IFITM2

interferon induced transmembrane protein 2, the group of Interferon induced transmembrane proteins

Basic information

Region (hg38): 11:303655-309397

Links

ENSG00000185201 ∙ NCBI:10581 ∙ OMIM:605578 ∙ HGNC:5413 ∙ Uniprot:Q01629 ∙ 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 IFITM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFITM2 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in IFITM2

This is a list of pathogenic ClinVar variants found in the IFITM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-308214-T-A		not specified	Uncertain significance (Nov 06, 2023)
11-308214-T-C		not specified	Uncertain significance (Jan 26, 2022)
11-308242-C-A		not specified	Uncertain significance (Aug 28, 2024)
11-308270-G-C		not specified	Likely benign (Dec 15, 2023)
11-308289-G-A		not specified	Uncertain significance (Dec 20, 2023)
11-308295-C-T		not specified	Uncertain significance (Jun 06, 2023)
11-308311-C-T		not specified	Uncertain significance (Jan 21, 2025)
11-308315-G-A		not specified	Uncertain significance (Apr 14, 2022)
11-308334-C-T		not specified	Uncertain significance (Nov 14, 2024)
11-308340-G-A		not specified	Uncertain significance (Mar 12, 2024)
11-308364-G-A		not specified	Uncertain significance (Jan 18, 2025)
11-308364-G-C		not specified	Uncertain significance (Feb 02, 2025)
11-308391-A-G		not specified	Uncertain significance (Jul 09, 2021)
11-308433-G-A		not specified	Uncertain significance (Apr 24, 2023)
11-309041-T-C		not specified	Uncertain significance (Jun 23, 2023)
11-309053-A-C		not specified	Uncertain significance (Feb 19, 2025)
11-309114-G-A		not specified	Uncertain significance (Jun 03, 2024)
11-309133-A-C		not specified	Uncertain significance (Apr 18, 2023)
11-309140-T-A		not specified	Uncertain significance (Jun 17, 2024)
11-309140-T-C		not specified	Uncertain significance (May 08, 2024)
11-309148-G-A		not specified	Uncertain significance (Jan 14, 2025)
11-309148-G-C		not specified	Uncertain significance (Nov 18, 2022)
11-309161-G-A		not specified	Uncertain significance (Feb 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFITM2	protein_coding	protein_coding	ENST00000399817	2	7642

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00515	0.481	124757	0	27	124784	0.000108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.315	89	81.0	1.10	0.00000463	868
Missense in Polyphen		9	14.692	0.61258		202
Synonymous	-1.63	47	34.8	1.35	0.00000228	261
Loss of Function	-0.201	3	2.65	1.13	1.15e-7	25

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00109	0.00109
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000177
Middle Eastern	0.000111	0.000111
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: IFN-induced antiviral protein which inhibits the entry of viruses to the host cell cytoplasm, permitting endocytosis, but preventing subsequent viral fusion and release of viral contents into the cytosol. Active against multiple viruses, including influenza A virus, SARS coronavirus (SARS-CoV), Marburg virus (MARV), 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. Induces cell cycle arrest and mediates apoptosis by caspase activation and in p53-independent manner. {ECO:0000269|PubMed:19544527, ECO:0000269|PubMed:20064371, ECO:0000269|PubMed:20534863, ECO:0000269|PubMed:20943977, ECO:0000269|PubMed:21177806, ECO:0000269|PubMed:21253575, ECO:0000269|PubMed:22479637}.
• Pathway: Cytokine Signaling in Immune system;Immune System;Interferon alpha/beta signaling;Interferon Signaling (Consensus)

Intolerance Scores

• loftool: 0.437
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.23

Haploinsufficiency Scores

• pHI: 0.233
• hipred: N
• hipred_score: 0.112
• ghis: 0.436

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.614

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ifitm2

Gene ontology

• Biological process: immune response;response to virus;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: plasma membrane;integral component of membrane;protein-containing complex