NM_001033855.3(DCLRE1C):c.959C>G (p.Ser320Cys) AND Histiocytic medullary reticulosis

Clinical significance:Benign (Last evaluated: Jan 12, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000348357.2

Allele description [Variation Report for NM_001033855.3(DCLRE1C):c.959C>G (p.Ser320Cys)]

NM_001033855.3(DCLRE1C):c.959C>G (p.Ser320Cys)

Gene:
DCLRE1C:DNA cross-link repair 1C [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10p13
Genomic location:
Preferred name:
NM_001033855.3(DCLRE1C):c.959C>G (p.Ser320Cys)
Other names:
p.S320C:TCC>TGC
HGVS:
  • NC_000010.11:g.14926856G>C
  • NG_007276.1:g.32240C>G
  • NM_001033855.3:c.959C>GMANE SELECT
  • NM_001033857.3:c.599C>G
  • NM_001033858.3:c.599C>G
  • NM_001289076.2:c.614C>G
  • NM_001289077.2:c.599C>G
  • NM_001289078.2:c.614C>G
  • NM_001289079.2:c.599C>G
  • NM_001350965.2:c.959C>G
  • NM_001350966.2:c.614C>G
  • NM_001350967.2:c.599C>G
  • NM_022487.4:c.614C>G
  • NP_001029027.1:p.Ser320Cys
  • NP_001029029.1:p.Ser200Cys
  • NP_001029030.1:p.Ser200Cys
  • NP_001276005.1:p.Ser205Cys
  • NP_001276006.1:p.Ser200Cys
  • NP_001276007.1:p.Ser205Cys
  • NP_001276008.1:p.Ser200Cys
  • NP_001337894.1:p.Ser320Cys
  • NP_001337895.1:p.Ser205Cys
  • NP_001337896.1:p.Ser200Cys
  • NP_071932.2:p.Ser205Cys
  • LRG_54t1:c.959C>G
  • LRG_54:g.32240C>G
  • NC_000010.10:g.14968855G>C
  • NM_001033855.1:c.959C>G
  • NM_001033855.2:c.959C>G
  • NM_022487.2:c.614C>G
  • NR_110297.2:n.1257C>G
  • NR_146961.2:n.1074C>G
  • NR_146962.1:n.1381C>G
  • Q96SD1:p.Ser320Cys
Protein change:
S200C
Links:
UniProtKB: Q96SD1#VAR_048894; dbSNP: rs41298896
NCBI 1000 Genomes Browser:
rs41298896
Molecular consequence:
  • NM_001033855.3:c.959C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001033857.3:c.599C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001033858.3:c.599C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001289076.2:c.614C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001289077.2:c.599C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001289078.2:c.614C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001289079.2:c.599C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001350965.2:c.959C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001350966.2:c.614C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001350967.2:c.599C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_022487.4:c.614C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_110297.2:n.1257C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146961.2:n.1074C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146962.1:n.1381C>G - 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
SCV000361552Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Benign
(Jan 12, 2018)
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 Clinical Services Laboratory,Illumina, SCV000361552.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

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

Last Updated: Jun 14, 2021

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