TMEM150A

protein-coding

transmembrane protein 150A

Gene summary

Involved in phosphatidylinositol phosphate biosynthetic process and protein localization to plasma membrane. Located in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

TMEM150

MANE transcript

NM_001031738.3

Inheritance

—

ClinVar variants

U:22B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.37

Max pathogenic AF

—

Genomic locus

chr2:85,598,547-85,603,196

External References & Databases

Ensembl (ENSG00000168890)

Transcript & Mutation Effects

hg38 • Region Span ~4.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TMEM150A variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 23

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001031738.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			22 clinvar	1 clinvar		23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	22	2	0	24

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 56 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001031738.3	RefSeq	NP_001026908.1	7	MANE Select
ENST00000334462.10	Ensembl	ENSP00000334708.5	7	MANE Select
NM_001369917.1	RefSeq	NP_001356846.1	7	Standard
NM_153342.4	RefSeq	NP_699173.2	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

catabolic process
regulation of autophagy
phosphatidylinositol phosphorylation
protein localization to plasma membrane

Molecular Function

protein binding

Cellular Component

lysosome
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409668
Coding exons: 7
Length: 4649
Individuals with no LoFs: 125719
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125729
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.42	113	164	0.688	0.00000908	1757
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.354

Gene Damage Prediction

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