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NM_001033855.3(DCLRE1C):c.2040A>T (p.Ile680=) AND Severe combined immunodeficiency due to DCLRE1C deficiency

Germline classification:
Likely benign (1 submission)
Last evaluated:
Apr 14, 2022
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:
RCV001444146.6

Allele description

NM_001033855.3(DCLRE1C):c.2040A>T (p.Ile680=)

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.2040A>T (p.Ile680=)
HGVS:
  • NC_000010.11:g.14908447T>A
  • NG_007276.1:g.50649A>T
  • NM_001033855.3:c.2040A>TMANE SELECT
  • NM_001033857.3:c.1680A>T
  • NM_001033858.3:c.1680A>T
  • NM_001289076.2:c.1695A>T
  • NM_001289077.2:c.1680A>T
  • NM_001289078.2:c.1695A>T
  • NM_001289079.2:c.1680A>T
  • NM_001350965.2:c.1782+258A>T
  • NM_001350966.2:c.1437+258A>T
  • NM_001350967.2:c.1422+258A>T
  • NM_022487.4:c.1695A>T
  • NP_001029027.1:p.Ile680=
  • NP_001029029.1:p.Ile560=
  • NP_001029030.1:p.Ile560=
  • NP_001276005.1:p.Ile565=
  • NP_001276006.1:p.Ile560=
  • NP_001276007.1:p.Ile565=
  • NP_001276008.1:p.Ile560=
  • NP_071932.2:p.Ile565=
  • LRG_54:g.50649A>T
  • NC_000010.10:g.14950446T>A
  • NR_110297.2:n.2479A>T
  • NR_146961.2:n.2220A>T
  • NR_146962.1:n.2527A>T
Links:
dbSNP: rs2131767938
NCBI 1000 Genomes Browser:
rs2131767938
Molecular consequence:
  • NM_001350965.2:c.1782+258A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001350966.2:c.1437+258A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001350967.2:c.1422+258A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NR_110297.2:n.2479A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146961.2:n.2220A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_146962.1:n.2527A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001033855.3:c.2040A>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001033857.3:c.1680A>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001033858.3:c.1680A>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001289076.2:c.1695A>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001289077.2:c.1680A>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001289078.2:c.1695A>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001289079.2:c.1680A>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_022487.4:c.1695A>T - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV001647141Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely benign
(Apr 14, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

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

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, SCV001647141.4

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

Last Updated: Feb 20, 2024