TMEM117

transmembrane protein 117

Basic information

Region (hg38): 12:43835966-44389762

Links

ENSG00000139173 ∙ NCBI:84216 ∙ ∙ HGNC:25308 ∙ Uniprot:Q9H0C3 ∙ 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 TMEM117 gene.

• Inborn genetic diseases (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM117 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in TMEM117

This is a list of pathogenic ClinVar variants found in the TMEM117 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-43844697-A-G		not specified	Uncertain significance (Mar 02, 2023)
12-43844715-G-A		not specified	Uncertain significance (Jan 23, 2024)
12-43844784-A-G		not specified	Uncertain significance (Mar 11, 2024)
12-43844810-T-G		not specified	Uncertain significance (Aug 12, 2021)
12-43944307-A-G		not specified	Uncertain significance (Apr 17, 2023)
12-43944315-C-T		not specified	Uncertain significance (Aug 17, 2021)
12-43944330-A-T		not specified	Uncertain significance (Mar 01, 2023)
12-44211310-G-C		not specified	Uncertain significance (Jan 23, 2023)
12-44299654-A-T		not specified	Uncertain significance (Nov 21, 2022)
12-44299657-G-A		not specified	Uncertain significance (Jun 21, 2022)
12-44299683-T-G		not specified	Uncertain significance (May 23, 2023)
12-44299723-T-A		not specified	Uncertain significance (Feb 16, 2023)
12-44376649-C-T		not specified	Uncertain significance (Aug 12, 2021)
12-44376700-G-C		not specified	Uncertain significance (Dec 20, 2023)
12-44376713-T-C		not specified	Uncertain significance (Jul 20, 2021)
12-44388185-A-G		not specified	Uncertain significance (Sep 29, 2023)
12-44388266-T-G		not specified	Uncertain significance (Jan 04, 2022)
12-44388271-C-T		not specified	Uncertain significance (Jun 21, 2021)
12-44388394-C-T		not specified	Uncertain significance (Feb 23, 2023)
12-44388425-G-T		not specified	Uncertain significance (Jan 26, 2022)
12-44388472-A-G		not specified	Uncertain significance (Feb 06, 2023)
12-44388491-C-T		not specified	Likely benign (Feb 27, 2024)
12-44388496-G-A		not specified	Uncertain significance (Dec 21, 2022)
12-44388580-T-G		not specified	Uncertain significance (Sep 01, 2021)
12-44388607-G-A		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM117	protein_coding	protein_coding	ENST00000266534	7	553776

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000296	0.985	125717	0	30	125747	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.56	208	282	0.738	0.0000148	3447
Missense in Polyphen		64	118.74	0.53898		1494
Synonymous	-0.0573	96	95.3	1.01	0.00000509	927
Loss of Function	2.21	13	24.9	0.523	0.00000146	265

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000164	0.000163
South Asian	0.000328	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in endoplasmic reticulum (ER) stress-induced cell death pathway. {ECO:0000269|PubMed:28285135}.

Intolerance Scores

• loftool: 0.733
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.181
• hipred: Y
• hipred_score: 0.522
• ghis: 0.566

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem117

Gene ontology

• Biological process: intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
• Cellular component: endoplasmic reticulum;plasma membrane;integral component of membrane
• Molecular function: molecular_function