NM_033629.6(TREX1):c.340C>T (p.Arg114Cys) AND Aicardi-Goutieres syndrome 1

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jul 15, 2014
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:: RCV000191136.1

Allele description [Variation Report for NM_033629.6(TREX1):c.340C>T (p.Arg114Cys)]

NM_033629.6(TREX1):c.340C>T (p.Arg114Cys)

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.340C>T (p.Arg114Cys)

HGVS:

NC_000003.12:g.48466995C>T
NG_009820.2:g.6166C>T
NG_033100.1:g.38866G>A
NG_041782.1:g.25286C>T
NM_001271023.2:c.*1441C>T
NM_007248.5:c.310C>T
NM_032166.4:c.*1441C>T
NM_033629.6:c.340C>TMANE SELECT
NM_130384.3:c.*1441C>TMANE SELECT
NP_009179.2:p.Arg104Cys
NP_338599.1:p.Arg114Cys
LRG_282t1:c.340C>T
LRG_282:g.6166C>T
LRG_282p1:p.Arg114Cys
NC_000003.11:g.48508394C>T
NM_033629.2:c.340C>T
NM_033629.4:c.340C>T
NR_153405.1:n.3649C>T

Protein change:

R104C

Links:

dbSNP: rs760838030

NCBI 1000 Genomes Browser:

rs760838030

Molecular consequence:

NM_001271023.2:c.*1441C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_032166.4:c.*1441C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_130384.3:c.*1441C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_007248.5:c.310C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_033629.6:c.340C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_153405.1:n.3649C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000245545	Baylor Genetics - Adult_WES	criteria provided, single submitter (Yang et al. 2013)	Likely pathogenic (Jul 15, 2014)	paternal	clinical testing	PubMed (2) [See all records that cite these PMIDs] 24088041, 26633545

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000245545

Baylor Genetics - Adult_WES

criteria provided, single submitter

(Yang et al. 2013)

Likely pathogenic
(Jul 15, 2014)

paternal

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	paternal	yes	1	1	not provided	not provided	not provided	clinical testing

Citations

PubMed

Clinical whole-exome sequencing for the diagnosis of mendelian disorders.

Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, Braxton A, Beuten J, Xia F, Niu Z, Hardison M, Person R, Bekheirnia MR, Leduc MS, Kirby A, Pham P, Scull J, Wang M, Ding Y, Plon SE, Lupski JR, Beaudet AL, et al.

N Engl J Med. 2013 Oct 17;369(16):1502-11. doi: 10.1056/NEJMoa1306555. Epub 2013 Oct 2.

PubMed [citation]

PMID:: 24088041
PMCID:: PMC4211433

Molecular diagnostic experience of whole-exome sequencing in adult patients.

Posey JE, Rosenfeld JA, James RA, Bainbridge M, Niu Z, Wang X, Dhar S, Wiszniewski W, Akdemir ZH, Gambin T, Xia F, Person RE, Walkiewicz M, Shaw CA, Sutton VR, Beaudet AL, Muzny D, Eng CM, Yang Y, Gibbs RA, Lupski JR, Boerwinkle E, et al.

Genet Med. 2016 Jul;18(7):678-85. doi: 10.1038/gim.2015.142. Epub 2015 Dec 3.

PubMed [citation]

PMID:: 26633545
PMCID:: PMC4892996

Details of each submission

From Baylor Genetics - Adult_WES, SCV000245545.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing (GTR000508680.4)	PubMed (2)

Description

Likely pathogenicity based on finding it once in our laboratory in trans with a pathogenic variant [V71fs] in an 18-year-old male with delayed development, neurologic regression, mineral deposition in the brain, adult-onset vision loss, inability to stand or walk, dystonia, abnormal teeth, maculopapular rash. This missense variant affects the same residue as another pathogenic variant reported in Aicardi-Goutieres syndrome (PMID 16845398, 18805785, 21270825, 21937424, 23881107). Father, who was heterozygous for this variant, had focal hand dystonia.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	paternal	yes	not provided	not provided	not provided	(GTR000508680.4)	1	not provided	1	not provided

Last Updated: Aug 5, 2023

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