IFITM3

interferon induced transmembrane protein 3, the group of Interferon induced transmembrane proteins

Basic information

Region (hg38): 11:319676-329475

Links

ENSG00000142089

∙ NCBI:10410 ∙ OMIM:605579 ∙ HGNC:5414 ∙ Uniprot:Q01628 ∙ 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 IFITM3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFITM3 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						0
missense			6 clinvar	1 clinvar		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	0

Variants in IFITM3

This is a list of pathogenic ClinVar variants found in the IFITM3 region.

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

Position	Phenotype	Significance	ClinVar
11-319873-C-T	not specified	Likely benign (Dec 13, 2023)	3108217
11-319893-A-C	not specified	Uncertain significance (Sep 06, 2022)	2310807
11-319960-T-A		Uncertain significance (-)	1050274
11-320672-T-C	not specified	Uncertain significance (Jan 03, 2024)	3108216
11-320681-C-T	not specified	Uncertain significance (Aug 22, 2023)	2603669
11-320689-G-T	not specified	Uncertain significance (Oct 10, 2023)	3108214
11-320692-G-A	not specified	Uncertain significance (Feb 24, 2022)	2277914
11-320713-G-A	not specified	Uncertain significance (Mar 19, 2024)	3285340
11-320749-A-G	not specified	Uncertain significance (Apr 07, 2023)	2534125
11-320772-A-G	Influenza, severe, susceptibility to	risk factor (Jan 06, 2014)	31527

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFITM3	protein_coding	protein_coding	ENST00000399808	2	7869

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0305	0.613	124777	0	4	124781	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.541	88	74.8	1.18	0.00000370	858
Missense in Polyphen		13	12.541	1.0366		181
Synonymous	-2.49	53	34.4	1.54	0.00000192	280
Loss of Function	0.208	2	2.34	0.853	1.01e-7	24

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000935	0.0000935
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000467	0.0000464
European (Non-Finnish)	0.00000885	0.00000883
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: IFN-induced antiviral protein which disrupts intracellular cholesterol homeostasis. Inhibits the entry of viruses to the host cell cytoplasm by preventing viral fusion with cholesterol depleted endosomes. May inactivate new enveloped viruses which buds out of the infected cell, by letting them go out with a cholesterol depleted membrane. Active against multiple viruses, including influenza A virus, SARS coronavirus (SARS-CoV), Marburg virus (MARV) and Ebola virus (EBOV), Dengue virus (DNV), West Nile virus (WNV), human immunodeficiency virus type 1 (HIV-1) and vesicular stomatitis virus (VSV). Can inhibit: influenza virus hemagglutinin protein-mediated viral entry, MARV and EBOV GP1,2- mediated viral entry, SARS-CoV S protein-mediated viral entry and VSV G protein-mediated viral entry. Plays a critical role in the structural stability and function of vacuolar ATPase (v-ATPase). Establishes physical contact with the v-ATPase of endosomes which is critical for proper clathrin localization and is also required for the function of the v-ATPase to lower the pH in phagocytic endosomes thus establishing an antiviral state. {ECO:0000269|PubMed:20064371, ECO:0000269|PubMed:20534863, ECO:0000269|PubMed:20943977, ECO:0000269|PubMed:21177806, ECO:0000269|PubMed:21253575, ECO:0000269|PubMed:22046135, ECO:0000269|PubMed:22479637, ECO:0000269|PubMed:23601107}.;
Pathway: Cytokine Signaling in Immune system;Immune System;Interferon alpha/beta signaling;Interferon Signaling (Consensus)

Intolerance Scores

loftool: 0.185
rvis_EVS: 0.13
rvis_percentile_EVS: 62.74

Haploinsufficiency Scores

pHI
hipred: N
hipred_score: 0.139
ghis: 0.405

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.0306

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ifitm3
Phenotype: immune system 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);

Gene ontology

Biological process: immune response;response to virus;negative regulation of viral transcription;response to interferon-gamma;response to interferon-alpha;response to interferon-beta;negative regulation of viral genome replication;negative regulation of viral entry into host cell;defense response to virus;type I interferon signaling pathway
Cellular component: lysosomal membrane;plasma membrane;integral component of membrane;late endosome membrane;protein-containing complex
Molecular function: protein binding