TMEM74

transmembrane protein 74

Basic information

Region (hg38): 8:108606850-108787594

Links

ENSG00000164841 ∙ NCBI:157753 ∙ OMIM:613935 ∙ HGNC:26409 ∙ Uniprot:Q96NL1 ∙ 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 TMEM74 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM74 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			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in TMEM74

This is a list of pathogenic ClinVar variants found in the TMEM74 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-108784215-A-G		not specified	Uncertain significance (Mar 30, 2024)
8-108784230-G-A		not specified	Uncertain significance (Aug 10, 2021)
8-108784300-A-G		not specified	Uncertain significance (Nov 24, 2024)
8-108784384-G-T		not specified	Uncertain significance (Sep 06, 2022)
8-108784410-C-A		not specified	Uncertain significance (Oct 27, 2023)
8-108784452-C-T		not specified	Uncertain significance (Sep 15, 2021)
8-108784471-C-T		not specified	Uncertain significance (Sep 27, 2024)
8-108784501-G-A		not specified	Uncertain significance (Jan 11, 2023)
8-108784540-T-G		not specified	Uncertain significance (Sep 03, 2024)
8-108784572-T-C		not specified	Uncertain significance (Oct 26, 2022)
8-108784582-A-C		not specified	Uncertain significance (Jan 23, 2024)
8-108784615-C-T		not specified	Uncertain significance (Jun 27, 2022)
8-108784617-T-C		not specified	Uncertain significance (Jul 05, 2023)
8-108784680-C-T		not specified	Uncertain significance (Oct 08, 2024)
8-108784791-C-T		not specified	Uncertain significance (Aug 06, 2024)
8-108784797-T-C		not specified	Uncertain significance (Aug 21, 2023)
8-108784815-G-A		not specified	Uncertain significance (Jun 22, 2021)
8-108784861-C-A		not specified	Likely benign (Mar 17, 2023)
8-108784873-G-A		not specified	Uncertain significance (Sep 15, 2021)
8-108784935-A-G		not specified	Uncertain significance (Feb 03, 2022)
8-108784945-C-T		not specified	Uncertain significance (Oct 07, 2024)
8-108784986-G-C		not specified	Uncertain significance (Sep 08, 2024)
8-108785007-G-A		not specified	Uncertain significance (Nov 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM74	protein_coding	protein_coding	ENST00000297459	1	180766

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000344	0.618	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0535	176	178	0.989	0.0000103	1992
Missense in Polyphen		50	57.426	0.87068		630
Synonymous	0.413	66	70.4	0.937	0.00000392	628
Loss of Function	0.646	6	7.97	0.753	4.00e-7	102

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000618	0.0000615
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000714	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.000196	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an essential role in autophagy. TMEM74-induced autophagy may involve PI3K signal transduction. {ECO:0000269|PubMed:18294959, ECO:0000269|PubMed:19029833}.

Recessive Scores

• pRec: 0.0991

Intolerance Scores

• loftool: 0.271
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.251
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.168

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem74

Gene ontology

• Biological process: macroautophagy
• Cellular component: autophagosome membrane;lysosomal membrane;integral component of membrane;cytoplasmic vesicle
• Molecular function: protein binding