TMEM120B

protein-coding

transmembrane protein 120B

Gene summary

Predicted to be involved in fat cell differentiation and protein heterooligomerization. Predicted to be located in membrane. Predicted to be active in nuclear inner membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001080825.2

Inheritance

—

ClinVar variants

U:62B:2

Top phenotype

Exstrophy-epispadias complex

gnomAD constraint

pLI —, LoF o/e 0.34

Max pathogenic AF

—

Genomic locus

chr12:121,712,752-121,783,001

External References & Databases

Ensembl (ENSG00000188735)

Transcript & Mutation Effects

hg38 • Region Span ~70.2 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 TMEM120B variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 55

not providedTotal: 1

Exstrophy-epispadias complexTotal: 1

TMEM120B-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001080825.2. 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 clinvar		2
missense			57 clinvar	1 clinvar		58
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	62	2	0	64

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001080825.2	RefSeq	NP_001074294.2	12	MANE Select
ENST00000449592.7	Ensembl	ENSP00000404991.2	12	MANE Select
ENST00000342607.10	Ensembl	ENSP00000345152.6	12	Standard
ENST00000540377.1	Ensembl	ENSP00000446159.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process
fat cell differentiation
protein heterooligomerization

Molecular Function

molecular_function
protein binding

Cellular Component

cellular_component
nuclear inner membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000449592
Coding exons: 12
Length: 70250
Individuals with no LoFs: 124781
Homozygous LoFs: 0
Heterozygous LoFs: 28
Defined: 124809
p: 0.000112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.966	156	194	0.805	0.0000112	2212
Missense (PolyPhen)		36	68.261	0.52738		797
Synonymous	-0.494	92	86.2	1.07	0.00000572	616
Loss of Function	2.98	8	23.6	0.339	0.00000108	261

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00039	0.00039	rare
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00021	0.00017	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Necessary for efficient adipogenesis. {ECO:0000250|UniProtKB:Q3TA38}.;

Recessive Scores

pRec: 0.0903

Intolerance Scores

LoFtool: 0.488
RVIS EVS: -0.11
RVIS percentile EVS: 45.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.131

Gene Damage Prediction

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