TMEM117

transmembrane protein 117

Basic information

Region (hg38): 12:43835967-44389762

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.

• not_specified (59 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. These statistics are base on transcript: NM_000032256.3. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			58	1		59
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	58	1	0

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