TXNDC5

thioredoxin domain containing 5, the group of Protein disulfide isomerases|Thioredoxin domain containing

Basic information

Region (hg38): 6:7881516-7910788

Links

ENSG00000239264 ∙ NCBI:81567 ∙ OMIM:616412 ∙ HGNC:21073 ∙ Uniprot:Q8NBS9 ∙ 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 TXNDC5 gene.

• Inborn genetic diseases (30 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TXNDC5 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			28	2	1	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	3	1

Variants in TXNDC5

This is a list of pathogenic ClinVar variants found in the TXNDC5 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-7883165-G-T		not specified	Likely benign (Dec 21, 2022)
6-7883179-G-A		not specified	Uncertain significance (Jun 21, 2021)
6-7883190-T-C		not specified	Uncertain significance (Aug 03, 2022)
6-7883235-C-T			Benign (May 14, 2018)
6-7884388-C-G		not specified	Uncertain significance (Mar 21, 2023)
6-7884465-G-C		not specified	Uncertain significance (Feb 05, 2024)
6-7888710-C-T		not specified	Uncertain significance (Mar 22, 2023)
6-7888713-C-A		not specified	Uncertain significance (Feb 13, 2024)
6-7888716-C-T		not specified	Uncertain significance (Mar 22, 2023)
6-7888736-G-A		not specified	Uncertain significance (Aug 02, 2023)
6-7888793-G-A		not specified	Likely benign (Aug 02, 2023)
6-7889564-G-C		not specified	Uncertain significance (Jul 13, 2022)
6-7891640-T-A		not specified	Uncertain significance (Feb 12, 2024)
6-7891641-C-T		not specified	Uncertain significance (Aug 16, 2021)
6-7891709-G-A		not specified	Uncertain significance (Dec 22, 2023)
6-7895175-T-C		not specified	Uncertain significance (May 11, 2022)
6-7899631-C-T		not specified	Uncertain significance (Jun 22, 2021)
6-7899640-T-C		not specified	Uncertain significance (Jun 22, 2023)
6-7904612-G-A			Likely benign (Jul 01, 2022)
6-7904674-T-G		not specified	Uncertain significance (Sep 27, 2021)
6-7904682-A-C		not specified	Uncertain significance (Feb 07, 2023)
6-7904692-A-G		not specified	Uncertain significance (Jun 03, 2022)
6-7904706-C-T		not specified	Uncertain significance (Mar 21, 2022)
6-7904716-G-C		not specified	Uncertain significance (Dec 20, 2023)
6-7910545-C-T		not specified	Uncertain significance (Mar 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TXNDC5	protein_coding	protein_coding	ENST00000379757	10	145164

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.87e-13	0.100	125673	0	75	125748	0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.416	244	226	1.08	0.0000136	2759
Missense in Polyphen		96	96.351	0.99636		1089
Synonymous	0.386	90	94.8	0.950	0.00000638	857
Loss of Function	0.654	21	24.5	0.857	0.00000141	257

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00145	0.00145
Ashkenazi Jewish	0.00	0.00
East Asian	0.00105	0.000979
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.00105	0.000979
South Asian	0.000229	0.000229
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possesses thioredoxin activity. Has been shown to reduce insulin disulfide bonds. Also complements protein disulfide- isomerase deficiency in yeast (By similarity). {ECO:0000250}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);Golgi Associated Vesicle Biogenesis;Lysosome Vesicle Biogenesis;Clathrin derived vesicle budding;Neutrophil degranulation;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.258

Intolerance Scores

• loftool: 0.977
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.69

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.342
• ghis: 0.493

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Txndc5
• Phenotype: endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system phenotype

Gene ontology

• Biological process: negative regulation of apoptotic process;apoptotic cell clearance;neutrophil degranulation;cell redox homeostasis
• Cellular component: extracellular region;endoplasmic reticulum;endoplasmic reticulum lumen;azurophil granule lumen;lysosomal lumen;extracellular exosome
• Molecular function: protein binding;isomerase activity