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NC_000003.11:g.(?_48507870)_(50340407_?)del AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 2, 2020
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:
RCV001380369.6

Allele description [Variation Report for NC_000003.11:g.(?_48507870)_(50340407_?)del]

NC_000003.11:g.(?_48507870)_(50340407_?)del

Genes:
  • PFKFB4:6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 [Gene - OMIM - HGNC]
  • ARIH2OS:ARIH2 opposite strand lncRNA [Gene - HGNC]
  • CAMKV:CaM kinase like vesicle associated [Gene - OMIM - HGNC]
  • DALRD3:DALR anticodon binding domain containing 3 [Gene - OMIM - HGNC]
  • GNAI2:G protein subunit alpha i2 [Gene - OMIM - HGNC]
  • GNAT1:G protein subunit alpha transducin 1 [Gene - OMIM - HGNC]
  • GMPPB:GDP-mannose pyrophosphorylase B [Gene - OMIM - HGNC]
  • MON1A:MON1 homolog A, secretory trafficking associated [Gene - OMIM - HGNC]
  • NAA80:N-alpha-acetyltransferase 80, NatH catalytic subunit [Gene - OMIM - HGNC]
  • NDUFAF3:NADH:ubiquinone oxidoreductase complex assembly factor 3 [Gene - OMIM - HGNC]
  • NCKIPSD:NCK interacting protein with SH3 domain [Gene - OMIM - HGNC]
  • RBM5:RNA binding motif protein 5 [Gene - OMIM - HGNC]
  • RBM6:RNA binding motif protein 6 [Gene - OMIM - HGNC]
  • SEMA3F-AS1:SEMA3F antisense RNA 1 [Gene - HGNC]
  • TCTA:T cell leukemia translocation altered [Gene - OMIM - HGNC]
  • TRAIP:TRAF interacting protein [Gene - OMIM - HGNC]
  • WDR6:WD repeat domain 6 [Gene - OMIM - HGNC]
  • APEH:acylaminoacyl-peptide hydrolase [Gene - OMIM - HGNC]
  • AMIGO3:adhesion molecule with Ig like domain 3 [Gene - OMIM - HGNC]
  • AMT:aminomethyltransferase [Gene - OMIM - HGNC]
  • ARIH2:ariadne RBR E3 ubiquitin protein ligase 2 [Gene - OMIM - HGNC]
  • BSN:bassoon presynaptic cytomatrix protein [Gene - OMIM - HGNC]
  • CELSR3:cadherin EGF LAG seven-pass G-type receptor 3 [Gene - OMIM - HGNC]
  • CDHR4:cadherin related family member 4 [Gene - HGNC]
  • C3orf62:chromosome 3 open reading frame 62 [Gene - HGNC]
  • CIMIP7:ciliary microtubule inner protein 7 [Gene - HGNC]
  • CCDC71:coiled-coil domain containing 71 [Gene - HGNC]
  • COL7A1:collagen type VII alpha 1 chain [Gene - OMIM - HGNC]
  • DAG1:dystroglycan 1 [Gene - OMIM - HGNC]
  • QRICH1:glutamine rich 1 [Gene - OMIM - HGNC]
  • QARS1:glutaminyl-tRNA synthetase 1 [Gene - OMIM - HGNC]
  • GPX1:glutathione peroxidase 1 [Gene - OMIM - HGNC]
  • HYAL1:hyaluronidase 1 [Gene - OMIM - HGNC]
  • HYAL3:hyaluronidase 3 [Gene - OMIM - HGNC]
  • INKA1:inka box actin regulator 1 [Gene - OMIM - HGNC]
  • IMPDH2:inosine monophosphate dehydrogenase 2 [Gene - OMIM - HGNC]
  • IP6K1:inositol hexakisphosphate kinase 1 [Gene - OMIM - HGNC]
  • IP6K2:inositol hexakisphosphate kinase 2 [Gene - OMIM - HGNC]
  • IHO1:interactor of HORMAD1 1 [Gene - OMIM - HGNC]
  • IFRD2:interferon related developmental regulator 2 [Gene - OMIM - HGNC]
  • KLHDC8B:kelch domain containing 8B [Gene - OMIM - HGNC]
  • LAMB2:laminin subunit beta 2 [Gene - OMIM - HGNC]
  • LSMEM2:leucine rich single-pass membrane protein 2 [Gene - HGNC]
  • MST1R:macrophage stimulating 1 receptor [Gene - OMIM - HGNC]
  • MST1:macrophage stimulating 1 [Gene - OMIM - HGNC]
  • MIR191:microRNA 191 [Gene - OMIM - HGNC]
  • NICN1:nicolin 1, tubulin polyglutamylase complex subunit [Gene - OMIM - HGNC]
  • P4HTM:prolyl 4-hydroxylase, transmembrane [Gene - OMIM - HGNC]
  • PRKAR2A:protein kinase cAMP-dependent type II regulatory subunit alpha [Gene - OMIM - HGNC]
  • RHOA:ras homolog family member A [Gene - OMIM - HGNC]
  • RNF123:ring finger protein 123 [Gene - OMIM - HGNC]
  • SEMA3B:semaphorin 3B [Gene - OMIM - HGNC]
  • SEMA3F:semaphorin 3F [Gene - OMIM - HGNC]
  • SHISA5:shisa family member 5 [Gene - OMIM - HGNC]
  • SLC25A20:solute carrier family 25 member 20 [Gene - OMIM - HGNC]
  • SLC26A6:solute carrier family 26 member 6 [Gene - OMIM - HGNC]
  • SLC38A3:solute carrier family 38 member 3 [Gene - OMIM - HGNC]
  • TREX1:three prime repair exonuclease 1 [Gene - OMIM - HGNC]
  • TMEM89:transmembrane protein 89 [Gene - HGNC]
  • UQCRC1:ubiquinol-cytochrome c reductase core protein 1 [Gene - OMIM - HGNC]
  • UBA7:ubiquitin like modifier activating enzyme 7 [Gene - OMIM - HGNC]
  • USP19:ubiquitin specific peptidase 19 [Gene - OMIM - HGNC]
  • USP4:ubiquitin specific peptidase 4 [Gene - OMIM - HGNC]
  • UCN2:urocortin 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
3p21.31
Genomic location:
Chr3: 48507870 - 50340407 (on Assembly GRCh37)
Preferred name:
NC_000003.11:g.(?_48507870)_(50340407_?)del
HGVS:
NC_000003.11:g.(?_48507870)_(50340407_?)del

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
SCV001578401Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Aug 2, 2020) 		germlineclinical testing

PubMed (2)
[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

Mutations in the gene encoding the 3'-5' DNA exonuclease TREX1 cause Aicardi-Goutières syndrome at the AGS1 locus.

Crow YJ, Hayward BE, Parmar R, Robins P, Leitch A, Ali M, Black DN, van Bokhoven H, Brunner HG, Hamel BC, Corry PC, Cowan FM, Frints SG, Klepper J, Livingston JH, Lynch SA, Massey RF, Meritet JF, Michaud JL, Ponsot G, Voit T, Lebon P, et al.

Nat Genet. 2006 Aug;38(8):917-20. Epub 2006 Jul 16.

PubMed [citation]
PMID:
16845398

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001578401.4

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

Description

A gross deletion of the genomic region encompassing the full coding sequence of the TREX1 gene has been identified. The boundaries of this event are unknown as the deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals with TREX1-related conditions. Loss-of-function variants in TREX1 are known to be pathogenic (PMID: 16845398). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024