FITM2

fat storage inducing transmembrane protein 2

Basic information

Region (hg38): 20:44302840-44311202

Previous symbols: [ "C20orf142" ]

Links

ENSG00000197296 ∙ NCBI:128486 ∙ OMIM:612029 ∙ HGNC:16135 ∙ Uniprot:Q8N6M3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Siddiqi syndrome (Strong), mode of inheritance: AR
• Siddiqi syndrome (Strong), mode of inheritance: AR
• Siddiqi syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Siddiqi syndrome	AR	Audiologic/Otolaryngologic	Among other findings, individuals may have prelingual hearing loss, and early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic; Craniofacial; Dermatologic; Musculoskeletal; Neurologic	28067622; 30214770; 30288795

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FITM2 gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FITM2 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			14	4		18
nonsense	1	1				2
start loss		2				2
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	2	2	5
Total	1	4	15	8	2

Variants in FITM2

This is a list of pathogenic ClinVar variants found in the FITM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-44306494-A-G			Benign (May 17, 2021)
20-44306640-A-C		not specified	Uncertain significance (Aug 17, 2021)
20-44306641-T-C		FITM2-related disorder	Likely benign (May 11, 2021)
20-44306664-G-A		FITM2-related disorder	Likely benign (Nov 26, 2019)
20-44306698-G-A		not specified	Likely benign (Oct 26, 2022)
20-44306716-G-A			Uncertain significance (Feb 15, 2024)
20-44306720-C-T		Siddiqi syndrome	Conflicting classifications of pathogenicity (Feb 02, 2020)
20-44306762-G-A		Siddiqi syndrome	Pathogenic (Oct 24, 2019)
20-44306837-CA-C		Siddiqi syndrome	Likely pathogenic (May 07, 2021)
20-44306856-G-A			Likely benign (Jul 01, 2022)
20-44306876-G-A		FITM2-related disorder	Likely pathogenic (Jun 04, 2024)
20-44306881-G-A		not specified	Uncertain significance (Mar 03, 2025)
20-44306915-C-T		not specified	Uncertain significance (Jan 06, 2025)
20-44306927-C-T		not specified	Uncertain significance (Aug 05, 2024)
20-44306949-G-C		not specified	Uncertain significance (Apr 24, 2025)
20-44306973-C-G		not specified	Uncertain significance (Feb 28, 2025)
20-44307013-T-C			Uncertain significance (Aug 07, 2024)
20-44307026-C-A		not specified	Uncertain significance (Aug 23, 2021)
20-44307032-C-T		not specified	Uncertain significance (Sep 29, 2022)
20-44307047-G-A		Siddiqi syndrome	Pathogenic (Apr 23, 2025)
20-44307060-C-T			Likely benign (Apr 01, 2022)
20-44307061-G-A			Uncertain significance (Mar 21, 2025)
20-44307066-G-T		not specified	Uncertain significance (Jul 30, 2024)
20-44307123-C-T		FITM2-related disorder	Benign (Aug 06, 2019)
20-44307162-G-A		FITM2-related disorder	Likely benign (Mar 24, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FITM2	protein_coding	protein_coding	ENST00000396825	2	8332

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000272	0.323	125723	0	24	125747	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.598	122	142	0.859	0.00000773	1683
Missense in Polyphen		40	50.804	0.78735		607
Synonymous	-0.717	73	65.6	1.11	0.00000392	536
Loss of Function	0.291	9	9.99	0.901	5.20e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000326	0.000326
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000890	0.0000879
Middle Eastern	0.000326	0.000326
South Asian	0.0000327	0.0000327
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an important role in lipid droplet accumulation. Plays a role in the regulation of cell morphology and cytoskeletal organization. {ECO:0000269|PubMed:18160536, ECO:0000269|PubMed:21834987}.
• Pathway: Metabolism of lipids;Metabolism;Lipid particle organization (Consensus)

Intolerance Scores

• loftool: 0.401
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.160
• hipred: N
• hipred_score: 0.335
• ghis: 0.490

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.714

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fitm2
• Phenotype: vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; pigmentation phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: fitm2
• Affected structure: pancreatic B cell
• Phenotype tag: abnormal
• Phenotype quality: decreased area

Gene ontology

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