TMEM125

transmembrane protein 125

Basic information

Region (hg38): 1:43269983-43274002

Links

ENSG00000179178 ∙ NCBI:128218 ∙ ∙ HGNC:28275 ∙ Uniprot:Q96AQ2 ∙ 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 TMEM125 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM125 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			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	0

Variants in TMEM125

This is a list of pathogenic ClinVar variants found in the TMEM125 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-43272763-T-G		not specified	Uncertain significance (Jun 07, 2024)
1-43272769-C-G		not specified	Uncertain significance (Feb 23, 2025)
1-43272769-C-T		not specified	Uncertain significance (May 03, 2023)
1-43272819-C-G		not specified	Uncertain significance (Mar 16, 2022)
1-43272820-G-A		not specified	Uncertain significance (Feb 12, 2025)
1-43272823-C-T		not specified	Uncertain significance (Mar 23, 2023)
1-43272828-C-T		not specified	Uncertain significance (Mar 28, 2024)
1-43272837-G-A		not specified	Uncertain significance (Dec 28, 2022)
1-43272855-G-A		not specified	Uncertain significance (Jul 27, 2024)
1-43272865-G-C		not specified	Uncertain significance (May 30, 2024)
1-43272873-G-A		not specified	Uncertain significance (Jan 24, 2024)
1-43272876-G-A		not specified	Uncertain significance (May 13, 2024)
1-43272879-G-A		not specified	Uncertain significance (Dec 24, 2024)
1-43272901-G-A		not specified	Uncertain significance (Nov 03, 2022)
1-43272906-C-T		not specified	Uncertain significance (Sep 26, 2023)
1-43272988-C-G		not specified	Uncertain significance (Jan 04, 2024)
1-43272988-C-T		not specified	Uncertain significance (Jul 05, 2024)
1-43273006-A-G		not specified	Uncertain significance (Feb 15, 2023)
1-43273014-C-T		not specified	Uncertain significance (Aug 15, 2023)
1-43273041-C-T		not specified	Uncertain significance (Feb 18, 2025)
1-43273042-G-A		not specified	Uncertain significance (Mar 18, 2024)
1-43273111-C-T		not specified	Uncertain significance (Feb 21, 2024)
1-43273147-G-A		not specified	Uncertain significance (Dec 10, 2024)
1-43273159-C-T		not specified	Uncertain significance (Jul 20, 2021)
1-43273170-G-T		not specified	Uncertain significance (Dec 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM125	protein_coding	protein_coding	ENST00000432792	1	4009

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000100	0.0554	125155	0	29	125184	0.000116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.535	121	139	0.872	0.00000940	1336
Missense in Polyphen		56	64.707	0.86544		659
Synonymous	0.238	65	67.5	0.963	0.00000481	541
Loss of Function	-1.95	7	3.22	2.17	1.39e-7	37

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000184	0.000182
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000196	0.000194
Middle Eastern	0.00	0.00
South Asian	0.000102	0.0000982
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.473
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.48

Haploinsufficiency Scores

• pHI: 0.262
• hipred: N
• hipred_score: 0.325
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem125

Gene ontology

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