TMEM150A

transmembrane protein 150A

Basic information

Region (hg38): 2:85598546-85603196

Previous symbols: [ "TMEM150" ]

Links

ENSG00000168890 ∙ NCBI:129303 ∙ OMIM:616757 ∙ HGNC:24677 ∙ Uniprot:Q86TG1 ∙ 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 TMEM150A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM150A 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in TMEM150A

This is a list of pathogenic ClinVar variants found in the TMEM150A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-85599125-C-G		not specified	Uncertain significance (May 03, 2023)
2-85599135-C-T		not specified	Uncertain significance (Oct 13, 2023)
2-85599153-G-A		not specified	Uncertain significance (Mar 29, 2024)
2-85599165-G-A		not specified	Uncertain significance (Oct 30, 2023)
2-85599650-G-A		not specified	Uncertain significance (Nov 03, 2023)
2-85599949-G-A		not specified	Uncertain significance (Apr 26, 2024)
2-85600015-G-A		not specified	Uncertain significance (Aug 10, 2021)
2-85601087-G-A		not specified	Uncertain significance (Jul 19, 2023)
2-85601445-C-T		not specified	Uncertain significance (Jul 11, 2023)
2-85601462-T-C		not specified	Uncertain significance (Dec 28, 2023)
2-85601942-C-T		not specified	Uncertain significance (Jan 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM150A	protein_coding	protein_coding	ENST00000409668	7	4649

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0236	0.964	125719	0	10	125729	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.42	113	164	0.688	0.00000908	1757
Missense in Polyphen		38	66.908	0.56795		723
Synonymous	0.988	61	71.6	0.851	0.00000456	574
Loss of Function	2.17	5	13.7	0.366	6.67e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000619	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates localization of phosphatidylinositol 4-kinase (PI4K) to the plasma membrane, possibly by reducing the association of TTC7 (TTC7A or TTC7B) with the PI4K complex (PubMed:25608530). Acts as a regulator of phosphatidylinositol 4- phosphate (PtdIns(4)P) synthesis (PubMed:25608530). May also play a role in fasting-induced catabolism (By similarity). {ECO:0000250|UniProtKB:Q9QZE9, ECO:0000269|PubMed:25608530}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.289
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.423
• hipred: N
• hipred_score: 0.429
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.354

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem150a

Gene ontology

• Biological process: catabolic process;regulation of autophagy;phosphatidylinositol phosphorylation;protein localization to plasma membrane
• Cellular component: lysosome;integral component of plasma membrane
• Molecular function: protein binding