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NM_001033855.3(DCLRE1C):c.668T>G (p.Leu223Ter) AND Severe combined immunodeficiency due to DCLRE1C deficiency

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 13, 2023
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:
RCV003859003.1

Allele description

NM_001033855.3(DCLRE1C):c.668T>G (p.Leu223Ter)

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.668T>G (p.Leu223Ter)
HGVS:
  • NC_000010.11:g.14934390A>C
  • NG_007276.1:g.24706T>G
  • NM_001033855.3:c.668T>GMANE SELECT
  • NM_001033857.3:c.308T>G
  • NM_001033858.3:c.308T>G
  • NM_001289076.2:c.323T>G
  • NM_001289077.2:c.308T>G
  • NM_001289078.2:c.323T>G
  • NM_001289079.2:c.308T>G
  • NM_001350965.2:c.668T>G
  • NM_001350966.2:c.323T>G
  • NM_001350967.2:c.308T>G
  • NM_022487.4:c.323T>G
  • NP_001029027.1:p.Leu223Ter
  • NP_001029027.1:p.Leu223Ter
  • NP_001029029.1:p.Leu103Ter
  • NP_001029030.1:p.Leu103Ter
  • NP_001276005.1:p.Leu108Ter
  • NP_001276006.1:p.Leu103Ter
  • NP_001276007.1:p.Leu108Ter
  • NP_001276008.1:p.Leu103Ter
  • NP_001337894.1:p.Leu223Ter
  • NP_001337895.1:p.Leu108Ter
  • NP_001337896.1:p.Leu103Ter
  • NP_071932.2:p.Leu108Ter
  • LRG_54t1:c.668T>G
  • LRG_54:g.24706T>G
  • LRG_54p1:p.Leu223Ter
  • NC_000010.10:g.14976389A>C
  • NM_001033855.1:c.668T>G
  • NR_110297.2:n.966T>G
  • NR_146960.1:n.1090T>G
  • NR_146961.2:n.783T>G
  • NR_146962.1:n.1090T>G
Protein change:
L103*
Molecular consequence:
  • NR_110297.2:n.966T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146960.1:n.1090T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146961.2:n.783T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146962.1:n.1090T>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001033855.3:c.668T>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001033857.3:c.308T>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001033858.3:c.308T>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001289076.2:c.323T>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001289077.2:c.308T>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001289078.2:c.323T>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001289079.2:c.308T>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001350965.2:c.668T>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001350966.2:c.323T>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001350967.2:c.308T>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_022487.4:c.323T>G - nonsense - [Sequence Ontology: SO:0001587]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004695922Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jan 13, 2023) 		germlineclinical testing

PubMed (3)
[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

Clinical and immunological manifestations of patients with atypical severe combined immunodeficiency.

Felgentreff K, Perez-Becker R, Speckmann C, Schwarz K, Kalwak K, Markelj G, Avcin T, Qasim W, Davies EG, Niehues T, Ehl S.

Clin Immunol. 2011 Oct;141(1):73-82. doi: 10.1016/j.clim.2011.05.007. Epub 2011 May 30. Review.

PubMed [citation]
PMID:
21664875

Hypomorphic interleukin-7 receptor α-chain mutations and T-cell deficiency: a delay in diagnosis.

Leiding JW, Sriaroon P, Ly JM, Petrovic A, Howard DL, Shamblott M, Kuehn HS, Fleisher TA.

Ann Allergy Asthma Immunol. 2015 Jul;115(1):1-3. doi: 10.1016/j.anai.2015.04.024. No abstract available.

PubMed [citation]
PMID:
26123418
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV004695922.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with DCLRE1C-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Leu223*) in the DCLRE1C gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DCLRE1C are known to be pathogenic (PMID: 21664875, 26123418).

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

Last Updated: Mar 5, 2024