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NM_033629.6(TREX1):c.907A>C (p.Thr303Pro) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 18, 2023
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:
RCV002513943.10

Allele description [Variation Report for NM_033629.6(TREX1):c.907A>C (p.Thr303Pro)]

NM_033629.6(TREX1):c.907A>C (p.Thr303Pro)

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.907A>C (p.Thr303Pro)
HGVS:
  • NC_000003.12:g.48467562A>C
  • NG_009820.2:g.6733A>C
  • NG_033100.1:g.38299T>G
  • NG_033100.2:g.42248T>G
  • NG_041782.1:g.25853A>C
  • NG_099340.1:g.623A>C
  • NM_001271022.2:c.*2008A>C
  • NM_001271023.2:c.*2008A>C
  • NM_007248.5:c.877A>C
  • NM_032166.4:c.*2008A>C
  • NM_033629.6:c.907A>CMANE SELECT
  • NM_130384.3:c.*2008A>CMANE SELECT
  • NP_009179.2:p.Thr293Pro
  • NP_338599.1:p.Thr303Pro
  • NP_338599.1:p.Thr303Pro
  • LRG_282t1:c.907A>C
  • AAK07616.1:p.Thr303Pro
  • AF319569.1:c.907A>C
  • LRG_282:g.6733A>C
  • LRG_282p1:p.Thr303Pro
  • NC_000003.11:g.48508961A>C
  • NM_033629.4:c.907A>C
  • NR_153405.1:n.4216A>C
  • Q9NSU2:p.Thr358Pro
Protein change:
T293P
Links:
UniProtKB: Q9NSU2#VAR_070902; dbSNP: rs76224909
NCBI 1000 Genomes Browser:
rs76224909
Molecular consequence:
  • NM_001271022.2:c.*2008A>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001271023.2:c.*2008A>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_032166.4:c.*2008A>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_130384.3:c.*2008A>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_007248.5:c.877A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033629.6:c.907A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_153405.1:n.4216A>C - 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
SCV000814211Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 18, 2023) 		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

Clinical and molecular phenotype of Aicardi-Goutieres syndrome.

Rice G, Patrick T, Parmar R, Taylor CF, Aeby A, Aicardi J, Artuch R, Montalto SA, Bacino CA, Barroso B, Baxter P, Benko WS, Bergmann C, Bertini E, Biancheri R, Blair EM, Blau N, Bonthron DT, Briggs T, Brueton LA, Brunner HG, Burke CJ, et al.

Am J Hum Genet. 2007 Oct;81(4):713-25. Epub 2007 Sep 4.

PubMed [citation]
PMID:
17846997
PMCID:
PMC2227922

Evaluation of the TREX1 gene in a large multi-ancestral lupus cohort.

Namjou B, Kothari PH, Kelly JA, Glenn SB, Ojwang JO, Adler A, Alarcón-Riquelme ME, Gallant CJ, Boackle SA, Criswell LA, Kimberly RP, Brown E, Edberg J, Stevens AM, Jacob CO, Tsao BP, Gilkeson GS, Kamen DL, Merrill JT, Petri M, Goldman RR, Vila LM, et al.

Genes Immun. 2011 Jun;12(4):270-9. doi: 10.1038/gene.2010.73. Epub 2011 Jan 27.

PubMed [citation]
PMID:
21270825
PMCID:
PMC3107387
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000814211.3

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

Description

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. This sequence change replaces threonine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 303 of the TREX1 protein (p.Thr303Pro). This variant is present in population databases (rs76224909, gnomAD 0.004%). This missense change has been observed in individual(s) with Aicardi-Goutieres syndrome (PMID: 17846997, 21270825). ClinVar contains an entry for this variant (Variation ID: 126394). 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.

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

Last Updated: Nov 24, 2024