TMEM116

transmembrane protein 116

Basic information

Region (hg38): 12:111931282-112013866

Links

ENSG00000198270 ∙ NCBI:89894 ∙ ∙ HGNC:25084 ∙ Uniprot:Q8NCL8 ∙ 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 TMEM116 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM116 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	20	1	0

Variants in TMEM116

This is a list of pathogenic ClinVar variants found in the TMEM116 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-111931719-T-C		not specified	Uncertain significance (Aug 28, 2023)
12-111931739-C-T		not specified	Uncertain significance (Jun 06, 2023)
12-111933892-C-T		not specified	Uncertain significance (Oct 08, 2024)
12-111933976-A-G		not specified	Uncertain significance (Nov 08, 2022)
12-111933981-G-A		not specified	Uncertain significance (Nov 13, 2024)
12-111936703-G-A		not specified	Uncertain significance (Jul 09, 2024)
12-111936763-A-G		not specified	Uncertain significance (Feb 06, 2025)
12-111936795-G-C		not specified	Uncertain significance (May 14, 2024)
12-111937166-C-G		not specified	Uncertain significance (Oct 20, 2023)
12-111937225-C-A		not specified	Uncertain significance (Sep 01, 2021)
12-111938197-G-C		not specified	Uncertain significance (Apr 27, 2024)
12-111938206-A-G		not specified	Uncertain significance (Dec 12, 2024)
12-111943321-A-C		not specified	Uncertain significance (Jun 07, 2023)
12-111943335-T-C		not specified	Uncertain significance (Mar 19, 2024)
12-111943336-T-C		not specified	Uncertain significance (Aug 01, 2024)
12-111943339-C-T		not specified	Likely benign (Mar 19, 2024)
12-111943354-A-G		not specified	Uncertain significance (Jan 30, 2024)
12-111991780-T-C		not specified	Uncertain significance (Mar 01, 2024)
12-111991797-A-C		not specified	Uncertain significance (Sep 17, 2021)
12-111991834-A-T		not specified	Uncertain significance (Dec 21, 2022)
12-111991838-A-G		not specified	Uncertain significance (Feb 24, 2023)
12-111991860-A-C		not specified	Uncertain significance (Jun 07, 2024)
12-112003828-A-G		not specified	Uncertain significance (Mar 14, 2023)
12-112013472-G-A		not specified	Uncertain significance (Jun 10, 2022)
12-112013478-G-A		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM116	protein_coding	protein_coding	ENST00000552374	10	81885

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.12e-13	0.0287	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.853	141	173	0.817	0.00000851	2174
Missense in Polyphen		45	52.339	0.85978		719
Synonymous	1.39	50	64.1	0.780	0.00000314	655
Loss of Function	0.0324	19	19.2	0.992	9.59e-7	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.000195	0.000185
European (Non-Finnish)	0.0000719	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.939
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.142
• hipred: N
• hipred_score: 0.170
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.683

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem116

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component;integral component of membrane
• Molecular function: molecular_function