TMX3

thioredoxin related transmembrane protein 3, the group of Protein disulfide isomerases|Thioredoxin domain containing

Basic information

Region (hg38): 18:68673687-68715108

Previous symbols: [ "TXNDC10" ]

Links

ENSG00000166479 ∙ NCBI:54495 ∙ OMIM:616102 ∙ HGNC:24718 ∙ Uniprot:Q96JJ7 ∙ 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 TMX3 gene.

• not provided (39 variants)
• Inborn genetic diseases (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMX3 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			7	1	1	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					37	37
Total	0	0	7	1	38

Variants in TMX3

This is a list of pathogenic ClinVar variants found in the TMX3 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-68676761-G-C			Benign (May 19, 2021)
18-68676890-T-C			Benign (May 20, 2021)
18-68676956-C-A		not specified	Uncertain significance (Oct 27, 2022)
18-68677084-T-C		not specified	Uncertain significance (Dec 22, 2023)
18-68677108-T-C		not specified	Uncertain significance (Oct 06, 2021)
18-68679468-T-C		not specified	Likely benign (Feb 10, 2022)
18-68679813-G-T			Benign (Nov 12, 2018)
18-68680890-T-G			Benign (May 20, 2021)
18-68681091-C-T		TMX3-related disorder	Likely benign (Feb 08, 2022)
18-68681214-C-T			Benign (May 19, 2021)
18-68681226-T-C			Benign (May 19, 2021)
18-68681335-T-C			Benign (May 23, 2021)
18-68682940-T-C		not specified	Uncertain significance (May 08, 2023)
18-68682944-T-C		not specified	Uncertain significance (Jul 27, 2021)
18-68682952-T-C		not specified	Uncertain significance (Dec 20, 2023)
18-68683027-G-A			Benign (May 23, 2021)
18-68684314-T-A			Benign (May 23, 2021)
18-68684474-C-T		not specified	Uncertain significance (Dec 22, 2023)
18-68687488-G-A			Benign (May 19, 2021)
18-68687521-A-G			Benign (May 19, 2021)
18-68687715-T-A		not specified	Uncertain significance (Mar 06, 2023)
18-68687756-T-C		not specified	Uncertain significance (Sep 26, 2023)
18-68687906-GCATA-G			Benign (May 28, 2021)
18-68691166-G-T			Benign (Nov 12, 2018)
18-68691247-C-T			Benign (May 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMX3	protein_coding	protein_coding	ENST00000299608	16	41611

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00440	0.995	125703	0	23	125726	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.19	173	223	0.776	0.0000102	2966
Missense in Polyphen		58	87.113	0.6658		1205
Synonymous	-0.00634	75	74.9	1.00	0.00000348	796
Loss of Function	3.18	9	26.7	0.337	0.00000134	347

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000241	0.000240
Ashkenazi Jewish	0.00	0.00
East Asian	0.000118	0.000109
Finnish	0.0000930	0.0000924
European (Non-Finnish)	0.000101	0.0000967
Middle Eastern	0.000118	0.000109
South Asian	0.0000716	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable disulfide isomerase, which participates in the folding of proteins containing disulfide bonds. May act as a dithiol oxidase. {ECO:0000269|PubMed:15623505}.
• Pathway: Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.726
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.37

Haploinsufficiency Scores

• pHI: 0.256
• hipred: N
• hipred_score: 0.492
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.602

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmx3

Zebrafish Information Network

• Gene name: tmx3a
• Affected structure: eye
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: platelet degranulation;peptidyl-cysteine oxidation;cell redox homeostasis
• Cellular component: endoplasmic reticulum membrane;plasma membrane;cell surface;integral component of membrane;platelet alpha granule membrane
• Molecular function: protein disulfide isomerase activity;protein binding;thiol oxidase activity