NC_000010.10:g.(?_14987084)_(14996009_?)del AND Severe combined immunodeficiency due to DCLRE1C deficiency

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 29, 2024
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:: RCV004580454.2

Allele description [Variation Report for NC_000010.10:g.(?_14987084)_(14996009_?)del]

NC_000010.10:g.(?_14987084)_(14996009_?)del

Gene:: DCLRE1C:DNA cross-link repair 1C [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 10p13
Genomic location:: Chr10: 14987084 - 14996009 (on Assembly GRCh37)
Preferred name:: NC_000010.10:g.(?_14987084)_(14996009_?)del
HGVS:: NC_000010.10:g.(?_14987084)_(14996009_?)del
This HGVS expression did not pass validation

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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IS66 family transposase [Paenibacillus elgii]
IS66 family transposase [Paenibacillus elgii]
gi|498179714|ref|WP_010493870.1|

Protein
type III-A CRISPR-associated protein Cas10/Csm1 [Paenibacillus elgii]
type III-A CRISPR-associated protein Cas10/Csm1 [Paenibacillus elgii]
gi|498187660|ref|WP_010501816.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005065738	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 29, 2024)	unknown	clinical testing	PubMed (4) [See all records that cite these PMIDs] 21664875, 26123418, 19912631, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005065738

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 29, 2024)

unknown

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV005065738.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 1-3 of the DCLRE1C gene, which includes the initiator codon. This deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. 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). A similar copy number variant has been observed in individuals with severe combined immunodeficiency (SCID) or Omenn syndrome (OS) (PMID: 19912631). For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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