FITM1

fat storage inducing transmembrane protein 1

Basic information

Region (hg38): 14:24130659-24132849

Links

ENSG00000139914 ∙ NCBI:161247 ∙ OMIM:612028 ∙ HGNC:33714 ∙ Uniprot:A5D6W6 ∙ 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 FITM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FITM1 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					2	2
missense			41	1	1	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	1	3

Variants in FITM1

This is a list of pathogenic ClinVar variants found in the FITM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-24131577-C-T		not specified	Uncertain significance (Feb 07, 2025)
14-24131603-G-A		not specified	Uncertain significance (Mar 07, 2023)
14-24131610-G-A		not specified	Uncertain significance (Jun 29, 2023)
14-24131619-C-T		not specified	Uncertain significance (Aug 16, 2021)
14-24131642-G-A		not specified	Uncertain significance (Dec 06, 2024)
14-24131693-G-A		not specified	Uncertain significance (May 24, 2023)
14-24131709-G-C		not specified	Uncertain significance (Apr 08, 2022)
14-24131721-G-A		not specified	Uncertain significance (Sep 01, 2021)
14-24131723-C-T		not specified	Uncertain significance (Mar 02, 2023)
14-24131724-G-A		not specified	Uncertain significance (Mar 12, 2024)
14-24131733-A-G		not specified	Uncertain significance (Aug 20, 2024)
14-24131745-C-T		not specified	Uncertain significance (Jun 22, 2024)
14-24131747-G-A		not specified	Uncertain significance (Apr 26, 2024)
14-24131813-G-A		not specified	Uncertain significance (Nov 14, 2023)
14-24132227-G-A		not specified	Uncertain significance (Mar 28, 2024)
14-24132238-G-C		not specified	Uncertain significance (May 02, 2024)
14-24132256-G-A			Benign (Dec 31, 2019)
14-24132278-T-G		not specified	Uncertain significance (Feb 09, 2025)
14-24132282-T-G		not specified	Uncertain significance (Aug 12, 2021)
14-24132291-G-A		not specified	Uncertain significance (May 31, 2023)
14-24132296-G-A		not specified	Uncertain significance (Jan 30, 2024)
14-24132326-C-A		not specified	Uncertain significance (Apr 04, 2024)
14-24132344-G-A			Benign (Dec 11, 2018)
14-24132359-G-A		not specified	Uncertain significance (Feb 28, 2023)
14-24132362-C-G		not specified	Uncertain significance (Feb 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FITM1	protein_coding	protein_coding	ENST00000267426	2	1575

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000259	0.790	125665	0	83	125748	0.000330

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0702	184	187	0.986	0.0000121	1823
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000245	0.000243
Ashkenazi Jewish	0.000103	0.0000992
East Asian	0.000163	0.000163
Finnish	0.00165	0.00162
European (Non-Finnish)	0.000206	0.000202
Middle Eastern	0.000163	0.000163
South Asian	0.000425	0.000425
Other	0.000495	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an important role in lipid droplet accumulation. {ECO:0000269|PubMed:18160536}.
• Pathway: Metabolism of lipids;Metabolism;Lipid particle organization (Consensus)

Intolerance Scores

• loftool: 0.251
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.56

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.383
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.440

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fitm1

Gene ontology

• Biological process: phospholipid biosynthetic process;positive regulation of sequestering of triglyceride;lipid storage;lipid droplet organization
• Cellular component: endoplasmic reticulum membrane;integral component of endoplasmic reticulum membrane
• Molecular function: molecular_function