TMEM59

transmembrane protein 59

Basic information

Region (hg38): 1:54026681-54053504

Previous symbols: [ "C1orf8" ]

Links

ENSG00000116209 ∙ NCBI:9528 ∙ OMIM:617084 ∙ HGNC:1239 ∙ Uniprot:Q9BXS4 ∙ 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 TMEM59 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM59 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in TMEM59

This is a list of pathogenic ClinVar variants found in the TMEM59 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-54032127-C-T		Estrogen resistance syndrome	risk factor (Aug 31, 2018)
1-54032190-G-C		not specified	Uncertain significance (Sep 16, 2021)
1-54032260-G-T		not specified	Uncertain significance (Apr 13, 2022)
1-54032290-C-T		not specified	Uncertain significance (Feb 22, 2023)
1-54036666-G-A		not specified	Uncertain significance (Dec 07, 2021)
1-54036672-C-T		not specified	Uncertain significance (Mar 04, 2024)
1-54041780-G-T		not specified	Uncertain significance (Jan 31, 2023)
1-54041783-G-A		not specified	Uncertain significance (Feb 22, 2024)
1-54043408-G-T		not specified	Uncertain significance (Dec 28, 2022)
1-54043454-C-T		not specified	Uncertain significance (Mar 16, 2024)
1-54047276-A-T		not specified	Uncertain significance (Feb 28, 2023)
1-54053004-G-A		not specified	Uncertain significance (May 31, 2023)
1-54053005-G-A		not specified	Uncertain significance (Jun 17, 2024)
1-54053185-C-T		not specified	Uncertain significance (Dec 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM59	protein_coding	protein_coding	ENST00000234831	8	21831

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.41e-12	0.0369	125592	0	155	125747	0.000617

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.438	151	167	0.905	0.00000782	2093
Missense in Polyphen		60	66.032	0.90865		819
Synonymous	0.225	65	67.4	0.965	0.00000353	620
Loss of Function	0.0446	18	18.2	0.989	8.36e-7	219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000161	0.000161
Ashkenazi Jewish	0.0103	0.0103
East Asian	0.000165	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000301	0.000299
Middle Eastern	0.000165	0.000163
South Asian	0.0000656	0.0000653
Other	0.00132	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a regulator of autophagy in response to S.aureus infection by promoting activation of LC3 (MAP1LC3A, MAP1LC3B or MAP1LC3C). Acts by interacting with ATG16L1, leading to promote a functional complex between LC3 and ATG16L1 and promoting LC3 lipidation and subsequent activation of autophagy (PubMed:27273576, PubMed:23376921). Modulates the O-glycosylation and complex N-glycosylation steps occurring during the Golgi maturation of several proteins such as APP, BACE1, SEAP or PRNP (PubMed:20427278). Inhibits APP transport to the cell surface and further shedding (PubMed:20427278). {ECO:0000269|PubMed:20427278, ECO:0000269|PubMed:23376921, ECO:0000269|PubMed:27273576}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in squamous cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.840
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.782
• hipred: N
• hipred_score: 0.282
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.808

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem59
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: proteolysis;autophagy;positive regulation of autophagy;negative regulation of protein processing;negative regulation of protein glycosylation in Golgi;negative regulation of protein localization to plasma membrane
• Cellular component: Golgi cis cisterna;Golgi trans cisterna;Golgi membrane;lysosome;lysosomal membrane;late endosome;Golgi medial cisterna;plasma membrane;integral component of membrane;late endosome membrane;extracellular exosome
• Molecular function: endopeptidase activity;protein binding