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NM_022168.4(IFIH1):c.2465G>A (p.Arg822Gln) AND Singleton-Merten syndrome 1

Germline classification:
Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:
Jul 28, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000169754.16

Allele description [Variation Report for NM_022168.4(IFIH1):c.2465G>A (p.Arg822Gln)]

NM_022168.4(IFIH1):c.2465G>A (p.Arg822Gln)

Gene:
IFIH1:interferon induced with helicase C domain 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q24.2
Genomic location:
Preferred name:
NM_022168.4(IFIH1):c.2465G>A (p.Arg822Gln)
Other names:
IFIH1, ARG822GLN (rs376048533)
HGVS:
  • NC_000002.12:g.162272377C>T
  • NG_011495.1:g.51153G>A
  • NM_022168.4:c.2465G>AMANE SELECT
  • NP_071451.2:p.Arg822Gln
  • LRG_1235t1:c.2465G>A
  • LRG_1235:g.51153G>A
  • LRG_1235p1:p.Arg822Gln
  • NC_000002.11:g.163128887C>T
  • NM_022168.3:c.2465G>A
  • Q9BYX4:p.Arg822Gln
Protein change:
R822Q; ARG822GLN
Links:
UniProtKB: Q9BYX4#VAR_073666; OMIM: 606951.0009; dbSNP: rs376048533
NCBI 1000 Genomes Browser:
rs376048533
Molecular consequence:
  • NM_022168.4:c.2465G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Singleton-Merten syndrome 1 (SGMRT1)
Synonyms:
Widened medullary cavities of bone, aortic calcification, abnormal dentition, and muscular weakness; Syndrome of widened medullary cavities of the metacarpals and phalanges, aortic calcification and abnormal dentition
Identifiers:
MONDO: MONDO:0024535; MedGen: C4225427; Orphanet: 85191; OMIM: 182250

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000221304OMIM
no assertion criteria provided
Pathogenic
(Feb 5, 2015)
germlineliterature only

PubMed (4)
[See all records that cite these PMIDs]

Feigenbaum, A., Kumar, A., Weksberg, R. Singleton-Merten (S-M) syndrome: autosomal dominant transmission with variable expression. (Abstract) Am. J. Hum. Genet. 43: A48-only, 1988.,

SCV0040137743billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicunknownclinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV004026603Molecular Medicine, University of Pavia
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Jul 28, 2023)
paternalresearch

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedunknownyes1not providednot providednot providednot providedclinical testing
not providedpaternalyes11not providednot providednot providedresearch

Citations

PubMed

Singleton-merten syndrome and impaired cardiac function.

Valverde I, Rosenthal E, Tzifa A, Desai P, Bell A, Pushparajah K, Qureshi S, Beerbaum P, Simpson J.

J Am Coll Cardiol. 2010 Nov 16;56(21):1760. doi: 10.1016/j.jacc.2010.02.078. No abstract available.

PubMed [citation]
PMID:
21070929

Oral Phenotype of Singleton-Merten Syndrome: A Systematic Review Illustrated With a Case Report.

Riou MC, de La Dure-Molla M, Kerner S, Rondeau S, Legendre A, Cormier-Daire V, Fournier BPJ.

Front Genet. 2022;13:875490. doi: 10.3389/fgene.2022.875490.

PubMed [citation]
PMID:
35754802
PMCID:
PMC9218817
See all PubMed Citations (5)

Details of each submission

From OMIM, SCV000221304.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)

Description

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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From 3billion, SCV004013774.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (2)

Description

The variant is observed at an allele frequency greater than expected for the associated disorder in the gnomAD v2.1.1 dataset. Missense changes are a common disease-causing mechanism. Functional studies provide moderate evidence of the variant having a damaging effect on the gene or gene product (PMID: 25620204). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.98; 3Cnet: 0.92). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000189338 / PMID: 25620204). The variant has been previously reported as de novo in a similarly affected individual (PMID: 25620204). The variant has been observed in at least two similarly affected unrelated individuals (PMID: 25620204). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

From Molecular Medicine, University of Pavia, SCV004026603.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1paternalyesnot providednot providednot provided1not provided1not provided

Last Updated: May 12, 2024