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NM_001033855.3(DCLRE1C):c.959C>G (p.Ser320Cys) AND Severe combined immunodeficiency due to DCLRE1C deficiency

Germline classification:
Benign (2 submissions)
Last evaluated:
Nov 14, 2023
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
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:
RCV001083680.16

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; NM_001033855.3(DCLRE1C):c.959C>G
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:
Severe combined immunodeficiency due to DCLRE1C deficiency (RS-SCID)
Synonyms:
Severe combined immunodeficiency with sensitivity to ionizing radiation; SCID, AUTOSOMAL RECESSIVE, T CELL-NEGATIVE, B CELL-NEGATIVE, NK CELL-POSITIVE, WITH SENSITIVITY TO IONIZING RADIATION
Identifiers:
MONDO: MONDO:0011225; MedGen: C1865370; Orphanet: 275; OMIM: 602450

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000645230Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Benign
(Jan 31, 2024)
germlineclinical testing

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

SCV004102780ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen
reviewed by expert panel

(ClinGen SCID ACMG Specifications DCLRE1C V1.0.0)
Benign
(Nov 14, 2023)
germlinecuration

Citation Link

Summary from all submissions

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

Citations

PubMed

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 Invitae, SCV000645230.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen, SCV004102780.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The NM_001033855.3:c.959C>G variant in DCLRE1C is a missense variant predicted to cause substitution of serine by cysteine at amino acid 320 (p.Ser320Cys). This variant has an allele frequency of 0.03553 in the African / African American population in gnomAD, which is above the threshold for BA1 set by the ClinGen SCID VCEP for DCLRE1C (>0.00346). In addition, 16 adult homozygous individuals with this variant are present in gnomAD v2.1.1 (in African/African American population)(BS2_Supporting). In summary, this variant meets the criteria to be classified as Benign for autosomal recessive SCID based on the ACMG criteria applied: BA1 and BS2_Supporting as specified by the ClinGen SCID VCEP (VCEP specifications version 1).

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

Last Updated: Jul 15, 2024