NM_001033855.3(DCLRE1C):c.457G>A (p.Gly153Arg) AND not provided

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: Feb 1, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000224125.33

Allele description [Variation Report for NM_001033855.3(DCLRE1C):c.457G>A (p.Gly153Arg)]

NM_001033855.3(DCLRE1C):c.457G>A (p.Gly153Arg)

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.457G>A (p.Gly153Arg)

Other names:

NM_001033855.3(DCLRE1C):c.457G>A

HGVS:

NC_000010.11:g.14935470C>T
NG_007276.1:g.23626G>A
NM_001033855.3:c.457G>AMANE SELECT
NM_001033857.3:c.97G>A
NM_001033858.3:c.97G>A
NM_001289076.2:c.112G>A
NM_001289077.2:c.97G>A
NM_001289078.2:c.112G>A
NM_001289079.2:c.97G>A
NM_001350965.2:c.457G>A
NM_001350966.2:c.112G>A
NM_001350967.2:c.97G>A
NM_022487.4:c.112G>A
NP_001029027.1:p.Gly153Arg
NP_001029029.1:p.Gly33Arg
NP_001029030.1:p.Gly33Arg
NP_001276005.1:p.Gly38Arg
NP_001276006.1:p.Gly33Arg
NP_001276007.1:p.Gly38Arg
NP_001276008.1:p.Gly33Arg
NP_001337894.1:p.Gly153Arg
NP_001337895.1:p.Gly38Arg
NP_001337896.1:p.Gly33Arg
NP_071932.2:p.Gly38Arg
LRG_54t1:c.457G>A
LRG_54:g.23626G>A
NC_000010.10:g.14977469C>T
NM_001033855.1:c.457G>A
NM_001033855.2:c.457G>A
NM_001033857.1:c.97G>A
NM_001033858.1:c.97G>A
NR_110297.2:n.755G>A
NR_146960.1:n.879G>A
NR_146961.2:n.572G>A
NR_146962.1:n.879G>A

Protein change:

G153R

Links:

dbSNP: rs41297018

NCBI 1000 Genomes Browser:

rs41297018

Molecular consequence:

NM_001033855.3:c.457G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001033857.3:c.97G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001033858.3:c.97G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001289076.2:c.112G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001289077.2:c.97G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001289078.2:c.112G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001289079.2:c.97G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001350965.2:c.457G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001350966.2:c.112G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001350967.2:c.97G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_022487.4:c.112G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_110297.2:n.755G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146960.1:n.879G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146961.2:n.572G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_146962.1:n.879G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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granzyme A [Rattus norvegicus]
granzyme A [Rattus norvegicus]
gi|23307121|dbj|BAC16549.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000280758	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely Benign (Sep 2, 2015)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001156850	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Benign (Aug 28, 2023)	germline	clinical testing	Citation Link,
SCV001931715	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing
SCV002544412	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Benign (Feb 1, 2024)	germline	clinical testing	Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	11	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000280758.1

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

Description

Converted during submission to Likely benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	0.010762	not provided	not provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV001156850.6

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

#	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

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001931715.1

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

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

From CeGaT Center for Human Genetics Tuebingen, SCV002544412.16

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	11	not provided	not provided	clinical testing	not provided

Description

DCLRE1C: BS1, BS2

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		11	not provided	not provided	not provided

Last Updated: Nov 3, 2024

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