TMX3

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

Basic information

Region (hg38): 18:68673688-68715108

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_specified (36 variants)
not_provided (14 variants)
TMX3-related_disorder (4 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. These statistics are base on transcript: NM_000019022.5. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			39 clinvar	3 clinvar	1 clinvar	43
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	44	3	1

Loading clinvar variants...

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
Phenotype

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