TXNDC2

thioredoxin domain containing 2, the group of Thioredoxin domain containing

Basic information

Region (hg38): 18:9885766-9889275

Links

ENSG00000168454 ∙ NCBI:84203 ∙ OMIM:617790 ∙ HGNC:16470 ∙ Uniprot:Q86VQ3 ∙ 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 TXNDC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TXNDC2 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				11	1	12
missense			28	7		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	28	18	1

Variants in TXNDC2

This is a list of pathogenic ClinVar variants found in the TXNDC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-9886189-G-C		not specified	Uncertain significance (Feb 28, 2023)
18-9886245-T-G		not specified	Uncertain significance (Jul 07, 2022)
18-9886575-G-GT			Benign (Jan 12, 2024)
18-9886622-C-T		not specified	Uncertain significance (Mar 21, 2022)
18-9886634-T-G		not specified	Uncertain significance (Oct 06, 2022)
18-9886673-T-C		not specified	Uncertain significance (Sep 16, 2021)
18-9886705-C-T		not specified	Uncertain significance (Jan 26, 2022)
18-9886763-A-G		not specified	Uncertain significance (Oct 05, 2023)
18-9886781-A-T		not specified	Uncertain significance (Jan 23, 2023)
18-9886838-C-A		not specified	Uncertain significance (Sep 27, 2021)
18-9886859-T-A		not specified	Likely benign (Dec 31, 2023)
18-9886893-A-G			Benign (Oct 15, 2018)
18-9886917-G-C		not specified	Uncertain significance (May 18, 2022)
18-9886925-T-C		not specified	Likely benign (Apr 06, 2023)
18-9886978-G-A		not specified	Uncertain significance (Jul 14, 2021)
18-9886984-G-A		not specified	Likely benign (Jun 24, 2022)
18-9887024-C-G		not specified	Uncertain significance (Sep 16, 2021)
18-9887125-C-T		not specified	Uncertain significance (Jan 18, 2023)
18-9887149-A-G		not specified	Uncertain significance (Sep 26, 2023)
18-9887179-C-A			Likely benign (Jul 01, 2022)
18-9887187-G-C		not specified	Uncertain significance (Aug 08, 2023)
18-9887225-C-A		not specified	Uncertain significance (Jan 05, 2022)
18-9887242-C-T		not specified	Uncertain significance (Jun 24, 2022)
18-9887258-A-G		not specified	Uncertain significance (May 08, 2023)
18-9887285-T-C		not specified	Likely benign (Apr 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TXNDC2	protein_coding	protein_coding	ENST00000306084	2	3510

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.634	0.339	125690	0	4	125694	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0622	282	279	1.01	0.0000134	3585
Missense in Polyphen		63	66.958	0.94088		960
Synonymous	-0.434	119	113	1.05	0.00000584	1053
Loss of Function	1.66	0	3.22	0.00	1.34e-7	49

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00000880	0.00000880
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably plays a regulatory role in sperm development. May participate in regulation of fibrous sheath (FS) assembly by supporting the formation of disulfide bonds during sperm tail morphogenesis. May also be required to rectify incorrect disulfide pairing and generate suitable pairs between the FS constituents. Can reduce disulfide bonds in vitro in the presence of NADP and thioredoxin reductase.

Intolerance Scores

• loftool: 0.826
• rvis_EVS: 1.31
• rvis_percentile_EVS: 94.05

Haploinsufficiency Scores

• pHI: 0.0320
• hipred: N
• hipred_score: 0.112
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0629

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Txndc2
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype; reproductive system phenotype; immune system phenotype

Gene ontology

• Biological process: glycerol ether metabolic process;multicellular organism development;spermatogenesis;cell differentiation;cell redox homeostasis;oxidation-reduction process;cellular oxidant detoxification
• Cellular component: cytoplasm
• Molecular function: thioredoxin-disulfide reductase activity;protein disulfide oxidoreductase activity