NM_033629.6(TREX1):c.137dup (p.Ser46fs) AND Chilblain lupus 1

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Oct 6, 2021
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:: RCV001730099.1

Allele description [Variation Report for NM_033629.6(TREX1):c.137dup (p.Ser46fs)]

NM_033629.6(TREX1):c.137dup (p.Ser46fs)

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:

Duplication

Cytogenetic location:

3p21.31

Genomic location:

Preferred name:

NM_033629.6(TREX1):c.137dup (p.Ser46fs)

HGVS:

NC_000003.12:g.48466792dup
NG_009820.2:g.5963dup
NG_033100.1:g.39069dup
NG_041782.1:g.25083dup
NM_001271022.2:c.*1238dup
NM_001271023.2:c.*1238dup
NM_007248.5:c.107dup
NM_032166.4:c.*1238dup
NM_033629.6:c.137dupMANE SELECT
NM_130384.3:c.*1238dupMANE SELECT
NP_009179.2:p.Ser36fs
NP_338599.1:p.Ser46fs
LRG_282t1:c.137dup
LRG_282:g.5963dup
LRG_282p1:p.Ser46fs
NC_000003.11:g.48508191dup
NM_033629.6:c.137dupGMANE SELECT
NR_153405.1:n.3446dup

Protein change:

S36fs

Links:

dbSNP: rs2107255865

NCBI 1000 Genomes Browser:

rs2107255865

Molecular consequence:

NM_001271022.2:c.*1238dup - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001271023.2:c.*1238dup - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_032166.4:c.*1238dup - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_130384.3:c.*1238dup - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_007248.5:c.107dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_033629.6:c.137dup - frameshift variant - [Sequence Ontology: SO:0001589]
NR_153405.1:n.3446dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Chilblain lupus 1 (CHBL1)
Identifiers:: MONDO: MONDO:0012500; MedGen: C0024145; OMIM: 610448

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001976930	Laboratory of Medical Genetics, National & Kapodistrian University of Athens	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 6, 2021)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001976930

Laboratory of Medical Genetics, National & Kapodistrian University of Athens

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Oct 6, 2021)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Laboratory of Medical Genetics, National & Kapodistrian University of Athens, SCV001976930.1

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

Description

PM1, PM2, PP3, PP4, PP5

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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