GeneBe

TMEM109

transmembrane protein 109

Basic information

Region (hg38): 11:60913907-60923443

Links

ENSG00000110108 ∙ NCBI:79073 ∙ OMIM:619168 ∙ HGNC:28771 ∙ Uniprot:Q9BVC6 ∙ 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 TMEM109 gene.

  • not_specified (30 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM109 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024092.3. 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.

EffectPLPVUSLBBSum
synonymous
0
missense
28
clinvar
2
clinvar
 30
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 28 2 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TMEM109protein_codingprotein_codingENST00000227525 39570
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.00007510.7661256941531257480.000215
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4891261420.8850.000008951487
Missense in Polyphen4655.2850.83205536
Synonymous-0.1716866.21.030.00000388587
Loss of Function1.10812.10.6599.25e-792

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0007540.000754
Ashkenazi Jewish0.0002020.000198
East Asian0.000.00
Finnish0.00009240.0000924
European (Non-Finnish)0.0001600.000158
Middle Eastern0.000.00
South Asian0.0001310.000131
Other0.0004940.000489

dbNSFP

Source: dbNSFP

Function
FUNCTION: May mediate cellular response to DNA damage by protecting against ultraviolet C-induced cell death (PubMed:23542032). Can form voltage-gated calcium and potassium channels in vitro (By similarity). {ECO:0000250|UniProtKB:O77751, ECO:0000269|PubMed:23542032}.;
Pathway
miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

pRec
0.0938

Intolerance Scores

loftool
0.243
rvis_EVS
-0.18
rvis_percentile_EVS
39.95

Haploinsufficiency Scores

pHI
0.122
hipred
N
hipred_score
0.172
ghis
0.588

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.200

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Tmem109
Phenotype
immune system phenotype; hematopoietic system phenotype; endocrine/exocrine gland phenotype; cellular phenotype;

Gene ontology

Biological process
ion transmembrane transport;regulation of ion transmembrane transport;intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator;negative regulation of cell death;cellular response to gamma radiation
Cellular component
nuclear outer membrane;integral component of membrane;sarcoplasmic reticulum membrane;extracellular exosome
Molecular function
molecular_function;voltage-gated ion channel activity;protein binding