TXNDC12

thioredoxin domain containing 12, the group of Protein disulfide isomerases|Thioredoxin domain containing

Basic information

Region (hg38): 1:52020130-52055191

Links

ENSG00000117862 ∙ NCBI:51060 ∙ OMIM:609448 ∙ HGNC:24626 ∙ Uniprot:O95881 ∙ 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 TXNDC12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TXNDC12 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						0
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			20	1		21
Total	0	0	24	1	0

Variants in TXNDC12

This is a list of pathogenic ClinVar variants found in the TXNDC12 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-52024519-G-C		not specified	Uncertain significance (Dec 07, 2021)
1-52028595-C-G		not specified	Uncertain significance (Sep 29, 2023)
1-52032710-T-C		not specified	Uncertain significance (May 30, 2022)
1-52032711-G-C		not specified	Uncertain significance (Dec 02, 2022)
1-52032761-T-C		not specified	Uncertain significance (Jul 25, 2023)
1-52032918-G-C		not specified	Uncertain significance (Dec 14, 2023)
1-52032943-C-A		not specified	Uncertain significance (Feb 22, 2023)
1-52032948-G-A		not specified	Uncertain significance (Aug 19, 2023)
1-52033008-G-C		not specified	Uncertain significance (Oct 12, 2021)
1-52033049-G-A		not specified	Uncertain significance (Feb 06, 2023)
1-52033082-C-T		not specified	Uncertain significance (Sep 01, 2021)
1-52033161-C-T		not specified	Likely benign (May 10, 2024)
1-52033164-A-C		not specified	Uncertain significance (Nov 09, 2023)
1-52033196-G-C		not specified	Uncertain significance (Apr 18, 2023)
1-52033265-G-A		not specified	Likely benign (Apr 13, 2022)
1-52033308-G-A		not specified	Uncertain significance (Feb 27, 2024)
1-52033339-G-C		not specified	Uncertain significance (Mar 01, 2024)
1-52033436-C-G		not specified	Uncertain significance (Jan 09, 2024)
1-52033455-A-C		not specified	Uncertain significance (Feb 02, 2024)
1-52033476-G-A		not specified	Uncertain significance (Oct 20, 2023)
1-52033508-T-C		not specified	Uncertain significance (Feb 16, 2023)
1-52033659-C-T		not specified	Uncertain significance (Jan 04, 2022)
1-52033712-C-T		not specified	Uncertain significance (Aug 26, 2022)
1-52033725-C-A		not specified	Uncertain significance (Jan 17, 2023)
1-52055075-C-T		not specified	Uncertain significance (Aug 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TXNDC12	protein_coding	protein_coding	ENST00000371626	7	36041

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000374	0.620	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.517	78	92.0	0.848	0.00000426	1136
Missense in Polyphen		23	34.059	0.67529		408
Synonymous	0.664	30	35.0	0.857	0.00000187	311
Loss of Function	0.801	8	10.8	0.738	5.58e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000511	0.000507
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000714	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.000166	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possesses significant protein thiol-disulfide oxidase activity. {ECO:0000269|PubMed:12761212}.
• Pathway: Glutathione metabolism - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.147

Intolerance Scores

• loftool: 0.594
• rvis_EVS: 0.73
• rvis_percentile_EVS: 85.98

Haploinsufficiency Scores

• pHI: 0.320
• hipred: N
• hipred_score: 0.276
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Txndc12
• Phenotype: normal phenotype

Gene ontology

• Biological process: cell redox homeostasis;oxidation-reduction process;negative regulation of cell death;negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
• Cellular component: endoplasmic reticulum;endoplasmic reticulum lumen
• Molecular function: protein binding;peptide disulfide oxidoreductase activity;protein-disulfide reductase (glutathione) activity