GeneBe

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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Siddiqi syndromeARAudiologic/OtolaryngologicAmong other findings, individuals may have prelingual hearing loss, and early recognition and treatment of hearing impairment may improve outcomes, including speech and language developmentAudiologic/Otolaryngologic; Craniofacial; Dermatologic; Musculoskeletal; Neurologic28067622; 30214770; 30288795

ClinVar

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

  • not_specified (26 variants)
  • not_provided (21 variants)
  • Siddiqi_syndrome (9 variants)
  • FITM2-related_disorder (8 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. These statistics are base on transcript: NM_001080472.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
6
clinvar
 6
missense
1
clinvar
30
clinvar
5
clinvar
 36
nonsense
4
clinvar
3
clinvar
 7
start loss
2
 2
frameshift
1
clinvar
1
clinvar
 2
splice donor/acceptor (+/-2bp)
0
Total 5 7 30 11 0

Highest pathogenic variant AF is 0.0000131378

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
FITM2protein_codingprotein_codingENST00000396825 28332
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.000002720.3231257230241257470.0000954
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.5981221420.8590.000007731683
Missense in Polyphen4050.8040.78735607
Synonymous-0.7177365.61.110.00000392536
Loss of Function0.29199.990.9015.20e-7101

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001190.000119
Ashkenazi Jewish0.00009920.0000992
East Asian0.0003260.000326
Finnish0.00004620.0000462
European (Non-Finnish)0.00008900.0000879
Middle Eastern0.0003260.000326
South Asian0.00003270.0000327
Other0.0003260.000326

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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