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NM_033629.6(TREX1):c.592G>A (p.Glu198Lys) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 2, 2024
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV001307854.5

Allele description [Variation Report for NM_033629.6(TREX1):c.592G>A (p.Glu198Lys)]

NM_033629.6(TREX1):c.592G>A (p.Glu198Lys)

Genes:
ATRIP:ATR interacting protein [Gene - OMIM - HGNC]
ATRIP-TREX1:ATRIP-TREX1 readthrough [Gene]
TREX1:three prime repair exonuclease 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p21.31
Genomic location:
Preferred name:
NM_033629.6(TREX1):c.592G>A (p.Glu198Lys)
HGVS:
  • NC_000003.12:g.48467247G>A
  • NG_009820.2:g.6418G>A
  • NG_033100.1:g.38614C>T
  • NG_033100.2:g.42563C>T
  • NG_041782.1:g.25538G>A
  • NG_099340.1:g.308G>A
  • NM_001271022.2:c.*1693G>A
  • NM_001271023.2:c.*1693G>A
  • NM_007248.5:c.562G>A
  • NM_032166.4:c.*1693G>A
  • NM_033629.6:c.592G>AMANE SELECT
  • NM_130384.3:c.*1693G>AMANE SELECT
  • NP_009179.2:p.Glu188Lys
  • NP_338599.1:p.Glu198Lys
  • NP_338599.1:p.Glu198Lys
  • LRG_282t1:c.592G>A
  • LRG_282:g.6418G>A
  • LRG_282p1:p.Glu198Lys
  • NC_000003.11:g.48508646G>A
  • NM_007248.5:c.562G>A
  • NM_033629.2:c.592G>A
  • NM_033629.4:c.592G>A
  • NR_153405.1:n.3901G>A
Protein change:
E188K
Links:
dbSNP: rs1416519719
NCBI 1000 Genomes Browser:
rs1416519719
Molecular consequence:
  • NM_001271022.2:c.*1693G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001271023.2:c.*1693G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_032166.4:c.*1693G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_130384.3:c.*1693G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_007248.5:c.562G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033629.6:c.592G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_153405.1:n.3901G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Aicardi-Goutieres syndrome 1
Synonyms:
CREE ENCEPHALITIS; ENCEPHALOPATHY, FAMILIAL INFANTILE, WITH INTRACRANIAL CALCIFICATION AND CHRONIC CEREBROSPINAL FLUID LYMPHOCYTOSIS; PSEUDOTOXOPLASMOSIS SYNDROME
Identifiers:
MONDO: MONDO:0009165; MedGen: C0796126; Orphanet: 51; OMIM: 225750
Name:
Chilblain lupus 1 (CHBL1)
Identifiers:
MONDO: MONDO:0012500; MedGen: C0024145; OMIM: 610448
Name:
Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations (RVCLS)
Synonyms:
Vasculopathy, retinal, with cerebral leukodystrophy; Cerebroretinal vasculopathy, hereditary; Retinopathy, vascular, with cerebral and renal involvement and Raynaud and migraine phenomena
Identifiers:
MONDO: MONDO:0008641; MedGen: C1860518; Orphanet: 3421; Orphanet: 63261; Orphanet: 71291; OMIM: 192315

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001497282Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jan 2, 2024) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Expanding the phenotypic spectrum of lupus erythematosus in Aicardi-Goutières syndrome.

Ramantani G, Kohlhase J, Hertzberg C, Innes AM, Engel K, Hunger S, Borozdin W, Mah JK, Ungerath K, Walkenhorst H, Richardt HH, Buckard J, Bevot A, Siegel C, von Stülpnagel C, Ikonomidou C, Thomas K, Proud V, Niemann F, Wieczorek D, Häusler M, Niggemann P, et al.

Arthritis Rheum. 2010 May;62(5):1469-77. doi: 10.1002/art.27367.

PubMed [citation]
PMID:
20131292

Rare variants in the TREX1 gene and susceptibility to autoimmune diseases.

Barizzone N, Monti S, Mellone S, Godi M, Marchini M, Scorza R, Danieli MG, D'Alfonso S.

Biomed Res Int. 2013;2013:471703. doi: 10.1155/2013/471703. Epub 2013 Oct 9.

PubMed [citation]
PMID:
24224166
PMCID:
PMC3810194
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001497282.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 198 of the TREX1 protein (p.Glu198Lys). This variant is present in population databases (no rsID available, gnomAD 0.0009%). This missense change has been observed in individual(s) with Aicardi-Goutieres Syndrome and Sjogren’s syndrome (PMID: 20131292, 24224166). ClinVar contains an entry for this variant (Variation ID: 1010253). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024