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NM_001033855.3(DCLRE1C):c.1903dup (p.Ser635fs) AND Histiocytic medullary reticulosis

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 31, 2017
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:
RCV000779020.4

Allele description [Variation Report for NM_001033855.3(DCLRE1C):c.1903dup (p.Ser635fs)]

NM_001033855.3(DCLRE1C):c.1903dup (p.Ser635fs)

Gene:
DCLRE1C:DNA cross-link repair 1C [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
10p13
Genomic location:
Preferred name:
NM_001033855.3(DCLRE1C):c.1903dup (p.Ser635fs)
HGVS:
  • NC_000010.11:g.14908589dup
  • NG_007276.1:g.50512dup
  • NM_001033855.3:c.1903dupMANE SELECT
  • NM_001033857.3:c.1543dup
  • NM_001033858.3:c.1543dup
  • NM_001289076.2:c.1558dup
  • NM_001289077.2:c.1543dup
  • NM_001289078.2:c.1558dup
  • NM_001289079.2:c.1543dup
  • NM_001350965.2:c.1782+116dup
  • NM_001350966.2:c.1437+116dup
  • NM_001350967.2:c.1422+116dup
  • NM_022487.4:c.1558dup
  • NP_001029027.1:p.Ser635fs
  • NP_001029029.1:p.Ser515fs
  • NP_001029030.1:p.Ser515fs
  • NP_001276005.1:p.Ser520fs
  • NP_001276006.1:p.Ser515fs
  • NP_001276007.1:p.Ser520fs
  • NP_001276008.1:p.Ser515fs
  • NP_071932.2:p.Ser520fs
  • LRG_54t1:c.1903dup
  • LRG_54:g.50512dup
  • NC_000010.10:g.14950582_14950583insT
  • NC_000010.10:g.14950588dup
  • NM_001033855.1:c.1903dupA
  • NM_001033855.2:c.1903dup
  • NM_001033855.2:c.1903dupA
  • NR_110297.2:n.2342dup
  • NR_146961.2:n.2083dup
  • NR_146962.1:n.2390dup
Protein change:
S515fs
Links:
dbSNP: rs760288938
NCBI 1000 Genomes Browser:
rs760288938
Molecular consequence:
  • NM_001033855.3:c.1903dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001033857.3:c.1543dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001033858.3:c.1543dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001289076.2:c.1558dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001289077.2:c.1543dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001289078.2:c.1558dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001289079.2:c.1543dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_022487.4:c.1558dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001350965.2:c.1782+116dup - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001350966.2:c.1437+116dup - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001350967.2:c.1422+116dup - intron variant - [Sequence Ontology: SO:0001627]
  • NR_110297.2:n.2342dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146961.2:n.2083dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146962.1:n.2390dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Histiocytic medullary reticulosis
Synonyms:
Omenn syndrome; Reticuloendotheliosis familial with eosinophilia; Severe combined immunodeficiency with hypereosinophilia
Identifiers:
MONDO: MONDO:0011338; MedGen: C2700553; Orphanet: 39041; OMIM: 603554

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000915464Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 09 May 2019)
Uncertain significance
(Aug 31, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000915464.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The DCLRE1C c.1903dupA (p.Ser635LysfsTer6) variant results in a frameshift, and is predicted to result in premature termination of the protein. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found based on this search. This variant has not therefore been reported in the literature in association with Omenn syndrome. The p.Ser635LysfsTer6 variant is reported at a frequency of 0.002465 in the Ashkenazi Jewish population from the Genome Aggregation Database. Based on the variant frequency, disease prevalence, disease penetrance, and inheritance mode, this variant could not be ruled out of causing disease. Based on the potential impact of frameshift variants and the lack of clarifying evidence, the p.Ser635LysfsTer6 variant is classified as a variant of unknown significance but suspicious for pathogenicity for Omenn syndrome. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

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

Last Updated: Feb 28, 2024