FITM1

protein-coding

fat storage inducing transmembrane protein 1

Gene summary

Predicted to enable diacylglycerol binding activity and triglyceride binding activity. Predicted to be involved in fat cell differentiation; lipid droplet formation; and phospholipid biosynthetic process. Predicted to be active in endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_203402.3

Inheritance

—

ClinVar variants

U:64B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr14:24,130,659-24,132,849

External References & Databases

Ensembl (ENSG00000139914)

Transcript & Mutation Effects

hg38 • Region Span ~2.2 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 FITM1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 65

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_203402.3. 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					2 clinvar	2
missense			64 clinvar	2 clinvar	1 clinvar	67
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	64	2	3	69

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_203402.3	RefSeq	NP_981947.1	2	MANE Select
ENST00000267426.6	Ensembl	ENSP00000267426.5	2	MANE Select
ENST00000559294.1	Ensembl	ENSP00000453741.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of lipids
Metabolism
Lipid particle organization

Biological Process

phospholipid biosynthetic process
positive regulation of sequestering of triglyceride
lipid storage
lipid droplet organization

Molecular Function

molecular_function

Cellular Component

endoplasmic reticulum membrane
integral component of endoplasmic reticulum membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000267426
Coding exons: 2
Length: 1575
Individuals with no LoFs: 125665
Homozygous LoFs: 0
Heterozygous LoFs: 83
Defined: 125748
p: 0.000330

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0702	184	187	0.986	0.0000121	1823
Missense (PolyPhen)		51	50.261	1.0147		517
Synonymous	0.404	81	85.8	0.944	0.00000539	680
Loss of Function	1.11	7	11.0	0.638	7.21e-7	90

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00016	0.00016	rare
Finnish	0.0017	0.0016	notable
European (Non-Finnish)	0.00021	0.00020	rare
South Asian	0.00042	0.00042	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays an important role in lipid droplet accumulation. {ECO:0000269|PubMed:18160536}.;

Intolerance Scores

LoFtool: 0.251
RVIS EVS: -0.34
RVIS percentile EVS: 30.56

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.440

Gene Damage Prediction

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