function	3.23	2	15.9	0.126	9.22e-7	186

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Active thioredoxin with a redox potential of about -250 mV. {ECO:0000269|PubMed:19349277}.

Recessive Scores

• pRec: 0.205

Intolerance Scores

• loftool: 0.372
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.28

Haploinsufficiency Scores

• pHI: 0.483
• hipred: Y
• hipred_score: 0.783
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.932

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Txnl1

Gene ontology

• Biological process: cell redox homeostasis;oxidation-reduction process
• Cellular component: proteasome complex;nucleus;cytoplasm;cytosol
• Molecular function: disulfide oxidoreductase activity