TMX4

thioredoxin related transmembrane protein 4, the group of Protein disulfide isomerases|Thioredoxin domain containing

Basic information

Region (hg38): 20:7977346-8019805

Previous symbols: [ "TXNDC13" ]

Links

ENSG00000125827 ∙ NCBI:56255 ∙ OMIM:616766 ∙ HGNC:25237 ∙ Uniprot:Q9H1E5 ∙ 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 TMX4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMX4 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in TMX4

This is a list of pathogenic ClinVar variants found in the TMX4 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-7982279-T-A		not specified	Uncertain significance (Jul 15, 2021)
20-7982343-C-A		not specified	Uncertain significance (Jun 04, 2024)
20-7982439-C-T		not specified	Uncertain significance (Jul 19, 2023)
20-7982508-C-T		not specified	Uncertain significance (Sep 14, 2022)
20-7982542-T-A		not specified	Uncertain significance (Dec 27, 2022)
20-7982554-A-T		not specified	Uncertain significance (Sep 22, 2023)
20-7982570-G-A		not specified	Uncertain significance (Sep 20, 2023)
20-7982574-C-T		not specified	Uncertain significance (Jun 21, 2023)
20-7982592-T-C		not specified	Uncertain significance (Jan 02, 2024)
20-7987325-A-T		not specified	Uncertain significance (Dec 18, 2023)
20-7987343-C-T		not specified	Uncertain significance (Oct 06, 2023)
20-7987380-T-A		not specified	Uncertain significance (Feb 10, 2022)
20-7999844-A-T		not specified	Uncertain significance (Apr 20, 2024)
20-7999847-T-C		not specified	Uncertain significance (Nov 08, 2022)
20-8010251-C-T		not specified	Uncertain significance (Nov 17, 2023)
20-8019529-C-T		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMX4	protein_coding	protein_coding	ENST00000246024	8	42482

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0442	0.951	125725	0	19	125744	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	141	180	0.783	0.00000976	2275
Missense in Polyphen		21	44.669	0.47012		535
Synonymous	-0.184	65	63.1	1.03	0.00000335	650
Loss of Function	2.45	5	15.4	0.325	7.48e-7	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000432	0.000431
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000548	0.0000544
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.0000452	0.0000440
Middle Eastern	0.0000548	0.0000544
South Asian	0.000168	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.795
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.66

Haploinsufficiency Scores

• pHI: 0.162
• hipred: N
• hipred_score: 0.199
• ghis: 0.450

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.410

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmx4

Gene ontology

• Biological process: cell redox homeostasis;oxidation-reduction process
• Cellular component: cell;integral component of membrane