TMX1

thioredoxin related transmembrane protein 1, the group of Protein disulfide isomerases|Thioredoxin domain containing

Basic information

Region (hg38): 14:51240162-51257655

Previous symbols: [ "TXNDC", "TXNDC1" ]

Links

ENSG00000139921 ∙ NCBI:81542 ∙ OMIM:610527 ∙ HGNC:15487 ∙ Uniprot:Q9H3N1 ∙ 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 TMX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMX1 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in TMX1

This is a list of pathogenic ClinVar variants found in the TMX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-51240315-C-G		not specified	Uncertain significance (Jan 18, 2025)
14-51240350-G-A		not specified	Uncertain significance (Oct 20, 2024)
14-51240426-G-A		not specified	Uncertain significance (Dec 06, 2022)
14-51243875-G-A		not specified	Uncertain significance (Feb 26, 2025)
14-51247149-A-G		not specified	Uncertain significance (Oct 20, 2024)
14-51247168-G-C		not specified	Uncertain significance (Apr 19, 2024)
14-51247198-T-C		not specified	Uncertain significance (Mar 01, 2024)
14-51247207-C-G		not specified	Uncertain significance (Aug 02, 2021)
14-51249352-A-G		not specified	Uncertain significance (Jan 29, 2025)
14-51249356-A-C		not specified	Likely benign (Jul 31, 2023)
14-51249520-A-G		not specified	Uncertain significance (May 18, 2023)
14-51249559-T-C		not specified	Uncertain significance (Nov 17, 2022)
14-51249736-G-A		not specified	Uncertain significance (Dec 04, 2024)
14-51249756-T-C		not specified	Uncertain significance (Dec 11, 2024)
14-51249757-A-G		not specified	Uncertain significance (Nov 26, 2024)
14-51254377-A-T		not specified	Uncertain significance (Mar 01, 2023)
14-51254425-A-C		not specified	Uncertain significance (Jan 08, 2025)
14-51254430-G-A		not specified	Uncertain significance (Dec 13, 2021)
14-51254472-A-G		not specified	Uncertain significance (Apr 26, 2023)
14-51254478-C-G		not specified	Uncertain significance (Dec 20, 2024)
14-51254515-C-A		not specified	Uncertain significance (May 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMX1	protein_coding	protein_coding	ENST00000457354	8	15880

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000746	0.983	124779	0	16	124795	0.0000641

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.230	159	151	1.05	0.00000760	1806
Missense in Polyphen		28	37.547	0.74574		434
Synonymous	-1.64	70	54.6	1.28	0.00000281	517
Loss of Function	2.12	8	17.6	0.454	8.45e-7	202

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000161	0.000161
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.0000558	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000621	0.0000530
Middle Eastern	0.0000558	0.0000556
South Asian	0.0000691	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May participate in various redox reactions through the reversible oxidation of its active center dithiol to a disulfide and catalyze dithiol-disulfide exchange reactions.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.535
• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.44

Haploinsufficiency Scores

• pHI: 0.828
• hipred: N
• hipred_score: 0.281
• ghis: 0.698

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.714

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmx1
• Phenotype: normal phenotype

Gene ontology

• Biological process: response to endoplasmic reticulum stress;cell redox homeostasis;oxidation-reduction process
• Cellular component: endoplasmic reticulum membrane;integral component of membrane
• Molecular function: disulfide oxidoreductase activity