TMEM129

transmembrane protein 129, E3 ubiquitin ligase

Basic information

Region (hg38): 4:1715952-1721358

Links

ENSG00000168936 ∙ NCBI:92305 ∙ OMIM:615975 ∙ HGNC:25137 ∙ Uniprot:A0AVI4 ∙ 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 TMEM129 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM129 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			40	4		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	4	0

Variants in TMEM129

This is a list of pathogenic ClinVar variants found in the TMEM129 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-1717190-G-A		not specified	Uncertain significance (Jun 28, 2022)
4-1717215-G-A		not specified	Uncertain significance (Sep 09, 2024)
4-1717218-C-T		not specified	Uncertain significance (Jan 18, 2022)
4-1717242-G-A		not specified	Uncertain significance (Oct 02, 2023)
4-1717252-C-A		not specified	Uncertain significance (Aug 21, 2023)
4-1717254-A-G		not specified	Uncertain significance (Jul 30, 2023)
4-1717268-A-G		not specified	Uncertain significance (Sep 13, 2023)
4-1717394-C-G		not specified	Uncertain significance (Dec 15, 2023)
4-1717394-C-T		not specified	Uncertain significance (Aug 01, 2024)
4-1717418-G-A		not specified	Uncertain significance (Aug 13, 2021)
4-1717541-G-A		not specified	Uncertain significance (Oct 27, 2021)
4-1717559-G-A		not specified	Uncertain significance (Mar 17, 2023)
4-1717568-G-A		not specified	Uncertain significance (May 17, 2023)
4-1717664-G-C		not specified	Uncertain significance (Apr 25, 2023)
4-1717673-A-C		not specified	Uncertain significance (Jun 02, 2023)
4-1718171-C-G		not specified	Uncertain significance (May 04, 2022)
4-1718194-C-T		not specified	Uncertain significance (Jul 12, 2023)
4-1718224-G-A		not specified	Uncertain significance (Jul 30, 2024)
4-1718227-T-A		not specified	Uncertain significance (Apr 07, 2022)
4-1718248-C-T		not specified	Likely benign (Oct 13, 2023)
4-1718249-G-A		not specified	Uncertain significance (Jul 17, 2023)
4-1718261-C-T		not specified	Uncertain significance (Jan 29, 2024)
4-1718276-C-A		not specified	Uncertain significance (Apr 09, 2024)
4-1718291-C-T		not specified	Uncertain significance (Jan 18, 2023)
4-1718299-C-T		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM129	protein_coding	protein_coding	ENST00000382936	4	5407

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.31e-11	0.0197	125019	0	17	125036	0.0000680

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.925	170	208	0.819	0.0000132	2271
Missense in Polyphen		46	64.179	0.71674		792
Synonymous	0.455	82	87.4	0.938	0.00000539	764
Loss of Function	-0.598	15	12.7	1.18	6.34e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000107	0.000106
Middle Eastern	0.000112	0.000109
South Asian	0.0000331	0.0000328
Other	0.000184	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase involved in ER-associated protein degradation, preferentially associates with the E2 enzyme UBE2J2. Exploited by viral US11 proteins to mediate HLA class I proteins degradation. {ECO:0000269|PubMed:24807418}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Protein ubiquitination;E3 ubiquitin ligases ubiquitinate target proteins (Consensus)

Intolerance Scores

• loftool: 0.886
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.251
• ghis: 0.562

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.469

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem129

Gene ontology

• Biological process: protein polyubiquitination;response to unfolded protein;protein ubiquitination;ubiquitin-dependent ERAD pathway;retrograde protein transport, ER to cytosol
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: metal ion binding;ubiquitin protein ligase activity