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NM_005419.4(STAT2):c.442C>T (p.Arg148Trp) AND Pseudo-TORCH syndrome 3

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 17, 2020
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001249565.1

Allele description [Variation Report for NM_005419.4(STAT2):c.442C>T (p.Arg148Trp)]

NM_005419.4(STAT2):c.442C>T (p.Arg148Trp)

Gene:
STAT2:signal transducer and activator of transcription 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q13.3
Genomic location:
Preferred name:
NM_005419.4(STAT2):c.442C>T (p.Arg148Trp)
HGVS:
  • NC_000012.12:g.56355472G>A
  • NG_046314.1:g.9782C>T
  • NM_005419.4:c.442C>TMANE SELECT
  • NM_198332.2:c.430C>T
  • NP_005410.1:p.Arg148Trp
  • NP_938146.1:p.Arg144Trp
  • LRG_1329t1:c.442C>T
  • LRG_1329:g.9782C>T
  • LRG_1329p1:p.Arg148Trp
  • NC_000012.11:g.56749256G>A
  • NM_005419.3:c.442C>T
Protein change:
R144W; ARG148TRP
Links:
OMIM: 600556.0003; dbSNP: rs1458224681
NCBI 1000 Genomes Browser:
rs1458224681
Molecular consequence:
  • NM_005419.4:c.442C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198332.2:c.430C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Pseudo-TORCH syndrome 3
Identifiers:
MONDO: MONDO:0030044; MedGen: C5394391; OMIM: 618886

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001423534OMIM
no assertion criteria provided
Pathogenic
(Jul 17, 2020)
germlineliterature only

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

Citations

PubMed

Severe type I interferonopathy and unrestrained interferon signaling due to a homozygous germline mutation in STAT2.

Duncan CJA, Thompson BJ, Chen R, Rice GI, Gothe F, Young DF, Lovell SC, Shuttleworth VG, Brocklebank V, Corner B, Skelton AJ, Bondet V, Coxhead J, Duffy D, Fourrage C, Livingston JH, Pavaine J, Cheesman E, Bitetti S, Grainger A, Acres M, Innes BA, et al.

Sci Immunol. 2019 Dec 13;4(42). doi:pii: eaav7501. 10.1126/sciimmunol.aav7501.

PubMed [citation]
PMID:
31836668
PMCID:
PMC7115903

Details of each submission

From OMIM, SCV001423534.1

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

Description

In 2 brothers, born of consanguineous Pakistani parents, with pseudo-TORCH syndrome-3 (PTORCH3; 618886), Duncan et al. (2019) identified a homozygous c.442C-T transition (c.442C-T, NM_005419.3) in the STAT2 gene, resulting in an arg148-to-trp (R148W) substitution at a highly conserved residue in the coiled-coil domain. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. It was found only in the heterozygous state at a very low frequency in the gnomAD database. STAT2 protein expression was unaffected in patient cells. RNA and RT-PCR analysis of patient blood showed increased IFN-stimulated gene (ISG) gene expression, consistent with a type I interferonopathy. Patient cells and STAT2-null cells transduced with the mutation showed a similar heightened sensitivity to IFNA1 (147660), consistent with an abnormally enhanced response upon exposure to interferon, rather than constitutive activation of STAT2. The abnormalities were associated with prolonged IFNAR (107450) signaling in patient cells, but not in parental cells carrying the heterozygous mutation, which the authors noted is unusual for gain-of-function mutations. Further in vitro studies showed that the R148W mutation impaired the interaction of STAT2 with the negative regulator USP18 (607057), resulting in desensitization to the negative regulation normally conferred by USP18. The findings were consistent with an inability of patient cells to properly restrain IFNAR signaling, which results in an inflammatory disease consistent with a type I interferonopathy. Duncan et al. (2019) noted that the loss of negative regulation of IFNAR signaling, due to the STAT2 mutation, behaves as a recessive trait with an overall gain-of-function effect on the IFN signaling pathway.

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

Last Updated: Apr 23, 2022