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.

• not_specified (68 variants)
• not_provided (15 variants)

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. These statistics are base on transcript: NM_000032243.6. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				11		11
missense			56	12		68
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	56	23	0

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