TMEM123

transmembrane protein 123

Basic information

Region (hg38): 11:102396331-102470384

Links

ENSG00000152558 ∙ NCBI:114908 ∙ OMIM:606356 ∙ HGNC:30138 ∙ Uniprot:Q8N131 ∙ 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 TMEM123 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM123 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			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in TMEM123

This is a list of pathogenic ClinVar variants found in the TMEM123 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-102401552-G-A		not specified	Uncertain significance (Nov 14, 2023)
11-102401653-T-A		not specified	Uncertain significance (May 05, 2023)
11-102401681-T-G		not specified	Uncertain significance (Feb 22, 2024)
11-102401954-T-C		not specified	Uncertain significance (Mar 19, 2024)
11-102402038-G-C		not specified	Uncertain significance (Aug 13, 2021)
11-102402072-T-C		not specified	Uncertain significance (Mar 25, 2024)
11-102402086-G-A		not specified	Uncertain significance (Nov 10, 2022)
11-102402144-G-A		not specified	Likely benign (Dec 28, 2022)
11-102402200-A-G		not specified	Uncertain significance (Jul 09, 2021)
11-102448844-C-G		not specified	Uncertain significance (Dec 11, 2023)
11-102448850-T-C		not specified	Uncertain significance (Nov 18, 2022)
11-102452548-C-A		not specified	Uncertain significance (Jan 29, 2024)
11-102452613-C-A		not specified	Uncertain significance (Aug 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM123	protein_coding	protein_coding	ENST00000398136	5	74053

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.646	0.348	124534	0	3	124537	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.513	124	109	1.14	0.00000524	1299
Missense in Polyphen		3	4.7145	0.63633		47
Synonymous	-0.575	47	42.2	1.11	0.00000219	454
Loss of Function	2.22	1	7.62	0.131	3.18e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000271	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Implicated in oncotic cell death, characterized by cell swelling, organelle swelling, vacuolization and increased membrane permeability. {ECO:0000269|PubMed:11481458}.

Recessive Scores

• pRec: 0.0760

Intolerance Scores

• loftool: 0.428
• rvis_EVS: 0.59
• rvis_percentile_EVS: 82.51

Haploinsufficiency Scores

• pHI: 0.0918
• hipred: N
• hipred_score: 0.172
• ghis: 0.426

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.919

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem123
• Phenotype: normal phenotype

Gene ontology

• Biological process: oncosis
• Cellular component: external side of plasma membrane;integral component of membrane;cytoplasmic vesicle
• Molecular function: protein binding;signaling receptor activity