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.

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.

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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in TMEM109

This is a list of pathogenic ClinVar variants found in the TMEM109 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-60919818-C-G		not specified	Uncertain significance (Feb 16, 2023)
11-60919850-G-T		not specified	Uncertain significance (Dec 20, 2023)
11-60919878-G-A		not specified	Uncertain significance (Jul 25, 2023)
11-60920955-G-A		not specified	Uncertain significance (Apr 28, 2023)
11-60921785-G-A		not specified	Likely benign (Sep 29, 2022)
11-60921942-C-A		not specified	Uncertain significance (Nov 17, 2022)
11-60921944-G-A		not specified	Uncertain significance (Jan 09, 2024)
11-60922034-C-T		not specified	Uncertain significance (Jun 27, 2022)
11-60922050-G-A		not specified	Uncertain significance (Feb 17, 2022)
11-60922066-A-C		not specified	Uncertain significance (May 26, 2022)
11-60922113-G-A		not specified	Uncertain significance (Jan 06, 2023)
11-60922118-C-T		not specified	Uncertain significance (Feb 16, 2023)
11-60922119-G-A		not specified	Uncertain significance (Sep 23, 2023)
11-60922128-G-C		not specified	Uncertain significance (Mar 16, 2022)
11-60922145-C-T		not specified	Uncertain significance (Jul 05, 2023)
11-60922146-G-A		not specified	Uncertain significance (Jun 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM109	protein_coding	protein_coding	ENST00000227525	3	9570

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000751	0.766	125694	1	53	125748	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.489	126	142	0.885	0.00000895	1487
Missense in Polyphen		46	55.285	0.83205		536
Synonymous	-0.171	68	66.2	1.03	0.00000388	587
Loss of Function	1.10	8	12.1	0.659	9.25e-7	92

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000754	0.000754
Ashkenazi Jewish	0.000202	0.000198
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.000494	0.000489

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

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

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