NM_000527.5(LDLR):c.313+1G>C AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Sep 29, 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:: RCV001699015.5

Allele description [Variation Report for NM_000527.5(LDLR):c.313+1G>C]

NM_000527.5(LDLR):c.313+1G>C

Gene:

LDLR:low density lipoprotein receptor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.2

Genomic location:

Preferred name:

NM_000527.5(LDLR):c.313+1G>C

HGVS:

NC_000019.10:g.11102787G>C
NG_009060.1:g.18407G>C
NG_140409.1:g.682G>C
NM_000527.5:c.313+1G>CMANE SELECT
NM_001195798.2:c.313+1G>C
NM_001195799.2:c.191-2433G>C
NM_001195800.2:c.313+1G>C
NM_001195803.2:c.313+1G>C
NM_001406861.1:c.572G>C
NP_001393790.1:p.Arg191Pro
LRG_274t1:c.313+1G>C
LRG_274:g.18407G>C
NC_000019.9:g.11213463G>C
NM_000527.4(LDLR):c.313+1G>C
NM_000527.4:c.313+1G>C
c.313+1G>C

Protein change:

R191P

Links:

LDLR-LOVD, British Heart Foundation: LDLR_001693; dbSNP: rs112029328

NCBI 1000 Genomes Browser:

rs112029328

Molecular consequence:

NM_001195799.2:c.191-2433G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001406861.1:c.572G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_000527.5:c.313+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001195798.2:c.313+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001195800.2:c.313+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001195803.2:c.313+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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RecName: Full=Protein arginine N-methyltransferase 9; AltName: Full=Protein argi...
RecName: Full=Protein arginine N-methyltransferase 9; AltName: Full=Protein arginine N-methyltransferase 10
gi|74758248|sp|Q6P2P2.1|ANM9_HUMAN

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001921130	Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001963019	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV002576992	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Sep 29, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001921130

Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided

Pathogenic

germline

clinical testing

SCV001963019

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus

no assertion criteria provided

Pathogenic

germline

clinical testing

SCV002576992

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Sep 29, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001921130.1

#	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 Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001963019.1

#	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 GeneDx, SCV002576992.2

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

Description

Canonical splice site variant expected to result in aberrant splicing, although in the absence of functional evidence the actual effect of this sequence change is unknown.; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 22244043, 22390909, 25525159, 19318025, 21935675, 10790219, 11668640, 15241806, 31589614, 32660911, 34037665, 33087929, 7616128)

#	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

Last Updated: Sep 29, 2024

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