TXNDC17

thioredoxin domain containing 17, the group of Thioredoxin domain containing

Basic information

Region (hg38): 17:6640985-6644541

Previous symbols: [ "TXNL5" ]

Links

ENSG00000129235 ∙ NCBI:84817 ∙ OMIM:616967 ∙ HGNC:28218 ∙ Uniprot:Q9BRA2 ∙ 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 TXNDC17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TXNDC17 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		1	5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	5	0	2

Variants in TXNDC17

This is a list of pathogenic ClinVar variants found in the TXNDC17 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-6641093-A-T		not specified	Uncertain significance (Aug 11, 2022)
17-6641101-G-A			Benign (Sep 14, 2018)
17-6641145-G-A			Benign (Jan 25, 2018)
17-6641173-T-C		not specified	Uncertain significance (Nov 20, 2024)
17-6641191-G-C		not specified	Uncertain significance (Jul 25, 2023)
17-6641191-G-T		not specified	Uncertain significance (Aug 26, 2024)
17-6641195-G-C		not specified	Uncertain significance (Feb 10, 2022)
17-6641221-G-A		not specified	Uncertain significance (Mar 15, 2024)
17-6642259-C-G		not specified	Uncertain significance (Dec 13, 2022)
17-6642308-T-C		not specified	Uncertain significance (Oct 21, 2024)
17-6642967-A-C		not specified	Uncertain significance (Aug 21, 2024)
17-6642979-T-G		not specified	Uncertain significance (Jul 25, 2024)
17-6644523-G-A		not specified	Uncertain significance (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TXNDC17	protein_coding	protein_coding	ENST00000250101	4	3784

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0389	0.849	125726	0	19	125745	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.160	63	66.7	0.945	0.00000289	805
Missense in Polyphen		22	19.607	1.122		253
Synonymous	-0.592	29	25.2	1.15	0.00000114	218
Loss of Function	1.28	3	6.54	0.459	2.83e-7	81

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000427	0.000427
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000800	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000698	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Disulfide reductase. May participate in various redox reactions through the reversible oxidation of its active center dithiol to a disulfide and catalyze dithiol-disulfide exchange reactions. Modulates TNF-alpha signaling and NF-kappa-B activation. Has peroxidase activity and may contribute to the elimination of cellular hydrogen peroxide. {ECO:0000269|PubMed:14607843, ECO:0000269|PubMed:14607844}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.558
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• pHI: 0.0877
• hipred: Y
• hipred_score: 0.517
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.652

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Txndc17

Gene ontology

• Biological process: tumor necrosis factor-mediated signaling pathway;oxidation-reduction process;cellular oxidant detoxification
• Cellular component: cytosol;extracellular exosome
• Molecular function: peroxidase activity;protein binding;protein-disulfide reductase activity