NM_001033855.3(DCLRE1C):c.1379AAG[2] (p.Glu462del) AND Severe combined immunodeficiency due to DCLRE1C deficiency

Germline classification:: Likely benign (1 submission)
Last evaluated:: Jan 31, 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:: RCV001085101.8

Allele description [Variation Report for NM_001033855.3(DCLRE1C):c.1379AAG[2] (p.Glu462del)]

NM_001033855.3(DCLRE1C):c.1379AAG[2] (p.Glu462del)

Gene:

DCLRE1C:DNA cross-link repair 1C [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

10p13

Genomic location:

Preferred name:

NM_001033855.3(DCLRE1C):c.1379AAG[2] (p.Glu462del)

HGVS:

NC_000010.11:g.14909101TTC[2]
NG_007276.1:g.49988AAG[2]
NM_001033855.3:c.1379AAG[2]MANE SELECT
NM_001033857.3:c.1019AAG[2]
NM_001033858.3:c.1019AAG[2]
NM_001289076.2:c.1034AAG[2]
NM_001289077.2:c.1019AAG[2]
NM_001289078.2:c.1034AAG[2]
NM_001289079.2:c.1019AAG[2]
NM_001350965.2:c.1379AAG[2]
NM_001350966.2:c.1034AAG[2]
NM_001350967.2:c.1019AAG[2]
NM_022487.4:c.1034AAG[2]
NP_001029027.1:p.Glu462del
NP_001029029.1:p.Glu342del
NP_001029030.1:p.Glu342del
NP_001276005.1:p.Glu347del
NP_001276006.1:p.Glu342del
NP_001276007.1:p.Glu347del
NP_001276008.1:p.Glu342del
NP_001337894.1:p.Glu462del
NP_001337895.1:p.Glu347del
NP_001337896.1:p.Glu342del
NP_071932.2:p.Glu347del
LRG_54t1:c.1385_1387del
LRG_54:g.49988AAG[2]
NC_000010.10:g.14951099_14951101del
NC_000010.10:g.14951100TTC[2]
NM_001033855.1:c.1385_1387delAAG
NM_001033855.2:c.1385_1387del
NM_001033855.2:c.1385_1387delAAG
NR_110297.2:n.1818AAG[2]
NR_146960.1:n.1746AAG[2]
NR_146961.2:n.1559AAG[2]
NR_146962.1:n.1866AAG[2]

Protein change:

E342del

Links:

dbSNP: rs373709012

NCBI 1000 Genomes Browser:

rs373709012

Molecular consequence:

NM_001033855.3:c.1379AAG[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001033857.3:c.1019AAG[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001033858.3:c.1019AAG[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001289076.2:c.1034AAG[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001289077.2:c.1019AAG[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001289078.2:c.1034AAG[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001289079.2:c.1019AAG[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001350965.2:c.1379AAG[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001350966.2:c.1034AAG[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001350967.2:c.1019AAG[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_022487.4:c.1034AAG[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_110297.2:n.1818AAG[2] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146960.1:n.1746AAG[2] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146961.2:n.1559AAG[2] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146962.1:n.1866AAG[2] - 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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Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/BRA/RJ-DCVN1/2020, complete genome
gi|1883806255|gb|MT827202.1|

Nucleotide
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Terminally Ill
Terminally Ill
Persons with an incurable or irreversible illness at the end stage that will result in death within a short time. (From O'Leary et al., Lexikon: Dictionary of Health Care Term...<br/>Year introduced: 1997

MeSH
PAPPA-AS1 PAPPA antisense RNA 1 [Homo sapiens]
PAPPA-AS1 PAPPA antisense RNA 1 [Homo sapiens]
Gene ID:493913

Gene
PHTF1 putative homeodomain transcription factor 1 [Bos taurus]
PHTF1 putative homeodomain transcription factor 1 [Bos taurus]
Gene ID:536504

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000766518	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 31, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000766518

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 31, 2024)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000766518.7

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

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

Last Updated: Oct 13, 2024

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