Alternative titles; symbols
HGNC Approved Gene Symbol: IFIH1
Cytogenetic location: 2q24.2 Genomic coordinates (GRCh38) : 2:162,267,074-162,318,684 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 2q24.2 | Aicardi-Goutieres syndrome 7 | 615846 | Autosomal dominant | 3 |
| Immunodeficiency 95 | 619773 | Autosomal recessive | 3 | |
| Singleton-Merten syndrome 1 | 182250 | Autosomal dominant | 3 |
The IFIH1 gene encodes a cytoplasmic receptor that senses dsRNA viral products to activate type I interferon signaling through the MAVS (609676) adaptor molecule. This can inhibit virus replication and modulate cellular immune responses. IFIH1 may also help recognize and limit the replication of ssRNA viruses (summary by Rice et al., 2014 and Lamborn et al., 2017).
By screening a melanoma differentiation-subtracted library and a placenta cDNA library, followed by 5-prime RACE, Kang et al. (2002) isolated a full-length cDNA encoding IFIH1, which they called MDA5. The deduced 1,025-amino acid protein contains an N-terminal CARD motif and a C-terminal DExH/D RNA helicase domain closely related to that of RIGI (DDX58; 609631). SDS-PAGE and Western blot analysis showed expression of a 120-kD protein. Northern blot analysis revealed that treatment of melanoma cells or skin fibroblasts with beta-interferon (IFNB; 147640) enhanced MDA5 expression 3-fold more than did treatment with IFNA (147660), IFNG (147570), or tumor necrosis factor (TNF; 191160). Other differentiation reagents had little or no effect. Expression of MDA5 was further upregulated in the presence of mezerein (MEZ). In tissues, expression of MDA5 was low overall, with highest levels in placenta, pancreas, and spleen, and undetectable levels in brain, lung, and testis. Confocal microscopy demonstrated cytoplasmic expression corresponding with the absence of a nuclear localization signal in the primary amino acid sequence. Ectopic expression of MDA5 in melanoma cells resulted in reduced colony formation, suggesting an interaction of the CARD and apoptotic signal molecules. Functional analysis indicated that MDA5 is an RNA-dependent ATPase.
By fluorescence immunohistochemistry, Rutsch et al. (2015) detected MDA5 in human cardiac myocytes, epidermis, and cartilage chondrocytes. Analysis of mouse mandibles demonstrated localization of Mda5 in ameloblasts, odontoblasts, and the periodontal ligament, as well as in active osteoblasts at the surface of alveolar bone.
Kang et al. (2004) determined that the IFIH1 gene contains 16 exons.
By radiation hybrid and genomic sequence analyses, Kang et al. (2004) mapped the IFIH1 gene to chromosome 2q24.
Using Northern blot analysis, Kang et al. (2004) showed that human MDA5 was a general type I IFN-inducible gene with rapid temporal induction kinetics and limited basal expression in normal tissue. The JAK (see 147795)/STAT (see 600555) signaling pathway was directly involved in IFN-induced MDA5 expression. Overexpression of MDA5 induced apoptotic cell death in HO-1 melanoma cells. Mutation analysis showed that the CARD and ATPase domains of MDA5 were involved in cellular growth and survival.
Colli et al. (2010) evaluated whether modulation of MDA5 and PTPN2 (176887), 2 candidate genes for type 1 diabetes, affects beta-cell responses to double-stranded RNA (dsRNA), a by-product of viral replication. INS-1E cells and primary fluorescence-activated cell sorting-purified rat beta-cells were transfected with small interference RNAs (siRNAs) targeting MDA5 or PTPN2 and subsequently exposed to intracellular synthetic dsRNA polyinosinic-polycytidylic acid (PIC). PIC increased MDA5 and PTPN2 mRNA expression, which was inhibited by the specific siRNAs. PIC triggered apoptosis in INS-1E and primary beta-cells and this was augmented by PTPN2 knockdown, although inhibition of MDA5 did not modify PIC-induced apoptosis. In contrast, MDA5 silencing decreased PIC-induced cytokine and chemokine expression, although inhibition of PTPN2 induced minor or no changes in these inflammatory mediators. Colli et al. (2010) concluded that changes in MDA5 and PTPN2 expression modify beta-cell responses to dsRNA. MDA5 regulates inflammatory signals, whereas PTPN2 may function as a defense mechanism against proapoptotic signals generated by dsRNA.
To determine the specific of RNA editing by ADAR1 (146920), Liddicoat et al. (2015) generated mice with an editing-deficient knockin mutation, Adar1(E861A). Adar1(E861A/E861A) embryos died at approximately embryonic day 13.5, with activated interferon (see 147660) and dsRNA-sensing pathways. Genomewide analysis of the in vivo substrates of ADAR1 identified clustered hyperediting within long dsRNA stem loops within 3-prime untranslated regions of endogenous transcripts. Concurrent deletion of the cytosolic sensor of dsRNA MDA5 rescued embryonic death and other phenotypes of Adar1(E861A/E861A). Liddicoat et al. (2015) concluded that adenosine-to-inosine editing of endogenous dsRNA is the essential function of ADAR1, preventing the activation of the cytosolic dsRNA response by endogenous transcripts.
Crystal Structure
Motz et al. (2013) determined the crystal structure of the MDA5 ATP-hydrolysis domain in complex with the viral inhibitor V protein. The V protein unfolded the ATP-hydrolysis domain of MDA5 via a beta-hairpin motif and recognized a structural motif of MDA5 that is normally buried in the conserved helicase fold. This leads to disruption of the MDA5 ATP-hydrolysis site and prevention of RNA-bound MDA5 filament formation. Motz et al. (2013) explained why V proteins inactivate MDA5, but not RIGI (609631), and mutating only 2 amino acids in RIGI induces robust V protein binding.
Singleton-Merten Syndrome 1
In affected individuals from 3 unrelated families with early and extreme aortic and valvular calcification, dental anomalies, osteopenia, and acroosteolysis (SGMRT1; 182250), Rutsch et al. (2015) performed whole-exome sequencing and identified heterozygosity for a missense mutation in the IFIH1 gene (R822Q; 606951.0009) that segregated with disease in each family. Functional analysis demonstrated that R822Q is a gain-of-function substitution that triggers production of type 1 interferon, resulting in a heightened inflammatory state.
In a French father with Singleton-Merten syndrome and his 2 affected sons with a variable neurologic presentation, Bursztejn et al. (2015) identified heterozygosity for a missense mutation in the IFIH1 gene (A489T; 606951.0015).
In 5 affected individuals from 2 unrelated families with Singleton-Merten syndrome, de Carvalho et al. (2017) sequenced the IFIH1 gene and identified heterozygosity for 2 different missense mutations at the same residue: a T331I substitution (606951.0016) in family 1938, and a T331R substitution (606951.0017) in family 1972. Both variants resulted in markedly increased levels of IFN signaling.
In a 10-year-old boy with Singleton-Merten syndrome, Riou et al. (2022) identified heterozygosity for the recurrent R822Q mutation in the IFIH1 gene.
Aicardi-Goutieres Syndrome 7
In 8 probands with Aicardi-Goutieres syndrome 7 (AGS7; 615846), Rice et al. (2014) identified 6 different heterozygous mutations in the IFIH1 gene (606951.0001-606951.0006). The first 3 mutations were found by whole-exome sequencing. The mutations in 5 probands occurred de novo, whereas in 2 they were paternally transmitted; for 1 proband parental DNA was unavailable. In 1 family, 2 mutation carriers remained clinically unaffected as adults. In vitro functional expression assays in HEK293T cells showed that the mutations caused marked induction of interferon signaling in response to short 162-bp double-stranded RNA (dsRNA), whereas control cells did not. The mutations also conferred 4- to 10-fold higher levels of basal signaling activity even in the absence of exogenous ligand. The mutated residues were located on the surface of the RNA-binding and ATP-binding sites in conserved helicase domains, but ATP hydrolysis activity of the mutants was comparable to wildtype. Structural modeling and biochemical studies indicated that the mutations enhance the stability of the activated IFIH1 filament by increasing affinity for dsRNA. These findings were consistent with a gain of function, resulting in increased interferon signaling. The findings also suggested the presence of an undefined endogenous dsRNA capable of stimulating mutant receptors.
In 3 unrelated Japanese patients with AGS7, Oda et al. (2014) identified 3 different de novo heterozygous missense mutations in the IFIH1 gene (606951.0002, 606951.0007, and 606951.0008). The mutations were found by trio-based whole-exome sequencing. Peripheral blood cells from the patients showed a type 1 interferon signature, and expression of each of the mutations in a human hepatoma cell line resulted in increased activation of the IFNB1 (147640) promoter compared to wildtype, consistent with increased type I interferon production. In vitro studies showed that the mutant IFIH1 proteins lacked ligand-specific responsiveness.
In a 6-year-old boy with bilateral spasticity, developmental delay, and basal ganglia calcification, Buers et al. (2017) identified heterozygosity for the recurrent R822Q mutation in the IFIH1 gene (606951.0009), previously reported in patients with Singleton-Merten syndrome. The authors concluded that both diseases are part of an 'interferonopathy grouping,' and that the R822Q mutation can cause a spectrum of disease, including neurologic involvement.
In a female infant with AGS7, Amari et al. (2020) identified a de novo heterozygous mutation in the IFIH1 gene (E813D; 606951.0010). The mutation was identified by whole-exome sequencing and confirmed by Sanger sequencing.
Immunodeficiency 95
In a 5-year-old girl from Burma with immunodeficiency-95 (IMD95; 619773), Lamborn et al. (2017), identified a homozygous missense mutation in the IFIH1 gene (K365E; 606951.0011). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was present in the heterozygous state in the unaffected parents and brother. In vitro functional expression studies of patient cells and cells transfected with the mutation showed that the K365E mutant had minimal IFNB1 (147640) and NFKB (see 164011) promoter activity after stimulation with poly(I:C) compared to wildtype. Cotransfection of the mutant with wildtype showed no dominant-negative effects; the findings were consistent with a loss of function. Cells with the mutation and cells with silencing of the IFIH1 gene demonstrated increased replication of human rhinovirus (HRV) and impaired interferon signaling compared to controls. However, these cells did not show increased viral replication of influenza or RSV. Transduction with wildtype, but not mutant, IFIH1 improved control of HRV replication. The findings were consistent with impaired viral recognition and antiviral responses specific for HRV.
In a 6-year-old girl, born of consanguineous Egyptian parents, with IMD95, Zaki et al. (2017) identified a homozygous nonsense mutation in the IFIH1 gene (K889X; 606951.0012). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was present in the heterozygous state in the unaffected parents and sib. Western blot analysis of patient fibroblasts showed significantly decreased IFIH1 protein levels compared to controls, suggesting that the mutant transcript undergoes nonsense-mediated mRNA decay and results in a loss of function. In addition to IMD95, manifest as recurrent severe viral respiratory infections and persistent EBV infection, the patient also had a severe neurodevelopmental disorder with seizures and microcephaly associated with a homozygous missense mutation in the PHGDH gene (V425M; 606879.0002).
In 3-year-old girl (patient 1), born of consanguineous Moroccan parents, with IMD95, Cananzi et al. (2021) identified a homozygous frameshift mutation in the IFIH1 gene (606951.0013). It was predicted to result in nonsense-mediated mRNA decay or produce a truncated protein lacking important functional domains. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was present in the heterozygous state in each unaffected parent. In vitro functional studies using a luciferase reporter assay showed that mutant IFIH1 failed to activate the IFNB1 (147640) promoter following stimulation, consistent with a loss-of-function effect. In addition to recurrent and severe infections, including with CMV, the patient also had very early-onset inflammatory bowel disease (VEOIBD) in the first weeks of life.
In a girl (PRI_022) with IMD95, Asgari et al. (2017) identified a homozygous splice site mutation in the IFIH1 gene (606951.0014). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was present at a low frequency in the gnomAD database (0.64%), including 7 homozygotes. Western blot analysis of patient cells showed that the mutant protein was expressed upon in vitro RSV infection. In vitro functional expression studies in HEK293T cells transfected with the mutation showed that the mutant protein was unstable, failed to lead to IFNB1 (147640) production, and had no detectable ATPase activity compared to wildtype, consistent with a loss-of-function effect. There was also evidence for a dominant-negative effect on the wildtype protein. Additional in vitro studies showed that RSV and HRV replication levels were increased in cells transduced with the mutation, indicating a central role for IFIH1 in innate immune recognition of RSV and HRV and in controlling these infections. Three additional children with severe early-onset viral HRC or RSV respiratory infections were heterozygous for the splice site variant and 4 further children were heterozygous for other loss-of-function variants in the IFIH1 gene, suggesting that heterozygosity may confer susceptibility to the disease. However, carrier parents were unaffected. The patients were part of a cohort of 120 children with severe manifestations of common viral respiratory infections who underwent exome sequencing.
Associations Pending Confirmation
For discussion of a possible association between variation in the IFIH1 gene and type 1 diabetes, see IDDM19 (610155).
For discussion of a possible association between variation in the IFIH1 gene and Graves disease, see 275000.
For discussion of a possible association between variation in the IFIH1 gene and selective immunoglobulin A deficiency, see IGAD1 (137100).
Robinson et al. (2011) studied the impact of the IFIH1 946A-T SNP (rs1990760) in 563 American patients of various ethnicities with systemic lupus erythematosus (SLE; 152700). They found that the T allele of rs1990760 was associated with anti-double-stranded DNA (dsDNA) antibodies in all groups, and that, among those with anti-dsDNA antibodies, the T allele was associated with lower serum IFNA. The T allele was also associated with increased IFN-induced gene expression in peripheral blood mononuclear cells in response to serum IFNA in anti-dsDNA antibody-positive patients, independent of the STAT4 (600558) genotype. Robinson et al. (2011) suggested that the T allele of rs1990760 may have a role in SLE pathogenesis.
Gorman et al. (2017) noted that the 946A-T variant has been associated with multiple autoimmune diseases. The authors found that peripheral blood mononuclear cells (PBMCs) from healthy donors with the 946A-T variant had increased interferon production in response to the ligand poly(I:C). Homozygotes also had significantly increased expression of interferon-stimulated genes. The authors showed that mice with a knockin 946A-T variant had increased basal interferon expression and better survived a viral challenge but had autoimmunity-related phenotypes including increased risk of diabetes and lupus. The authors suggested that survival of the variant in human populations is likely a case of balanced selection between response to viral infection versus risks from autoimmune diseases.
In 7 unrelated patients (patients 2-8) of various ethnic origins with very early-onset inflammatory bowel disease (VEOIBD), Cananzi et al. (2021) identified heterozygous loss-of-function variants in the IFIH1 gene (see, e.g., 606951.0014). The variants, which were found by whole-exome sequencing and confirmed by Sanger sequencing, were present at low frequencies in the gnomAD database. There were 2 nonsense, 1 frameshift, and 1 splice site variant. The variants were inherited from an unaffected parent in 6 cases, consistent with incomplete penetrance and suggesting that the variants may confer susceptibility to the disease. The patients were diagnosed with Crohn disease (4), ulcerative colitis (2), and IBD with diffuse colonic nodular lymphatic hyperplasia (1). The median age at onset was 24 months (range, 3 months to 6 years), and the patients presented with bloody, mucous, protein-losing inflammatory diarrhea and poor overall growth. Colonoscopy showed multiple linear deep ulcers separated by skip areas of normal mucosa, and histology showed ileal and colonic inflammation with villous atrophy, crypt distortion, mucinous hyperplasia of colonocytes, and Paneth cell metaplasia. Laboratory studies showed elevated inflammatory markers such as ESR and CRP, anemia, and hypoalbuminemia. Cananzi et al. (2021) proposed that compromised microbacterial sensing due to the variants impairs IFIH1 activation and interferon production, leading to impairment of innate immune defenses and chronic intestinal inflammation. Additional environmental and genetic factors likely modify the risk of developing the disease.
Using mice deficient in MDA5, Kato et al. (2006) showed that MDA5 and RIGI (609631) recognize different types of double-stranded RNAs: MDA5 recognizes PIC and RIGI detects in vitro transcribed double-stranded RNAs. RNA viruses are also differentially recognized by RIGI and MDA5. Kato et al. (2006) found that RIGI is essential for the production of interferons in response to RNA viruses including paramyxoviruses, influenza virus, and Japanese encephalitis virus, whereas MDA5 is critical for picornavirus detection. Furthermore, Rig1-null and Mda5-null mice are highly susceptible to infection with these respective RNA viruses compared to control mice. Kato et al. (2006) concluded that, taken together, their data show that RIGI and MDA5 distinguish different RNA viruses and are critical for host antiviral responses.
Using chemical mutagenesis, Funabiki et al. (2014) generated mice with a mutation in exon 13 of Mda5, resulting in a gly821-to-ser (G821S) substitution. These mice spontaneously developed lupus-like nephritis and systemic autoimmune symptoms without viral infection. Mutant mice that also lacked Mavs failed to develop nephritis, and mutant mice that also lacked Ifnar1 (107450) had a partially ameliorated nephritis. The G821S mutant could activate signaling in the absence of its ligand, but it was defective for ligand- and virus-induced signaling, suggesting a possible conformational change in Mda5. Funabiki et al. (2014) concluded that dysregulation of the innate immune sensor MDA5 causes autoimmune disorders.
Soda et al. (2019) found that mice with the constitutively active Mda5 G821S mutation exhibited growth retardation and decreased bone mineralization due to attenuated bone formation from osteoblasts and bone resorption by osteoclasts. The Mda5 G821S mutation did not intrinsically affect osteoclast function, but osteoclast differentiation from osteoclast precursor cells was extrinsically affected by exogenous type I Ifn that was induced by Mda5/Mavs signaling and played a central role in abnormal bone metabolism.
In 2 unrelated patients of European descent with Aicardi-Goutieres syndrome-7 (AGS7; 615846), Rice et al. (2014) identified a de novo heterozygous c.2159G-A transition in exon 11 of the IFIH1 gene, resulting in an arg720-to-gln (R720Q) substitution at a highly conserved residue in the core helicase-2 domain. The mutation in the first patient was found by whole-exome sequencing and confirmed by Sanger sequencing. It was not present in the Exome Sequencing Project database or in over 300 in-house control exomes. In vitro functional expression assays in HEK293T cells showed that the mutation caused marked induction of interferon signaling in response to short 162-bp double-stranded RNA (dsRNA) compared to controls. The mutation conferred 4- to 10-fold higher levels of basal signaling activity even in the absence of exogenous ligand. These findings were consistent with a gain of function, resulting in increased interferon signaling.
In 2 unrelated patients with Aicardi-Goutieres syndrome-7 (AGS7; 615846), Rice et al. (2014) identified a heterozygous c.2336G-A transition in exon 12 of the IFIH1 gene, resulting in an arg779-to-his (R779H) substitution at a highly conserved residue in the core helicase-2 domain. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was not present in the Exome Sequencing Project database or in over 300 in-house control exomes. The mutation occurred de novo in 1 patient. In the second family, the clinically asymptomatic father and paternal grandmother also carried the mutation, suggesting incomplete penetrance. However, all 3 mutation carriers in this family had a robust interferon signature. Rice et al. (2014) suggested that the phenotypic variability in this family may have resulted from additional environmental or genetic factors. In vitro functional expression assays in HEK293T cells showed that the mutation caused marked induction of interferon signaling in response to short 162-bp double-stranded RNA (dsRNA) compared to controls. The mutation conferred 4- to 10-fold higher levels of basal signaling activity even in the absence of exogenous ligand. These findings were consistent with a gain of function, resulting in increased interferon signaling.
Oda et al. (2014) identified a de novo heterozygous R779H mutation in a Japanese girl with AGS7. The mutation was found by trio-based whole-exome sequencing and confirmed by Sanger sequencing.
In a European American patient with Aicardi-Goutieres syndrome-7 (AGS7; 615846), Rice et al. (2014) identified a de novo heterozygous c.1009A-G transition in exon 5 of the IFIH1 gene, resulting in an arg337-to-gly (R337G) substitution at a highly conserved residue in the core helicase-1 domain. The mutation was not found in the Exome Sequencing Project database or in over 300 in-house control exomes. In vitro functional expression assays in HEK293T cells showed that the mutation caused marked induction of interferon signaling in response to short 162-bp double-stranded RNA (dsRNA) compared to controls. The mutation conferred 4- to 10-fold higher levels of basal signaling activity even in the absence of exogenous ligand. These findings were consistent with a gain of function, resulting in increased interferon signaling.
Adang et al. (2018) identified this mutation in a 16-year-old boy with AGS7 who died from cardiopulmonary arrest. Pulmonary hypertension was identified at autopsy. The mutation was shown to have occurred de novo.
In a patient of British descent with Aicardi-Goutieres syndrome-7 (AGS7; 615846), Rice et al. (2014) identified a heterozygous c.2335C-T transition in exon 12 of the IFIH1 gene, resulting in an arg779-to-cys (R779C) substitution at a highly conserved residue in the core helicase-2 domain. The mutation was not found in the Exome Sequencing Project database or in over 300 in-house control exomes. In vitro functional expression assays in HEK293T cells showed that the mutation caused marked induction of interferon signaling in response to short 162-bp double-stranded RNA (dsRNA) compared to controls. The mutation conferred 4- to 10-fold higher levels of basal signaling activity even in the absence of exogenous ligand. These findings were consistent with a gain of function, resulting in increased interferon signaling.
In a British father and daughter (F524) with Aicardi-Goutieres syndrome-7 (AGS7; 615846), Rice et al. (2014) identified a heterozygous c.1483G-A transition in exon 7 of the IFIH1 gene, resulting in a gly495-to-arg (G495R) substitution at a conserved residue in the core helicase-1 domain. The mutation was not found in the Exome Sequencing Project database or in over 300 in-house control exomes. The mutation occurred de novo in the father. In vitro functional expression assays in HEK293T cells showed that the mutation caused marked induction of interferon signaling in response to short 162-bp double-stranded RNA (dsRNA) compared to controls. The mutation conferred 4- to 10-fold higher levels of basal signaling activity even in the absence of exogenous ligand. These findings were consistent with a gain of function, resulting in increased interferon signaling. The patients had a unique phenotype characterized mainly by early-onset spastic paraparesis; the daughter also developed had a multisystem inflammatory process with brain imaging abnormalities. The British father was also reported by Crow et al. (2014). He had onset of motor symptoms around 2 years of age when he developed toe-walking and frequent falls after normal early development. He was diagnosed with cerebral palsy, but the disorder was slowly progressive. At age 33 years, he showed lower limb spasticity without upper limb involvement. Brain imaging and cognition were normal at the age of 29 years. Laboratory studies showed persistently increased interferon. Crow et al. (2014) emphasized the phenotypic variability associated with AGS, noting that neurologic dysfunction is not always marked in this disorder.
In an Italian patient with Aicardi-Goutieres syndrome-7 (AGS7; 615846), Rice et al. (2014) identified a de novo heterozygous c.1178A-T transversion in exon 6 of the IFIH1 gene, resulting in an asp393-to-val (D393V) substitution at a highly conserved residue in the core helicase-1 domain. The mutation was not found in the Exome Sequencing Project database or in over 300 in-house control exomes. In vitro functional expression assays in HEK293T cells showed that the mutation caused marked induction of interferon signaling in response to short 162-bp double-stranded RNA (dsRNA) compared to controls. The mutation conferred 4- to 10-fold higher levels of basal signaling activity even in the absence of exogenous ligand. These findings were consistent with a gain of function, resulting in increased interferon signaling.
In a Japanese boy with Aicardi-Goutieres syndrome-7 (AGS7; 615846), Oda et al. (2014) identified a de novo heterozygous c.1354G-A transition in the IFIH1 gene, resulting in an ala452-to-thr (A452T) substitution at a conserved residue in the helicase domain. The mutation, which was found by trio-based exome sequencing, was filtered against the dbSNP (build 137) database and was not present in an in-house exome database of 312 Japanese individuals.
In a Japanese boy with Aicardi-Goutieres syndrome-7 (AGS7; 615846), Oda et al. (2014) identified a de novo heterozygous c.1114C-T transition in the IFIH1 gene, resulting in a leu372-to-phe (L372F) substitution at a conserved residue in the helicase domain. The mutation, which was found by trio-based exome sequencing, was filtered against the dbSNP (build 137) database and was not present in an in-house exome database of 312 Japanese individuals.
Singleton-Merten Syndrome 1
In affected individuals from 3 unrelated families with early and extreme aortic and valvular calcification, dental anomalies, osteopenia, and acroosteolysis (SGMRT1; 182250), previously reported by Feigenbaum et al. (1988), Rutsch et al. (2005), and Valverde et al. (2010), respectively, Rutsch et al. (2015) performed whole-exome sequencing and identified heterozygosity for a c.2465G-A transition in the IFIH1 gene, resulting in an arg822-to-gln (R822Q) substitution at a highly conserved residue in 1 of 2 core helicase domains. The mutation, which segregated with disease in each family, was not found in any unaffected family members; analysis of 17 additional family members from the largest family showed that all but 1 individual with dental anomalies carried the mutation, and 1 individual with only psoriasis carried the mutation, whereas 3 others with only psoriasis did not. The authors noted that the IFIH1 c.2465G-A variant has been reported as a SNP (rs376048533) in 1 individual with 'cardiac and pulmonary phenotypes' from among 6,517 individuals in the NHLBI Exome Variant Server database, and is listed in the Exome Aggregation Consortium Browser with an allele frequency of 0.00002481. In vitro functional analysis revealed that the R822Q mutant enhanced MDA5 function in interferon-beta (IFNB1; 147640) induction, and interferon signature genes were upregulated in patient blood and dental cells. Rutsch et al. (2015) concluded that R822Q is a gain-of-function substitution that causes Singleton-Merten syndrome through dysregulation of the human innate immune response.
In a 10-year-old boy with Singleton-Merten syndrome, Riou et al. (2022) identified heterozygosity for the recurrent R822Q mutation (c.2465G-A, NM_022168.4) in the IFIH1 gene. The mutation arose de novo.
Aicardi-Goutieres Syndrome 7
In a 6-year-old boy with bilateral spasticity, developmental delay, and basal ganglia calcification (AGS7; 615846), Buers et al. (2017) identified heterozygosity for the R822Q mutation in the IFIH1 gene. The mutation was not present in parental DNA and was considered to have arisen de novo.
In a female infant with Aicardi-Goutieres syndrome-7 (AGS7; 615846), Amari et al. (2020) identified a de novo heterozygous c.2439A-T transversion (c.2439A-T, NM_022168) in exon 12 of the IFIH1 gene, resulting in a glu813-to-asp (E813D) substitution in the HEL2 domain. The mutation was identified by whole-exome sequencing and confirmed by Sanger sequencing. The mutation was not present in the gnomAD database or in an in-house database. Functional studies were not performed. The patient had prenatal findings including cardiomegaly, pericardial effusion, and intracranial calcifications.
In a 5-year-old girl from Burma with immunodeficiency-95 (IMD95; 619773), Lamborn et al. (2017), identified a homozygous c.1093A-G transition (c.1093A-G, NM_022168.3) in the IFIH1 gene, resulting in a lys365-to-glu (K365E) substitution at a conserved residue in the Hel1 domain. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was found at a low frequency in the ExAC database (0.06%) only in the heterozygous state and mainly in Asian populations. Both unaffected parents and an unaffected brother were heterozygous for the mutation. Patient cells showed normal protein levels, but the mutant protein was unable to bind to the poly(I:C) ligand, suggesting improper assembly and impaired downstream signaling. In vitro functional expression studies using a luciferase reporter assay demonstrated that the K365E mutant had minimal IFNB1 (147640) and NFKB (see 164011) promoter activity after stimulation with poly(I:C) compared to wildtype. Cotransfection of the mutant with wildtype showed no dominant-negative effects; the findings were consistent with a loss of function. Increased human rhinovirus (HRV) replication was observed in patient primary respiratory nasal epithelial cells compared to controls. However, these cells did not show increased viral replication of influenza or RSV. Similarly, silencing of IFIH1 in a respiratory epithelial cell line resulted in increased HRV transcripts, increased production of infectious virus, and decreased levels of IFN-regulated transcripts after HRV infection compared to controls, consistent with impaired viral recognition and antiviral responses. Transduction with wildtype, but not mutant, IFIH1 improved control of HRV replication. Similar to patient cells, silencing of IFIH1 did not increase replication of influenza or RSV in vitro. Overall, these findings indicated that IFIH1 has a nonredundant role in immunity against respiratory infections specifically caused by HRV. The patient had early-onset recurrent viral respiratory infections often requiring hospitalization. She also carried a heterozygous 4-bp deletion in the TM4SF20 gene (615404.0001) that likely explained her delays in motor and language development. Genetic analysis also identified 14 other homozygous missense mutations, 2 compound heterozygous missense mutations, and 3 de novo missense mutations, but the IFIH1 mutation was computationally predicted and functionally demonstrated to be deleterious.
In a 6-year-old girl, born of consanguineous Egyptian parents, with immunodeficiency-95 (IMD95; 619773), Zaki et al. (2017) identified a homozygous c.2665A-T transversion (c.2665A-T, NM_022168.2) in exon 14 of the IFIH1 gene, resulting in a lys889-to-ter (K889X) substitution. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was present in the heterozygous state in the unaffected parents and sib. It was not present in the ExAC or 1TGP databases. Western blot analysis of patient fibroblasts showed significantly decreased IFIH1 protein levels compared to controls, suggesting that the mutant transcript undergoes nonsense-mediated mRNA decay and results in a loss of function. In addition to IMD95, manifest as recurrent severe viral respiratory infections and persistent EBV infection, the patient also had a severe neurodevelopmental disorder with seizures and microcephaly associated with a homozygous missense mutation in the PHGDH gene (V425M; 606879.0002).
In 3-year-old girl (patient 1), born of consanguineous Moroccan parents, with immunodeficiency-95 (IMD95; 619773), Cananzi et al. (2021) identified a homozygous 1-bp deletion (c.2016delA, NM_022168) in exon 10 of the IFIH1 gene, resulting in a frameshift and premature termination (Asp673IlefsTer5) in the Hel2i domain. It was predicted to result in nonsense-mediated mRNA decay or produce a truncated protein lacking important functional domains. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was present in the heterozygous state in each unaffected parent. The mutation was found at a low frequency in the gnomAD database (2.99 x 10(-4)). In vitro functional studies using a luciferase reporter assay showed that mutant IFIH1 failed to activate the IFNB1 (147640) promoter following stimulation, consistent with a loss-of-function effect. In addition to recurrent and severe infections, including with CMV, the patient also had very early-onset inflammatory bowel disease (VEOIBD) in the first weeks of life.
In a 16-month-old girl (PRI_022) with immunodeficiency-95 (IMD95; 619773), Asgari et al. (2017) identified a homozygous splice site mutation in the IFIH1 gene, resulting in a splicing defect, the skipping of exon 14, a frameshift, and premature termination (Ile872Ter). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was present at a low frequency in the gnomAD database (0.64%). The mutation was inherited from her unaffected parents. In vitro functional expression studies in HEK293T cells transfected with the mutation showed that the mutant protein was unstable, failed to lead to IFNB1 (147640) production, and had no detectable ATPase activity compared to wildtype, consistent with a loss-of-function effect. There was also evidence for a dominant-negative effect on the wildtype protein. Additional in vitro studies showed that RSV and HRV replication levels were increased in cells transduced with the mutation, indicating a central role for IFIH1 in innate immune recognition of RSV and HRV and in controlling these infections. The patient presented with early-onset respiratory failure associated with RSV infection. Three additional children with severe early-onset viral HRC or RSV respiratory infections were heterozygous for the splice site variant; however, 2 patient inherited the variant from an unaffected parent. These findings suggested that heterozygosity for loss-of-function IFIH1 variants may confer susceptibility to the disease.
Association Pending Confirmation
In 2 unrelated patients (P3 and P7) with very early-onset inflammatory bowel disease (VEOIBD), Cananzi et al. (2021) identified the same intron 14 splice site mutation (c.2807+1G-A, NM_022168) in heterozygous state. This variant, which was identified by whole-exome sequencing, was inherited from an unaffected parent in both families, suggesting incomplete penetrance. In vitro functional expression studies using a luciferase reporter assay showed that the variant IFIH1 failed to activate the IFNB1 promoter following stimulation, consistent with a loss-of-function effect. Both patients with VEOIBD and the c.2807+1G-A mutation also carried an inherited T702I missense variant (one in trans, the other in cis) in the IFIH1 gene that had no functional effect.
In a French father and 2 sons with Singleton-Merten syndrome (SGMRT1; 182250), Bursztejn et al. (2015) identified heterozygosity for a c.1465G-A transition in the IFIH1 gene, resulting in an ala489-to-thr (A489T) substitution at a highly conserved residue within the core helicase Hel1 domain. The mutation, which was not found in the ExAC database, was also not present in the paternal grandparents, indicating a de novo origin or gonadal mosaicism. The A489T mutant showed impaired ATP hydrolysis activity compared to wildtype IFIH1, and the mutant protein-RNA complex showed increased stability in the presence of ATP compared to wildtype. Analysis of transfected HEK293T cells revealed that basal levels of interferon signaling were markedly increased in the absence of exogenous RNA with the A489T mutant. In addition, mutant IFIH1 displayed marked interferon induction following stimulation with either long or short double-stranded RNA.
In an 18-year-old girl, her mother, and maternal aunt (family 1938) with Singleton-Merten syndrome (SGMRT1; 182250), de Carvalho et al. (2017) identified heterozygosity for a c.992C-T transition (c.992C-T, NM_022168) in the IFIH1 gene, resulting in a thr331-to-ile (T331I) substitution at a highly conserved residue within the Hel1 core helicase domain. Familial segregation was not reported. The variant was not found in the ExAC database. Studies in HEK293T cells showed that basal levels of IFN signaling were markedly increased with the T331I mutant in the absence of endogenous dsRNA ligand, consistent with constitutive activation of MDA5.
In a 9-year-old girl and her affected father (family 1972) with Singleton-Merten syndrome (SGMRT1; 182250), de Carvalho et al. (2017) identified heterozygosity for a c.992C-G transition (c.992C-G, NM_022168) in the IFIH1 gene, resulting in a thr331-to-arg (T331R) substitution at a highly conserved residue within the Hel1 core helicase domain. Familial segregation was not reported. The variant was not found in the ExAC database. Studies in HEK293T cells showed that basal levels of IFN signaling were markedly increased with the T331R mutant in the absence of endogenous dsRNA ligand, consistent with constitutive activation of MDA5.
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